Starting phenix.real_space_refine on Sat Sep 12 08:59:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ty9_20582/09_2026/6ty9_20582.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ty9_20582/09_2026/6ty9_20582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ty9_20582/09_2026/6ty9_20582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ty9_20582/09_2026/6ty9_20582.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ty9_20582/09_2026/6ty9_20582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ty9_20582/09_2026/6ty9_20582.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ty9_20582/09_2026/6ty9_20582.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ty9_20582/09_2026/6ty9_20582.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 44 5.49 5 Mg 3 5.21 5 S 54 5.16 5 C 9100 2.51 5 N 2482 2.21 5 O 2876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14559 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9667 Classifications: {'peptide': 1208} Link IDs: {'PTRANS': 38, 'TRANS': 1169} Chain: "B" Number of atoms: 4007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 4007 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 482} Chain breaks: 2 Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna2p_pur': 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 418 Unusual residues: {'GTA': 1} Classifications: {'RNAv2': 18, 'undetermined': 1} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 15} Link IDs: {'rna3p': 17, None: 1} Not linked: pdbres="GTA N 1 " pdbres=" G N 2 " Chain: "T" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 410 Classifications: {'RNAv2': 19} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 15, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 16} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.18, per 1000 atoms: 0.22 Number of scatterers: 14559 At special positions: 0 Unit cell: (105.138, 143.37, 106.2, 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 54 16.00 P 44 15.00 Mg 3 11.99 O 2876 8.00 N 2482 7.00 C 9100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 604.7 milliseconds 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 15 sheets defined 52.5% alpha, 9.0% beta 9 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.665A pdb=" N THR A 10 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 21 through 36 removed outlier: 3.622A pdb=" N LEU A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 45 removed outlier: 3.755A pdb=" N ARG A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.691A pdb=" N THR A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.721A pdb=" N TYR A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.794A pdb=" N LEU A 112 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 135 removed outlier: 3.619A pdb=" N LYS A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 Processing helix chain 'A' and resid 165 through 176 removed outlier: 4.069A pdb=" N THR A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 219 removed outlier: 3.701A pdb=" N PHE A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 238 removed outlier: 3.671A pdb=" N ILE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 250 removed outlier: 3.602A pdb=" N LYS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 removed outlier: 4.035A pdb=" N GLY A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 307 removed outlier: 4.374A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.579A pdb=" N TYR A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 340 removed outlier: 3.647A pdb=" N VAL A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 removed outlier: 3.710A pdb=" N PHE A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 398 removed outlier: 3.957A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 410 removed outlier: 3.665A pdb=" N GLY A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 421 Processing helix chain 'A' and resid 431 through 439 Processing helix chain 'A' and resid 440 through 446 Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 463 through 468 removed outlier: 4.001A pdb=" N PHE A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 removed outlier: 3.751A pdb=" N SER A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 removed outlier: 3.825A pdb=" N GLN A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 513 Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 529 through 536 Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'A' and resid 560 through 573 removed outlier: 3.715A pdb=" N PHE A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 Processing helix chain 'A' and resid 643 through 665 removed outlier: 3.840A pdb=" N HIS A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 661 " --> pdb=" O ARG A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 706 Processing helix chain 'A' and resid 735 through 739 removed outlier: 3.528A pdb=" N ILE A 739 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 766 Processing helix chain 'A' and resid 767 through 771 removed outlier: 3.536A pdb=" N VAL A 771 " --> pdb=" O LEU A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 788 removed outlier: 3.515A pdb=" N MET A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 809 Processing helix chain 'A' and resid 833 through 839 Processing helix chain 'A' and resid 868 through 871 removed outlier: 3.507A pdb=" N LYS A 871 " --> pdb=" O GLY A 868 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 868 through 871' Processing helix chain 'A' and resid 872 through 878 removed outlier: 4.329A pdb=" N TYR A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 888 removed outlier: 3.534A pdb=" N