Starting phenix.real_space_refine on Fri Jun 13 10:01:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ty9_20582/06_2025/6ty9_20582.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ty9_20582/06_2025/6ty9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ty9_20582/06_2025/6ty9_20582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ty9_20582/06_2025/6ty9_20582.map" model { file = "/net/cci-nas-00/data/ceres_data/6ty9_20582/06_2025/6ty9_20582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ty9_20582/06_2025/6ty9_20582.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.009 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'RNA': 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: {'RNA': 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: {'RNA': 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: 8.44, per 1000 atoms: 0.58 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: 3.58 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 4.73 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: 5.21 Time building geometry restraints manager: 4.26 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: 20374 4.30 - 8.60: 48 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: 8710 34.09 - 68.18: 253 68.18 - 102.27: 15 102.27 - 136.36: 3 136.36 - 170.45: 2 Dihedral angle restraints: 8983 sinusoidal: 3951 harmonic: 5032 Sorted by residual: dihedral pdb=" O2G GTP M 2 " pdb=" O3B GTP M 2 " pdb=" PG GTP M 2 " pdb=" PB GTP M 2 " ideal model delta sinusoidal sigma weight residual 177.30 -12.25 -170.45 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O3A GTP M 2 " pdb=" O3B GTP M 2 " pdb=" PB GTP M 2 " pdb=" PG GTP M 2 " ideal model delta sinusoidal sigma weight residual -56.21 70.96 -127.16 1 2.00e+01 2.50e-03 3.85e+01 dihedral pdb=" C8 GTP M 2 " pdb=" C1' GTP M 2 " pdb=" N9 GTP M 2 " pdb=" O4' GTP M 2 " ideal model delta sinusoidal sigma weight residual 104.59 0.79 103.81 1 2.00e+01 2.50e-03 2.97e+01 ... (remaining 8980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2103 0.069 - 0.139: 199 0.139 - 0.208: 11 0.208 - 0.277: 0 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=" CA ILE A 433 " pdb=" N ILE A 433 " pdb=" C ILE A 433 " pdb=" CB ILE A 433 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.25e-01 chirality pdb=" CB VAL A 199 " pdb=" CA VAL A 199 " pdb=" CG1 VAL A 199 " pdb=" CG2 VAL A 199 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.02e-01 ... (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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 37.170 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 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 : 0.008 0.288 14950 Z= 0.400 Angle : 0.775 21.509 20437 Z= 0.408 Chirality : 0.043 0.346 2314 Planarity : 0.004 0.038 2458 Dihedral : 15.641 170.453 5749 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.002 TRP A 256 HIS 0.006 0.001 HIS B 490 PHE 0.018 0.002 PHE A 344 TYR 0.014 0.002 TYR B 178 ARG 0.011 0.001 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.29301 ( 594) hydrogen bonds : angle 9.15918 ( 1653) covalent geometry : bond 0.00850 (14949) covalent geometry : angle 0.77452 (20437) Misc. bond : bond 0.00001 ( 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 : 1.605 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: 2.1643 time to fit residues: 617.5985 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 : 2.628 ------------------------------------------------------------------------------- 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 145 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 156 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 137 GLN A 378 HIS A 387 ASN A 394 GLN A 412 HIS A 514 ASN A 617 GLN A 939 GLN A1020 HIS ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN B 53 HIS B 180 GLN B 346 ASN B 542 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.128502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.094028 restraints weight = 17624.551| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.45 r_work: 0.2837 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14950 Z= 0.151 Angle : 0.547 10.221 20437 Z= 0.283 Chirality : 0.041 0.148 2314 Planarity : 0.004 0.044 2458 Dihedral : 12.767 169.793 2501 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.02 % Allowed : 12.97 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.18), residues: 1701 helix: -1.29 (0.16), residues: 833 sheet: -1.12 (0.37), residues: 174 loop : -1.27 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.005 0.001 HIS B 59 PHE 0.013 0.001 PHE A 206 TYR 0.013 0.001 TYR A 563 ARG 0.005 0.001 ARG B 518 Details of bonding type rmsd hydrogen bonds : bond 0.04918 ( 594) hydrogen bonds : angle 4.87630 ( 1653) covalent geometry : bond 0.00349 (14949) covalent geometry : angle 0.54650 (20437) Misc. bond : bond 0.00062 ( 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 252 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 