GLN A 886 " --> pdb=" O ARG A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 900 Processing helix chain 'A' and resid 901 through 912 removed outlier: 4.091A pdb=" N ASN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 923 removed outlier: 3.819A pdb=" N VAL A 920 " --> pdb=" O LEU A 916 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 939 removed outlier: 3.777A pdb=" N GLN A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 958 Processing helix chain 'A' and resid 971 through 983 removed outlier: 3.795A pdb=" N LYS A 976 " --> pdb=" O GLY A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1006 removed outlier: 3.648A pdb=" N LYS A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1020 Processing helix chain 'A' and resid 1034 through 1038 Processing helix chain 'A' and resid 1053 through 1063 Processing helix chain 'A' and resid 1066 through 1078 removed outlier: 3.516A pdb=" N LEU A1072 " --> pdb=" O SER A1068 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A1078 " --> pdb=" O LEU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1103 removed outlier: 3.624A pdb=" N ILE A1099 " --> pdb=" O GLN A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1114 Processing helix chain 'A' and resid 1117 through 1132 removed outlier: 3.526A pdb=" N TYR A1130 " --> pdb=" O ARG A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1159 Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 3.571A pdb=" N TYR A1169 " --> pdb=" O PRO A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1189 removed outlier: 3.507A pdb=" N HIS A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A1187 " --> pdb=" O TYR A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1193 Processing helix chain 'A' and resid 1203 through 1212 removed outlier: 3.737A pdb=" N GLY A1212 " --> pdb=" O ALA A1208 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 16 removed outlier: 3.706A pdb=" N TYR B 13 " --> pdb=" O HIS B 9 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 61 removed outlier: 3.533A pdb=" N LYS B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.534A pdb=" N LEU B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 removed outlier: 3.555A pdb=" N LEU B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.552A pdb=" N LEU B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 removed outlier: 3.518A pdb=" N SER B 200 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 243 removed outlier: 3.543A pdb=" N TYR B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 325 through 341 removed outlier: 3.918A pdb=" N ALA B 338 " --> pdb=" O LYS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 375 removed outlier: 3.676A pdb=" N PHE B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.789A pdb=" N LYS B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 416 through 429 removed outlier: 3.577A pdb=" N HIS B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 441 through 458 removed outlier: 3.953A pdb=" N GLU B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 491 through 497 removed outlier: 3.572A pdb=" N ALA B 496 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 519 Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 546 through 557 removed outlier: 4.036A pdb=" N ILE B 554 " --> pdb=" O MET B 550 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 186 Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.685A pdb=" N GLY A 280 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 384 removed outlier: 6.571A pdb=" N LYS A 382 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 590 " --> pdb=" O SER A 374 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 475 through 477 removed outlier: 3.578A pdb=" N LYS A 475 " --> pdb=" O GLY A 491 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 672 through 678 removed outlier: 7.029A pdb=" N ILE A 685 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 675 " --> pdb=" O MET A 683 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N MET A 683 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE A 677 " --> pdb=" O ASP A 681 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASP A 681 " --> pdb=" O ILE A 677 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 547 through 548 removed outlier: 3.868A pdb=" N ASP A 547 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 712 " --> pdb=" O ASP A 547 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 621 through 624 Processing sheet with id=AA9, first strand: chain 'A' and resid 720 through 721 removed outlier: 4.003A pdb=" N LEU A 726 " --> pdb=" O TRP A 733 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 791 through 797 removed outlier: 3.920A pdb=" N THR A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1022 through 1030 removed outlier: 4.919A pdb=" N ARG A1197 " --> pdb=" O GLU A1027 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 157 through 159 removed outlier: 6.743A pdb=" N ILE B 158 " --> pdb=" O ILE B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 204 through 208 Processing sheet with id=AB5, first strand: chain 'B' and resid 297 through 299 removed outlier: 6.667A pdb=" N GLY B 255 " --> pdb=" O PRO B 318 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 257 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE B 316 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR B 259 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 378 through 381 removed outlier: 6.558A pdb=" N ALA B 347 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL B 487 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU B 349 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLY B 489 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 351 " --> pdb=" O GLY B 489 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N VAL B 505 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 350 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU B 507 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR B 352 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR B 543 " --> pdb=" O THR B 504 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2287 1.31 - 1.43: 4353 1.43 - 1.56: 8124 1.56 - 1.68: 89 1.68 - 1.81: 96 Bond restraints: 14949 Sorted by residual: bond pdb=" C2' GTP M 2 " pdb=" C3' GTP M 2 " ideal model delta sigma weight residual 1.524 1.236 0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C1B GTA N 1 " pdb=" C2B GTA N 1 " ideal model delta sigma weight residual 1.530 1.300 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C1B GTA N 1 " pdb=" O4B GTA N 1 " ideal model delta sigma weight residual 1.395 1.612 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C3A GTA N 1 " pdb=" C4A GTA N 1 " ideal model delta sigma weight residual 1.525 1.349 0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" C4A GTA N 1 " pdb=" O4A GTA N 1 " ideal model delta sigma weight residual 1.433 1.607 -0.174 2.00e-02 2.50e+03 7.56e+01 ... (remaining 14944 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 20369 4.30 - 8.60: 53 8.60 - 12.91: 9 12.91 - 17.21: 4 17.21 - 21.51: 2 Bond angle restraints: 20437 Sorted by residual: angle pdb=" N1C GTA N 1 " pdb=" C6C GTA N 1 " pdb=" N6C GTA N 1 " ideal model delta sigma weight residual 119.40 97.89 21.51 3.00e+00 1.11e-01 5.14e+01 angle pdb=" N GLY A 440 " pdb=" CA GLY A 440 " pdb=" C GLY A 440 " ideal model delta sigma weight residual 111.34 123.76 -12.42 1.82e+00 3.02e-01 4.65e+01 angle pdb=" C5C GTA N 1 " pdb=" C6C GTA N 1 " pdb=" N6C GTA N 1 " ideal model delta sigma weight residual 122.62 142.11 -19.49 3.00e+00 1.11e-01 4.22e+01 angle pdb=" C1B GTA N 1 " pdb=" N9C GTA N 1 " pdb=" C8C GTA N 1 " ideal model delta sigma weight residual 127.31 111.22 16.09 3.00e+00 1.11e-01 2.88e+01 angle pdb=" O13 GTA N 1 " pdb=" P2 GTA N 1 " pdb=" O23 GTA N 1 " ideal model delta sigma weight residual 93.83 109.09 -15.26 3.00e+00 1.11e-01 2.59e+01 ... (remaining 20432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.09: 8628 34.09 - 68.18: 253 68.18 - 102.27: 16 102.27 - 136.36: 2 136.36 - 170.45: 2 Dihedral angle restraints: 8901 sinusoidal: 3869 harmonic: 5032 Sorted by residual: dihedral pdb=" C4' U T 16 " pdb=" C3' U T 16 " pdb=" C2' U T 16 " pdb=" C1' U T 16 " ideal model delta sinusoidal sigma weight residual 36.34 -36.61 72.95 1 3.10e+00 1.04e-01 7.06e+02 dihedral pdb=" C4' U T 15 " pdb=" C3' U T 15 " pdb=" C2' U T 15 " pdb=" C1' U T 15 " ideal model delta sinusoidal sigma weight residual 36.35 -35.37 71.71 1 3.10e+00 1.04e-01 6.85e+02 dihedral pdb=" C4' A M 1 " pdb=" C3' A M 1 " pdb=" C2' A M 1 " pdb=" C1' A M 1 " ideal model delta sinusoidal sigma weight residual 36.34 -34.83 71.17 1 3.10e+00 1.04e-01 6.77e+02 ... (remaining 8898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2058 0.069 - 0.139: 200 0.139 - 0.208: 12 0.208 - 0.277: 43 0.277 - 0.346: 1 Chirality restraints: 2314 Sorted by residual: chirality pdb=" C3A GTA N 1 " pdb=" C2A GTA N 1 " pdb=" C4A GTA N 1 " pdb=" O3A GTA N 1 " both_signs ideal model delta sigma weight residual False -2.72 -2.37 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C2' U T 16 " pdb=" C3' U T 16 " pdb=" O2' U T 16 " pdb=" C1' U T 16 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C2' U T 15 " pdb=" C3' U T 15 " pdb=" O2' U T 15 " pdb=" C1' U T 15 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2311 not shown) Planarity restraints: 2458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 430 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C LEU A 430 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU A 430 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 431 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 431 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C THR A 431 " -0.042 2.00e-02 2.50e+03 pdb=" O THR A 431 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 432 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 203 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 204 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.021 5.00e-02 4.00e+02 ... (remaining 2455 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 101 2.56 - 3.15: 11303 3.15 - 3.73: 21851 3.73 - 4.32: 34139 4.32 - 4.90: 53835 Nonbonded interactions: 121229 Sorted by model distance: nonbonded pdb=" OD2 ASP A 680 " pdb="MG MG A1302 " model vdw 1.980 2.170 nonbonded pdb=" O1A GTP M 2 " pdb="MG MG A1301 " model vdw 2.056 2.170 nonbonded pdb=" NE2 GLN A 939 " pdb=" O ILE B 68 " model vdw 2.206 3.120 nonbonded pdb=" O VAL A 548 " pdb="MG MG A1302 " model vdw 2.207 2.170 nonbonded pdb=" OG1 THR A 209 " pdb=" OD2 ASP A 341 " model vdw 2.226 3.040 ... (remaining 121224 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.370 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.288 14950 Z= 0.401 Angle : 0.802 21.509 20437 Z= 0.414 Chirality : 0.054 0.346 2314 Planarity : 0.004 0.038 2458 Dihedral : 15.566 170.453 5667 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.20 % Allowed : 6.52 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.19 (0.16), residues: 1701 helix: -3.67 (0.10), residues: 812 sheet: -1.49 (0.35), residues: 177 loop : -1.74 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 168 TYR 0.014 0.002 TYR B 178 PHE 0.018 0.002 PHE A 344 TRP 0.011 0.002 TRP A 256 HIS 0.006 0.001 HIS B 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00852 / 0.40 (14949) covalent geometry : angle 0.80174 / 0.41 (20437) hydrogen bonds : bond 0.29301 / 20.14 ( 594) hydrogen bonds : angle 9.15918 / 6.35 ( 1653) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 261 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 8 TYR cc_start: 0.8388 (p90) cc_final: 0.7828 (p90) REVERT: A 92 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7879 (mt-10) REVERT: A 484 ARG cc_start: 0.7628 (mtt180) cc_final: 0.7242 (ttp80) REVERT: A 947 GLU cc_start: 0.7241 (tm-30) cc_final: 0.7018 (tm-30) REVERT: A 1009 TYR cc_start: 0.8260 (t80) cc_final: 0.7802 (t80) REVERT: B 132 ILE cc_start: 0.8888 (mm) cc_final: 0.8592 (tt) REVERT: B 251 ILE cc_start: 0.9004 (pt) cc_final: 0.8636 (mt) outliers start: 3 outliers final: 2 residues processed: 263 average time/residue: 0.7523 time to fit residues: 213.7691 Evaluate side-chains 197 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 195 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 895 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.0060 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN A 378 HIS A 387 ASN A 394 GLN A 412 HIS A 617 GLN A 939 GLN A 999 HIS A1020 HIS ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN B 53 HIS B 180 GLN B 346 ASN B 429 HIS B 459 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.098537 restraints weight = 17468.902| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.37 r_work: 0.2883 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14950 Z= 0.111 Angle : 0.578 11.517 20437 Z= 0.279 Chirality : 0.044 0.465 2314 Planarity : 0.004 0.043 2458 Dihedral : 11.349 165.285 2419 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.61 % Allowed : 13.10 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.18), residues: 1701 helix: -1.24 (0.16), residues: 839 sheet: -1.09 (0.37), residues: 170 loop : -1.21 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 841 TYR 0.012 0.001 TYR A 165 PHE 0.011 0.001 PHE A 206 TRP 0.010 0.001 TRP B 260 HIS 0.005 0.001 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (14949) covalent geometry : angle 0.57833 / 0.28 (20437) hydrogen bonds : bond 0.04116 / 2.78 ( 594) hydrogen bonds : angle 4.77352 / 3.43 ( 1653) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 0.560 Fit side-chains REVERT: A 8 TYR cc_start: 0.8783 (p90) cc_final: 0.8151 (p90) REVERT: A 92 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8570 (mt-10) REVERT: A 468 LYS cc_start: 0.8660 (mtpm) cc_final: 0.8307 (mtmm) REVERT: A 484 ARG cc_start: 0.7961 (mtt180) cc_final: 0.6891 (ttp80) REVERT: A 485 ARG cc_start: 0.7556 (mtp180) cc_final: 0.6997 (mtm-85) REVERT: A 789 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8633 (pt) REVERT: A 918 ASP cc_start: 0.8610 (m-30) cc_final: 0.8317 (m-30) REVERT: A 947 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7051 (tm-30) REVERT: A 999 HIS cc_start: 0.8638 (t-90) cc_final: 0.8275 (t-170) REVERT: A 1009 TYR cc_start: 0.8066 (t80) cc_final: 0.7350 (t80) REVERT: A 1175 ARG cc_start: 0.8222 (ttm170) cc_final: 0.8005 (ttt180) REVERT: B 212 ASN cc_start: 0.8321 (t0) cc_final: 0.8108 (t0) REVERT: B 251 ILE cc_start: 0.9154 (pt) cc_final: 0.8693 (mt) REVERT: B 276 ARG cc_start: 0.8571 (ttp-170) cc_final: 0.8340 (ttm170) outliers start: 24 outliers final: 8 residues processed: 244 average time/residue: 0.6862 time to fit residues: 183.0188 Evaluate side-chains 210 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 201 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 442 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 67 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 170 optimal weight: 50.0000 chunk 122 optimal weight: 0.0670 chunk 158 optimal weight: 0.0040 chunk 86 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 overall best weight: 5.8136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN A 486 GLN A 514 ASN A 724 GLN B 542 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.128307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.093095 restraints weight = 17627.290| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.46 r_work: 0.2816 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14950 Z= 0.187 Angle : 0.584 8.959 20437 Z= 0.287 Chirality : 0.044 0.225 2314 Planarity : 0.004 0.041 2458 Dihedral : 11.209 172.141 2416 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.63 % Allowed : 13.78 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.19), residues: 1701 helix: -0.25 (0.17), residues: 836 sheet: -0.79 (0.38), residues: 164 loop : -1.08 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 310 TYR 0.013 0.002 TYR A 563 PHE 0.014 0.001 PHE A 206 TRP 0.011 0.001 TRP A 256 HIS 0.005 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (14949) covalent geometry : angle 0.58353 / 0.29 (20437) hydrogen bonds : bond 0.04711 / 3.22 ( 594) hydrogen bonds : angle 4.50595 / 3.22 ( 1653) Misc. bond : bond 0.00051 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 202 time to evaluate : 0.538 Fit side-chains REVERT: A 8 TYR cc_start: 0.8805 (p90) cc_final: 0.8156 (p90) REVERT: A 54 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: A 468 LYS cc_start: 0.8688 (mtpm) cc_final: 0.8277 (mtmm) REVERT: A 484 ARG cc_start: 0.8046 (mtt180) cc_final: 0.6891 (ttp80) REVERT: A 485 ARG cc_start: 0.7681 (mtp180) cc_final: 0.7081 (mtm-85) REVERT: A 703 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9141 (tp) REVERT: A 789 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8693 (pt) REVERT: A 899 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: A 918 ASP cc_start: 0.8631 (m-30) cc_final: 0.8306 (m-30) REVERT: A 1009 TYR cc_start: 0.8077 (t80) cc_final: 0.7254 (t80) REVERT: A 1109 ASP cc_start: 0.8201 (t70) cc_final: 0.7873 (t0) REVERT: A 1138 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7438 (tt0) REVERT: A 1159 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: A 1175 ARG cc_start: 0.8258 (ttm170) cc_final: 0.8012 (ttt180) REVERT: B 212 ASN cc_start: 0.8421 (t0) cc_final: 0.8147 (t0) REVERT: B 251 ILE cc_start: 0.9169 (pt) cc_final: 0.8676 (mt) REVERT: B 276 ARG cc_start: 0.8545 (ttp-170) cc_final: 0.8310 (ttm170) REVERT: B 517 MET cc_start: 0.9036 (mmp) cc_final: 0.8722 (mmp) outliers start: 54 outliers final: 19 residues processed: 234 average time/residue: 0.6628 time to fit residues: 169.1927 Evaluate side-chains 225 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 3 optimal weight: 0.4980 chunk 115 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 724 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.129022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.093873 restraints weight = 17586.361| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.45 r_work: 0.2812 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14950 Z= 0.163 Angle : 0.556 9.385 20437 Z= 0.273 Chirality : 0.044 0.242 2314 Planarity : 0.004 0.038 2458 Dihedral : 10.765 168.065 2416 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.97 % Allowed : 14.72 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1701 helix: 0.29 (0.18), residues: 824 sheet: -0.63 (0.39), residues: 164 loop : -0.88 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 841 TYR 0.012 0.001 TYR A 563 PHE 0.012 0.001 PHE A 206 TRP 0.011 0.001 TRP B 260 HIS 0.005 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (14949) covalent geometry : angle 0.55641 / 0.27 (20437) hydrogen bonds : bond 0.04145 / 2.82 ( 594) hydrogen bonds : angle 4.30900 / 3.08 ( 1653) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 211 time to evaluate : 0.545 Fit side-chains REVERT: A 8 TYR cc_start: 0.8810 (p90) cc_final: 0.8172 (p90) REVERT: A 54 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: A 92 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8467 (mt-10) REVERT: A 263 ASN cc_start: 0.9039 (OUTLIER) cc_final: 0.8678 (m110) REVERT: A 313 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7836 (mm-30) REVERT: A 468 LYS cc_start: 0.8676 (mtpm) cc_final: 0.8293 (mtmm) REVERT: A 484 ARG cc_start: 0.8006 (mtt180) cc_final: 0.6879 (ttp80) REVERT: A 485 ARG cc_start: 0.7528 (mtp180) cc_final: 0.7050 (mtm-85) REVERT: A 681 ASP cc_start: 0.9025 (OUTLIER) cc_final: 0.8773 (t0) REVERT: A 703 ILE cc_start: 0.9370 (tt) cc_final: 0.9159 (tp) REVERT: A 789 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8585 (pt) REVERT: A 827 LEU cc_start: 0.8015 (pt) cc_final: 0.7591 (mt) REVERT: A 894 ASP cc_start: 0.7926 (m-30) cc_final: 0.7713 (m-30) REVERT: A 918 ASP cc_start: 0.8592 (m-30) cc_final: 0.8236 (m-30) REVERT: A 978 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7161 (tp40) REVERT: A 999 HIS cc_start: 0.8658 (t-90) cc_final: 0.8280 (t-170) REVERT: A 1009 TYR cc_start: 0.8023 (t80) cc_final: 0.7230 (t80) REVERT: A 1109 ASP cc_start: 0.8210 (t70) cc_final: 0.7906 (t0) REVERT: A 1138 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: A 1159 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: A 1175 ARG cc_start: 0.8263 (ttm170) cc_final: 0.8022 (ttt180) REVERT: B 212 ASN cc_start: 0.8381 (t0) cc_final: 0.8122 (t0) REVERT: B 251 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8657 (mt) REVERT: B 276 ARG cc_start: 0.8524 (ttp-170) cc_final: 0.8285 (ttm170) REVERT: B 359 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7989 (ptpt) REVERT: B 488 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8488 (mt-10) REVERT: B 517 MET cc_start: 0.9033 (mmp) cc_final: 0.8794 (mmp) outliers start: 59 outliers final: 32 residues processed: 248 average time/residue: 0.6847 time to fit residues: 185.8385 Evaluate side-chains 241 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 3 optimal weight: 6.9990 chunk 82 optimal weight: 50.0000 chunk 119 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 37 optimal weight: 0.0170 overall best weight: 5.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 387 ASN A 724 GLN A 807 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.096008 restraints weight = 17504.874| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.35 r_work: 0.2829 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14950 Z= 0.165 Angle : 0.554 8.937 20437 Z= 0.273 Chirality : 0.043 0.241 2314 Planarity : 0.004 0.038 2458 Dihedral : 10.513 165.100 2416 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.44 % Allowed : 14.05 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.20), residues: 1701 helix: 0.50 (0.18), residues: 827 sheet: -0.53 (0.40), residues: 164 loop : -0.81 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 841 TYR 0.012 0.001 TYR A 563 PHE 0.013 0.001 PHE A 206 TRP 0.011 0.001 TRP B 260 HIS 0.006 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (14949) covalent geometry : angle 0.55449 / 0.27 (20437) hydrogen bonds : bond 0.04139 / 2.81 ( 594) hydrogen bonds : angle 4.26875 / 3.05 ( 1653) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 206 time to evaluate : 0.569 Fit side-chains REVERT: A 8 TYR cc_start: 0.8807 (p90) cc_final: 0.8191 (p90) REVERT: A 54 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.8005 (m-30) REVERT: A 92 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8501 (mt-10) REVERT: A 203 