2.563 Fit side-chains revert: symmetry clash REVERT: A 8 TYR cc_start: 0.8805 (p90) cc_final: 0.8098 (p90) REVERT: A 92 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8605 (mt-10) REVERT: A 468 LYS cc_start: 0.8698 (mtpm) cc_final: 0.8329 (mtmm) REVERT: A 484 ARG cc_start: 0.8146 (mtt180) cc_final: 0.6927 (ttp80) REVERT: A 485 ARG cc_start: 0.7615 (mtp180) cc_final: 0.7011 (mtm-85) REVERT: A 789 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8718 (pt) REVERT: A 918 ASP cc_start: 0.8630 (m-30) cc_final: 0.8331 (m-30) REVERT: A 947 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6860 (tm-30) REVERT: A 1009 TYR cc_start: 0.8099 (t80) cc_final: 0.7351 (t80) REVERT: A 1033 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8636 (mp) REVERT: A 1105 THR cc_start: 0.8915 (t) cc_final: 0.8657 (p) REVERT: A 1175 ARG cc_start: 0.8254 (ttm170) cc_final: 0.8009 (ttt180) REVERT: B 212 ASN cc_start: 0.8439 (t0) cc_final: 0.8204 (t0) REVERT: B 251 ILE cc_start: 0.9176 (pt) cc_final: 0.8702 (mt) REVERT: B 276 ARG cc_start: 0.8567 (ttp-170) cc_final: 0.8333 (ttm170) outliers start: 30 outliers final: 13 residues processed: 238 average time/residue: 1.6385 time to fit residues: 426.1955 Evaluate side-chains 213 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 1.629 ------------------------------------------------------------------------------- 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 899 GLU Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 340 VAL 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 26 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 GLN A1070 ASN B 64 ASN B 182 HIS B 429 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.133188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.099352 restraints weight = 17554.209| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.36 r_work: 0.2902 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14950 Z= 0.089 Angle : 0.467 9.455 20437 Z= 0.237 Chirality : 0.038 0.130 2314 Planarity : 0.003 0.040 2458 Dihedral : 12.134 162.751 2498 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.55 % Allowed : 14.11 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.20), residues: 1701 helix: 0.03 (0.17), residues: 838 sheet: -0.77 (0.39), residues: 168 loop : -0.91 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 260 HIS 0.004 0.001 HIS A1203 PHE 0.010 0.001 PHE B 548 TYR 0.011 0.001 TYR A 165 ARG 0.006 0.000 ARG B 310 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 594) hydrogen bonds : angle 4.21716 ( 1653) covalent geometry : bond 0.00191 (14949) covalent geometry : angle 0.46656 (20437) Misc. bond : bond 0.00024 ( 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 258 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 1.715 Fit side-chains REVERT: A 8 TYR cc_start: 0.8709 (p90) cc_final: 0.8173 (p90) REVERT: A 54 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7992 (m-30) REVERT: A 92 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8280 (mt-10) REVERT: A 190 ASP cc_start: 0.8584 (t70) cc_final: 0.8152 (t0) REVERT: A 468 LYS cc_start: 0.8605 (mtpm) cc_final: 0.8224 (mtmm) REVERT: A 484 ARG cc_start: 0.8080 (mtt180) cc_final: 0.6951 (ttp80) REVERT: A 485 ARG cc_start: 0.7481 (mtp180) cc_final: 0.6727 (mtm-85) REVERT: A 757 MET cc_start: 0.9070 (tpt) cc_final: 0.8749 (tpp) REVERT: A 827 LEU cc_start: 0.7945 (pt) cc_final: 0.7560 (mt) REVERT: A 918 ASP cc_start: 0.8582 (m-30) cc_final: 0.8273 (m-30) REVERT: A 1009 TYR cc_start: 0.8061 (t80) cc_final: 0.7334 (t80) REVERT: A 1109 ASP cc_start: 0.8252 (t70) cc_final: 0.7926 (t0) REVERT: A 1138 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: A 1159 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: A 1175 ARG cc_start: 0.8220 (ttm170) cc_final: 0.7923 (ttt180) REVERT: B 212 ASN cc_start: 0.8173 (t0) cc_final: 0.7910 (t0) REVERT: B 251 ILE cc_start: 0.9128 (pt) cc_final: 0.8633 (mt) REVERT: B 276 ARG cc_start: 0.8547 (ttp-170) cc_final: 0.8325 (ttm170) REVERT: B 517 MET cc_start: 0.8999 (mmp) cc_final: 0.8707 (mmp) outliers start: 38 outliers final: 11 residues processed: 244 average time/residue: 1.3812 time to fit residues: 368.4542 Evaluate side-chains 213 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 1.532 ------------------------------------------------------------------------------- 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 789 LEU Chi-restraints excluded: chain A residue 908 LEU 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 256 CYS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 427 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.0020 chunk 152 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 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 = 0.3452 r_free = 0.3452 target = 0.131810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.096706 restraints weight = 17335.259| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.45 