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8961 (mp) REVERT: A 313 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7773 (mm-30) REVERT: A 468 LYS cc_start: 0.8694 (mtpm) cc_final: 0.8343 (mtmm) REVERT: A 484 ARG cc_start: 0.8032 (mtt180) cc_final: 0.6958 (ttp80) REVERT: A 485 ARG cc_start: 0.7595 (mtp180) cc_final: 0.7135 (mtm-85) REVERT: A 812 MET cc_start: 0.7842 (ptm) cc_final: 0.7569 (ptm) REVERT: A 827 LEU cc_start: 0.8098 (pt) cc_final: 0.7690 (mt) REVERT: A 918 ASP cc_start: 0.8578 (m-30) cc_final: 0.8202 (m-30) REVERT: A 1009 TYR cc_start: 0.8067 (t80) cc_final: 0.7284 (t80) REVERT: A 1109 ASP cc_start: 0.8170 (t70) cc_final: 0.7877 (t0) REVERT: A 1138 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: A 1159 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: A 1175 ARG cc_start: 0.8214 (ttm170) cc_final: 0.8006 (ttt180) REVERT: B 212 ASN cc_start: 0.8312 (t0) cc_final: 0.8067 (t0) REVERT: B 251 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8657 (mt) REVERT: B 276 ARG cc_start: 0.8517 (ttp-170) cc_final: 0.8285 (ttm170) REVERT: B 359 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7886 (ptpt) REVERT: B 443 ARG cc_start: 0.7107 (mtt90) cc_final: 0.6877 (mtt90) REVERT: B 488 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8457 (mt-10) REVERT: B 517 MET cc_start: 0.9004 (mmp) cc_final: 0.8661 (mmp) outliers start: 66 outliers final: 35 residues processed: 247 average time/residue: 0.6710 time to fit residues: 180.9283 Evaluate side-chains 238 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 135 optimal weight: 0.0010 chunk 152 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 170 optimal weight: 50.0000 chunk 123 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 724 GLN A 807 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.129195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.094031 restraints weight = 17409.012| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.45 r_work: 0.2821 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14950 Z= 0.150 Angle : 0.541 8.898 20437 Z= 0.266 Chirality : 0.043 0.249 2314 Planarity : 0.004 0.037 2458 Dihedral : 10.256 160.889 2416 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.44 % Allowed : 14.72 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1701 helix: 0.62 (0.18), residues: 831 sheet: -0.41 (0.40), residues: 162 loop : -0.74 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 841 TYR 0.011 0.001 TYR A 563 PHE 0.012 0.001 PHE B 548 TRP 0.010 0.001 TRP B 260 HIS 0.005 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (14949) covalent geometry : angle 0.54111 / 0.27 (20437) hydrogen bonds : bond 0.03897 / 2.65 ( 594) hydrogen bonds : angle 4.17935 / 2.98 ( 1653) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 208 time to evaluate : 0.388 Fit side-chains REVERT: A 8 TYR cc_start: 0.8795 (p90) cc_final: 0.8165 (p90) REVERT: A 54 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.8033 (m-30) REVERT: A 92 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8543 (mt-10) REVERT: A 203 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8981 (mp) REVERT: A 263 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8667 (m110) REVERT: A 313 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7757 (mm-30) REVERT: A 468 LYS cc_start: 0.8690 (mtpm) cc_final: 0.8292 (mtmm) REVERT: A 484 ARG cc_start: 0.8019 (mtt180) cc_final: 0.6875 (ttp80) REVERT: A 485 ARG cc_start: 0.7549 (mtp180) cc_final: 0.7005 (mtm-85) REVERT: A 681 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8817 (t0) REVERT: A 812 MET cc_start: 0.7911 (ptm) cc_final: 0.7616 (ptm) REVERT: A 827 LEU cc_start: 0.8053 (pt) cc_final: 0.7671 (mt) REVERT: A 918 ASP cc_start: 0.8592 (m-30) cc_final: 0.8167 (m-30) REVERT: A 956 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8510 (mp) REVERT: A 999 HIS cc_start: 0.8638 (t-90) cc_final: 0.8292 (t-170) REVERT: A 1009 TYR cc_start: 0.8014 (t80) cc_final: 0.7225 (t80) REVERT: A 1109 ASP cc_start: 0.8195 (t70) cc_final: 0.7478 (t0) REVERT: A 1138 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7413 (tt0) REVERT: A 1159 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: A 1175 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7984 (ttt180) REVERT: B 212 ASN cc_start: 0.8271 (t0) cc_final: 0.8001 (t0) REVERT: B 276 ARG cc_start: 0.8534 (ttp-170) cc_final: 0.8301 (ttm170) REVERT: B 359 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7918 (ptpt) REVERT: B 488 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8475 (mt-10) outliers start: 66 outliers final: 36 residues processed: 256 average time/residue: 0.6818 time to fit residues: 190.9692 Evaluate side-chains 244 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 153 optimal weight: 0.8980 chunk 127 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN A 387 ASN A 480 GLN A 486 GLN A 724 GLN A 807 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.128829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.094436 restraints weight = 17425.890| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.36 r_work: 0.2808 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14950 Z= 0.200 Angle : 0.589 8.756 20437 Z= 0.290 Chirality : 0.045 0.236 2314 Planarity : 0.004 0.039 2458 Dihedral : 10.299 161.356 2416 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.44 % Allowed : 15.12 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.20), residues: 1701 helix: 0.53 (0.18), residues: 828 sheet: -0.49 (0.40), residues: 164 loop : -0.71 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 882 TYR 0.012 0.002 TYR A 563 PHE 0.014 0.001 PHE A 206 TRP 0.011 0.001 TRP B 260 HIS 0.006 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (14949) covalent geometry : angle 0.58890 / 0.29 (20437) hydrogen bonds : bond 0.04406 / 3.00 ( 594) hydrogen bonds : angle 4.29691 / 3.05 ( 1653) Misc. bond : bond 0.00061 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 202 time to evaluate : 0.570 Fit side-chains REVERT: A 8 TYR cc_start: 0.8814 (p90) cc_final: 0.8187 (p90) REVERT: A 54 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8007 (m-30) REVERT: A 92 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8595 (mt-10) REVERT: A 203 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8983 (mp) REVERT: A 263 ASN cc_start: 0.9069 (OUTLIER) cc_final: 0.8674 (m110) REVERT: A 313 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7767 (mm-30) REVERT: A 468 LYS cc_start: 0.8748 (mtpm) cc_final: 0.8383 (mtmm) REVERT: A 484 ARG cc_start: 0.8067 (mtt180) cc_final: 0.6984 (ttp80) REVERT: A 485 ARG cc_start: 0.7529 (mtp180) cc_final: 0.6952 (mtm-85) REVERT: A 681 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8777 (t0) REVERT: A 812 MET cc_start: 0.7933 (ptm) cc_final: 0.7704 (ptm) REVERT: A 918 ASP cc_start: 0.8613 (m-30) cc_final: 0.8211 (m-30) REVERT: A 956 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8546 (mp) REVERT: A 1009 TYR cc_start: 0.8192 (t80) cc_final: 0.7389 (t80) REVERT: A 1109 ASP cc_start: 0.8161 (t70) cc_final: 0.7508 (t0) REVERT: A 1138 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: A 1175 ARG cc_start: 0.8251 (ttm170) cc_final: 0.8017 (ttt180) REVERT: B 212 ASN cc_start: 0.8317 (t0) cc_final: 0.7951 (t160) REVERT: B 276 ARG cc_start: 0.8550 (ttp-170) cc_final: 0.8324 (ttm170) REVERT: B 359 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8003 (ptpt) REVERT: B 517 MET cc_start: 0.9008 (mmp) cc_final: 0.8710 (mmp) outliers start: 66 outliers final: 37 residues processed: 250 average time/residue: 0.6576 time to fit residues: 179.9908 Evaluate side-chains 241 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 48 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 chunk 49 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN A 480 GLN A 724 GLN A 807 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.129346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.094977 restraints weight = 17370.572| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.36 r_work: 0.2824 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14950 Z= 0.160 Angle : 0.557 8.539 20437 Z= 0.274 Chirality : 0.043 0.262 2314 Planarity : 0.004 0.038 2458 Dihedral : 10.065 154.333 2416 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.23 % Allowed : 15.59 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.20), residues: 1701 helix: 0.64 (0.18), residues: 830 sheet: -0.41 (0.40), residues: 162 loop : -0.64 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 882 TYR 0.014 0.001 TYR A1083 PHE 0.013 0.001 PHE A 902 TRP 0.011 0.001 TRP B 260 HIS 0.005 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (14949) covalent geometry : angle 0.55718 / 0.27 (20437) hydrogen bonds : bond 0.03990 / 2.71 ( 594) hydrogen bonds : angle 4.18892 / 2.97 ( 1653) Misc. bond : bond 0.00052 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 204 time to evaluate : 0.589 Fit side-chains REVERT: A 8 TYR cc_start: 0.8786 (p90) cc_final: 0.8173 (p90) REVERT: A 54 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.8021 (m-30) REVERT: A 203 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8985 (mp) REVERT: A 263 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8674 (m110) REVERT: A 468 LYS cc_start: 0.8739 (mtpm) cc_final: 0.8387 (mtmm) REVERT: A 484 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7003 (ttt-90) REVERT: A 918 ASP cc_start: 0.8570 (m-30) cc_final: 0.8156 (m-30) REVERT: A 922 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8376 (tppp) REVERT: A 956 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8599 (mp) REVERT: A 1009 TYR cc_start: 0.8125 (t80) cc_final: 0.7349 (t80) REVERT: A 1109 ASP cc_start: 0.8160 (t70) cc_final: 0.7487 (t0) REVERT: A 1138 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: A 1159 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: A 1175 ARG cc_start: 0.8223 (ttm170) cc_final: 0.8022 (ttt180) REVERT: B 212 ASN cc_start: 0.8290 (t0) cc_final: 0.7920 (t0) REVERT: B 251 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8678 (mt) REVERT: B 276 ARG cc_start: 0.8555 (ttp-170) cc_final: 0.8326 (ttm170) REVERT: B 359 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8022 (ptpt) outliers start: 63 outliers final: 34 residues processed: 245 average time/residue: 0.6461 time to fit residues: 173.8387 Evaluate side-chains 239 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 54 optimal weight: 7.9990 chunk 158 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 166 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN A 387 ASN A 480 GLN A 486 GLN A 724 GLN A 807 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.093630 restraints weight = 17559.864| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.35 r_work: 0.2794 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14950 Z= 0.211 Angle : 0.601 8.727 20437 Z= 0.298 Chirality : 0.045 0.248 2314 Planarity : 0.004 0.040 2458 Dihedral : 10.143 154.681 2416 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.56 % Allowed : 16.53 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.20), residues: 1701 helix: 0.51 (0.18), residues: 828 sheet: -0.59 (0.39), residues: 164 loop : -0.69 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 882 TYR 0.014 0.002 TYR A1083 