r_work: 0.2868 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14950 Z= 0.102 Angle : 0.469 9.059 20437 Z= 0.237 Chirality : 0.038 0.142 2314 Planarity : 0.003 0.037 2458 Dihedral : 11.838 160.327 2498 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.96 % Allowed : 14.92 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1701 helix: 0.62 (0.18), residues: 828 sheet: -0.61 (0.38), residues: 168 loop : -0.74 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 256 HIS 0.006 0.001 HIS A 999 PHE 0.010 0.001 PHE B 548 TYR 0.011 0.001 TYR A 969 ARG 0.003 0.000 ARG B 310 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 594) hydrogen bonds : angle 4.07056 ( 1653) covalent geometry : bond 0.00232 (14949) covalent geometry : angle 0.46852 (20437) Misc. bond : bond 0.00024 ( 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 249 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 1.728 Fit side-chains REVERT: A 8 TYR cc_start: 0.8755 (p90) cc_final: 0.8213 (p90) REVERT: A 54 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: A 263 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8728 (m110) REVERT: A 313 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7749 (mm-30) REVERT: A 468 LYS cc_start: 0.8572 (mtpm) cc_final: 0.8156 (mtmm) REVERT: A 484 ARG cc_start: 0.8003 (mtt180) cc_final: 0.6894 (ttp80) REVERT: A 485 ARG cc_start: 0.7446 (mtp180) cc_final: 0.6875 (mtm-85) REVERT: A 757 MET cc_start: 0.9092 (tpt) cc_final: 0.8798 (tpp) REVERT: A 812 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.6944 (ptm) REVERT: A 827 LEU cc_start: 0.7962 (pt) cc_final: 0.7683 (mt) REVERT: A 918 ASP cc_start: 0.8543 (m-30) cc_final: 0.8135 (m-30) REVERT: A 999 HIS cc_start: 0.8765 (t-170) cc_final: 0.8380 (t-90) REVERT: A 1009 TYR cc_start: 0.8005 (t80) cc_final: 0.7225 (t80) REVERT: A 1109 ASP cc_start: 0.8245 (t70) cc_final: 0.7910 (t0) REVERT: A 1138 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: A 1159 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: A 1175 ARG cc_start: 0.8226 (ttm170) cc_final: 0.7891 (ttt180) REVERT: B 212 ASN cc_start: 0.8227 (t0) cc_final: 0.7940 (t0) REVERT: B 251 ILE cc_start: 0.9122 (pt) cc_final: 0.8628 (mt) REVERT: B 276 ARG cc_start: 0.8536 (ttp-170) cc_final: 0.8308 (ttm170) REVERT: B 359 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7952 (ptpt) REVERT: B 488 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8458 (mt-10) REVERT: B 517 MET cc_start: 0.8990 (mmp) cc_final: 0.8726 (mmp) outliers start: 44 outliers final: 21 residues processed: 237 average time/residue: 1.3984 time to fit residues: 363.1742 Evaluate side-chains 222 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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 263 ASN 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 489 ILE Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 812 MET 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 1044 ASN 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 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 479 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 9 optimal weight: 9.9990 chunk 157 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 82 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 514 ASN A 724 GLN A 807 ASN A1070 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.128174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.092856 restraints weight = 17424.726| |-----------------------------------------------------------------------------| r_work (start): 0.2911 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: 3.41 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2151 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= 0.185 Angle : 0.538 8.954 20437 Z= 0.273 Chirality : 0.041 0.167 2314 Planarity : 0.004 0.038 2458 Dihedral : 11.975 165.183 2498 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.90 % Allowed : 15.19 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1701 helix: 0.59 (0.18), residues: 823 sheet: -0.51 (0.40), residues: 164 loop : -0.79 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 256 HIS 0.006 0.001 HIS A1036 PHE 0.014 0.001 PHE A 206 TYR 0.012 0.002 TYR A 969 ARG 0.005 0.001 ARG A 841 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 594) hydrogen bonds : angle 4.24478 ( 1653) covalent geometry : bond 0.00444 (14949) covalent geometry : angle 0.53840 (20437) Misc. bond : bond 0.00049 ( 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 256 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 198 time to evaluate : 1.641 Fit side-chains REVERT: A 8 TYR cc_start: 0.8805 (p90) cc_final: 0.8173 (p90) REVERT: A 54 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.8003 (m-30) REVERT: A 92 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8535 (mt-10) REVERT: A 263 ASN cc_start: 0.9111 (OUTLIER) cc_final: 0.8753 (m110) REVERT: A 313 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7757 (mm-30) REVERT: A 468 LYS cc_start: 0.8679 (mtpm) cc_final: 0.8286 (mtmm) REVERT: A 484 ARG cc_start: 0.8063 (mtt180) cc_final: 0.6908 (ttp80) REVERT: A 485 ARG cc_start: 0.7568 (mtp180) cc_final: 0.6939 (mtm-85) REVERT: A 812 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7415 (ptm) REVERT: A 827 LEU cc_start: 0.8075 (pt) cc_final: 0.7620 (mt) REVERT: A 918 ASP cc_start: 0.8601 (m-30) cc_final: 0.8186 (m-30) REVERT: A 956 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8510 (mp) REVERT: A 999 HIS cc_start: 0.8780 (t-170) cc_final: 0.8403 (t-90) REVERT: A 1109 ASP cc_start: 0.8244 (t70) cc_final: 0.7524 (t0) REVERT: A 1138 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: A 1159 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: A 1175 ARG cc_start: 0.8231 (ttm170) cc_final: 0.8000 (ttt180) REVERT: B 212 ASN cc_start: 0.8363 (t0) cc_final: 0.8019 (t0) REVERT: B 276 ARG cc_start: 0.8524 (ttp-170) cc_final: 0.8286 (ttm170) REVERT: B 359 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7869 (ptpt) REVERT: B 488 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8494 (mt-10) REVERT: B 517 MET cc_start: 0.8999 (mmp) cc_final: 0.8768 (mmp) outliers start: 58 outliers final: 31 residues processed: 236 average time/residue: 1.4272 time to fit residues: 367.0656 Evaluate side-chains 234 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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 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 436 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 489 ILE 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 714 GLU Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 766 ASP Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 943 LEU 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 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 427 ILE 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 169 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 724 GLN A 807 ASN B 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.127826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.092473 restraints weight = 17504.689| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.46 r_work: 0.2847 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2243 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 : 0.523 8.816 20437 Z= 0.265 Chirality : 0.041 0.167 2314 Planarity : 0.004 0.037 2458 Dihedral : 11.800 161.615 2498 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.03 % Allowed : 15.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1701 helix: 0.65 (0.18), residues: 831 sheet: -0.38 (0.40), residues: 162 loop : -0.69 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 260 HIS 0.006 0.001 HIS A1036 PHE 0.013 0.001 PHE A 902 TYR 0.012 0.001 TYR A 969 ARG 0.006 0.001 ARG A1080 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 594) hydrogen bonds : angle 4.18342 ( 1653) covalent geometry : bond 0.00391 (14949) covalent geometry : angle 0.52335 (20437) Misc. bond : bond 0.00047 ( 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 262 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 202 time to evaluate : 1.691 Fit side-chains REVERT: A 8 TYR cc_start: 0.8783 (p90) cc_final: 0.8155 (p90) REVERT: A 54 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.8017 (m-30) REVERT: A 92 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8474 (mt-10) REVERT: A 203 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8973 (mp) REVERT: A 313 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7732 (mm-30) REVERT: A 468 LYS cc_start: 0.8669 (mtpm) cc_final: 0.8275 (mtmm) REVERT: A 484 ARG cc_start: 0.8010 (mtt180) cc_final: 0.6946 (ttt-90) REVERT: A 485 ARG cc_start: 0.7522 (mtp180) cc_final: 0.6938 (mtm-85) REVERT: A 681 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8812 (t0) REVERT: A 918 ASP cc_start: 0.8599 (m-30) cc_final: 0.8170 (m-30) REVERT: A 956 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8517 (mp) REVERT: A 999 HIS cc_start: 0.8782 (t-170) cc_final: 0.8432 (t-90) REVERT: A 1009 TYR cc_start: 0.8029 (t80) cc_final: 0.7173 (t80) REVERT: A 1109 ASP cc_start: 0.8245 (t70) cc_final: 0.7563 (t0) REVERT: A 1138 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7346 (tt0) REVERT: A 1159 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: A 1175 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7978 (ttt180) REVERT: B 212 ASN cc_start: 0.8370 (t0) cc_final: 0.8089 (t0) REVERT: B 276 ARG cc_start: 0.8535 (ttp-170) cc_final: 0.8297 (ttm170) REVERT: B 281 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7797 (t70) REVERT: B 359 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7842 (ptpt) REVERT: B 488 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8477 (mt-10) outliers start: 60 outliers final: 33 residues processed: 244 average time/residue: 1.4534 time to fit residues: 386.8071 Evaluate side-chains 237 