PHE 0.014 0.002 PHE A 206 TRP 0.012 0.001 TRP B 260 HIS 0.007 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.21 (14949) covalent geometry : angle 0.60094 / 0.30 (20437) hydrogen bonds : bond 0.04512 / 3.07 ( 594) hydrogen bonds : angle 4.29570 / 3.04 ( 1653) Misc. bond : bond 0.00067 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 198 time to evaluate : 0.604 Fit side-chains REVERT: A 8 TYR cc_start: 0.8829 (p90) cc_final: 0.8202 (p90) REVERT: A 54 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: A 263 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8705 (m110) REVERT: A 468 LYS cc_start: 0.8783 (mtpm) cc_final: 0.8398 (mtmm) REVERT: A 484 ARG cc_start: 0.8007 (mtt180) cc_final: 0.7050 (ttt-90) REVERT: A 812 MET cc_start: 0.7892 (ptm) cc_final: 0.7684 (ptm) REVERT: A 918 ASP cc_start: 0.8609 (m-30) cc_final: 0.8233 (m-30) REVERT: A 956 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8595 (mp) REVERT: A 1109 ASP cc_start: 0.8161 (t70) cc_final: 0.7511 (t0) REVERT: A 1138 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7506 (tt0) REVERT: A 1175 ARG cc_start: 0.8265 (ttm170) cc_final: 0.8052 (ttt180) REVERT: B 212 ASN cc_start: 0.8441 (t0) cc_final: 0.8086 (t0) REVERT: B 276 ARG cc_start: 0.8553 (ttp-170) cc_final: 0.8325 (ttm170) REVERT: B 359 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7996 (ptpt) outliers start: 53 outliers final: 35 residues processed: 234 average time/residue: 0.6707 time to fit residues: 172.1391 Evaluate side-chains 235 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 75 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN A 137 GLN A 480 GLN A 481 GLN A 807 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.129185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.094825 restraints weight = 17533.943| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.36 r_work: 0.2831 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14950 Z= 0.145 Angle : 0.547 9.249 20437 Z= 0.269 Chirality : 0.043 0.252 2314 Planarity : 0.004 0.037 2458 Dihedral : 9.857 146.923 2416 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.16 % Allowed : 17.07 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.20), residues: 1701 helix: 0.71 (0.18), residues: 829 sheet: -0.48 (0.39), residues: 162 loop : -0.62 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 882 TYR 0.011 0.001 TYR A 563 PHE 0.015 0.001 PHE A 902 TRP 0.011 0.001 TRP B 260 HIS 0.005 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (14949) covalent geometry : angle 0.54689 / 0.27 (20437) hydrogen bonds : bond 0.03829 / 2.61 ( 594) hydrogen bonds : angle 4.14913 / 2.94 ( 1653) Misc. bond : bond 0.00046 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 0.531 Fit side-chains REVERT: A 8 TYR cc_start: 0.8777 (p90) cc_final: 0.8174 (p90) REVERT: A 54 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: A 468 LYS cc_start: 0.8739 (mtpm) cc_final: 0.8365 (mtmm) REVERT: A 484 ARG cc_start: 0.7927 (mtt180) cc_final: 0.7037 (ttt-90) REVERT: A 918 ASP cc_start: 0.8538 (m-30) cc_final: 0.8107 (m-30) REVERT: A 956 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8567 (mp) REVERT: A 979 LYS cc_start: 0.8360 (mtpt) cc_final: 0.8051 (ttpp) REVERT: A 982 MET cc_start: 0.6761 (ptm) cc_final: 0.6385 (ppp) REVERT: A 999 HIS cc_start: 0.8645 (t-90) cc_final: 0.8346 (t-170) REVERT: A 1009 TYR cc_start: 0.8132 (t80) cc_final: 0.7349 (t80) REVERT: A 1109 ASP cc_start: 0.8170 (t70) cc_final: 0.7496 (t0) REVERT: A 1138 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: A 1159 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: A 1175 ARG cc_start: 0.8222 (ttm170) cc_final: 0.8021 (ttt180) REVERT: B 212 ASN cc_start: 0.8252 (t0) cc_final: 0.7882 (t0) REVERT: B 251 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8672 (mt) REVERT: B 276 ARG cc_start: 0.8556 (ttp-170) cc_final: 0.8331 (ttm170) REVERT: B 281 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7621 (t70) REVERT: B 359 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7819 (ptpt) REVERT: B 488 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8405 (mt-10) outliers start: 47 outliers final: 33 residues processed: 236 average time/residue: 0.6722 time to fit residues: 173.7538 Evaluate side-chains 238 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 118 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 171 optimal weight: 50.0000 chunk 135 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN A 137 GLN A 387 ASN A 807 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.128646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.094335 restraints weight = 17470.020| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.35 r_work: 0.2809 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14950 Z= 0.201 Angle : 0.590 9.078 20437 Z= 0.291 Chirality : 0.045 0.242 2314 Planarity : 0.004 0.039 2458 Dihedral : 9.986 148.014 2416 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.29 % Allowed : 17.00 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1701 helix: 0.59 (0.18), residues: 828 sheet: -0.59 (0.39), residues: 164 loop : -0.69 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 882 TYR 0.012 0.002 TYR A 563 PHE 0.015 0.001 PHE A 902 TRP 0.012 0.001 TRP B 260 HIS 0.007 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (14949) covalent geometry : angle 0.58982 / 0.29 (20437) hydrogen bonds : bond 0.04374 / 2.99 ( 594) hydrogen bonds : angle 4.25322 / 3.01 ( 1653) Misc. bond : bond 0.00064 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5277.87 seconds wall clock time: 90 minutes 46.46 seconds (5446.46 seconds total)