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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 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 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 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 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 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 411 THR Chi-restraints excluded: chain B residue 424 GLU 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 105 optimal weight: 0.7980 chunk 139 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN A 480 GLN A 486 GLN A 724 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 = 0.3391 r_free = 0.3391 target = 0.127345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.092110 restraints weight = 17476.919| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.45 r_work: 0.2832 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14950 Z= 0.184 Angle : 0.547 8.443 20437 Z= 0.278 Chirality : 0.042 0.174 2314 Planarity : 0.004 0.037 2458 Dihedral : 11.788 160.505 2498 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.44 % Allowed : 15.59 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1701 helix: 0.62 (0.18), residues: 829 sheet: -0.37 (0.41), residues: 162 loop : -0.68 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 260 HIS 0.006 0.001 HIS A1036 PHE 0.013 0.001 PHE A 902 TYR 0.012 0.002 TYR A 563 ARG 0.006 0.001 ARG A 841 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 594) hydrogen bonds : angle 4.22046 ( 1653) covalent geometry : bond 0.00444 (14949) covalent geometry : angle 0.54737 (20437) Misc. bond : bond 0.00050 ( 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 269 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 203 time to evaluate : 1.705 Fit side-chains REVERT: A 8 TYR cc_start: 0.8814 (p90) cc_final: 0.8173 (p90) REVERT: A 54 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: A 92 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8521 (mt-10) REVERT: A 203 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.8974 (mp) REVERT: A 263 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8700 (m110) REVERT: A 313 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 468 LYS cc_start: 0.8707 (mtpm) cc_final: 0.8310 (mtmm) REVERT: A 484 ARG cc_start: 0.8032 (mtt180) cc_final: 0.7004 (ttt-90) REVERT: A 485 ARG cc_start: 0.7377 (mtp180) cc_final: 0.6898 (mtm-85) REVERT: A 681 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8833 (t0) REVERT: A 714 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7312 (pt0) REVERT: A 812 MET cc_start: 0.7862 (ptm) cc_final: 0.7643 (ptm) REVERT: A 918 ASP cc_start: 0.8596 (m-30) cc_final: 0.8135 (m-30) REVERT: A 956 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8534 (mp) REVERT: A 999 HIS cc_start: 0.8782 (t-170) cc_final: 0.8414 (t-90) REVERT: A 1009 TYR cc_start: 0.8067 (t80) cc_final: 0.7251 (t80) REVERT: A 1109 ASP cc_start: 0.8222 (t70) cc_final: 0.7549 (t0) REVERT: A 1138 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: A 1175 ARG cc_start: 0.8220 (ttm170) cc_final: 0.7969 (ttt180) REVERT: B 212 ASN cc_start: 0.8413 (t0) cc_final: 0.8048 (t0) REVERT: B 276 ARG cc_start: 0.8542 (ttp-170) cc_final: 0.8304 (ttm170) REVERT: B 281 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7823 (t70) REVERT: B 359 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7873 (ptpt) REVERT: B 488 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8509 (mt-10) outliers start: 66 outliers final: 39 residues processed: 247 average time/residue: 1.4191 time to fit residues: 383.3061 Evaluate side-chains 243 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 1.794 ------------------------------------------------------------------------------- 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 431 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 471 LYS 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 714 GLU 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 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 196 THR 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 427 ILE 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 44 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 156 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN A 724 GLN A 807 ASN B 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.127562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.092380 restraints weight = 17346.542| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.44 r_work: 0.2846 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14950 Z= 0.174 Angle : 0.537 8.591 20437 Z= 0.273 Chirality : 0.041 0.168 2314 Planarity : 0.004 0.037 2458 Dihedral : 11.658 154.728 2498 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.90 % Allowed : 16.06 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1701 helix: 0.65 (0.18), residues: 829 sheet: -0.40 (0.40), residues: 162 loop : -0.65 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.006 0.001 HIS A1036 PHE 0.015 0.001 PHE A 902 TYR 0.012 0.001 TYR A 563 ARG 0.006 0.000 ARG A 841 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 594) hydrogen bonds : angle 4.16497 ( 1653) covalent geometry : bond 0.00419 (14949) covalent geometry : angle 0.53730 (20437) Misc. bond : bond 0.00051 ( 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 253 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 1.508 Fit side-chains REVERT: A 8 TYR cc_start: 0.8799 (p90) cc_final: 0.8166 (p90) REVERT: A 54 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: A 92 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8519 (mt-10) REVERT: A 203 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8980 (mp) REVERT: A 263 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8682 (m110) REVERT: A 313 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7732 (mm-30) REVERT: A 468 LYS cc_start: 0.8694 (mtpm) cc_final: 0.8298 (mtmm) REVERT: A 484 ARG cc_start: 0.7966 (mtt180) cc_final: 0.7000 (ttt-90) REVERT: A 485 ARG cc_start: 0.7388 (mtp180) cc_final: 0.6900 (mtm-85) REVERT: A 681 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8858 (t0) REVERT: A 714 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7298 (pt0) REVERT: A 812 MET cc_start: 0.7945 (ptm) cc_final: 0.7688 (ptm) REVERT: A 918 ASP cc_start: 0.8591 (m-30) cc_final: 0.8117 (m-30) REVERT: A 922 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8290 (tppp) REVERT: A 956 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8535 (mp) REVERT: A 999 HIS cc_start: 0.8784 (t-170) cc_final: 0.8423 (t-90) REVERT: A 1009 TYR cc_start: 0.8064 (t80) cc_final: 0.7256 (t80) REVERT: A 1109 ASP cc_start: 0.8213 (t70) cc_final: 0.7537 (t0) REVERT: A 1138 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7426 (tt0) REVERT: A 1159 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: A 1175 ARG cc_start: 0.8223 (ttm170) cc_final: 0.7982 (ttt180) REVERT: B 212 ASN cc_start: 0.8365 (t0) cc_final: 0.8062 (t0) REVERT: B 276 ARG cc_start: 0.8544 (ttp-170) cc_final: 0.8306 (ttm170) REVERT: B 281 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7843 (t70) REVERT: B 359 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7706 (ptpt) REVERT: B 488 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8478 (mt-10) outliers start: 58 outliers final: 37 residues processed: 235 average time/residue: 1.4114 time to fit residues: 362.4837 Evaluate side-chains 235 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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 431 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 471 LYS 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 714 GLU 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 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 86 VAL Chi-restraints excluded: chain B residue 196 THR 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 411 THR Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 427 ILE 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 69 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 113 optimal weight: 30.0000 chunk 102 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 overall best weight: 7.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN A 480 GLN A 481 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 = 0.3389 r_free = 0.3389 target = 0.126862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.091923 restraints weight = 17346.312| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.39 r_work: 0.2784 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14950 Z= 0.227 Angle : 0.586 8.749 20437 Z= 0.297 Chirality : 0.043 0.188 2314 Planarity : 0.004 0.039 2458 Dihedral : 11.813 154.303 2498 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.03 % Allowed : 16.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1701 helix: 0.52 (0.18), residues: 827 sheet: -0.54 (0.39), residues: 164 loop : -0.70 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 260 HIS 0.007 0.001 HIS A1036 PHE 0.014 0.002 PHE A 902 TYR 0.012 0.002 TYR A 563 ARG 0.006 0.001 ARG A 841 Details of bonding type rmsd hydrogen bonds : bond 0.04644 ( 594) hydrogen bonds : angle 4.28713 ( 1653) covalent geometry : bond 0.00549 (14949) covalent geometry : angle 0.58602 (20437) Misc. bond : bond 0.00065 ( 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 256 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 196 time to evaluate : 3.023 Fit side-chains REVERT: A 8 TYR cc_start: 0.8822 (p90) cc_final: 0.8177 (p90) REVERT: A 54 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.8045 (m-30) REVERT: A 92 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8588 (mt-10) REVERT: A 263 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8688 (m110) REVERT: A 313 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7749 (mm-30) REVERT: A 468 LYS cc_start: 0.8774 (mtpm) cc_final: 0.8358 (mtmm) REVERT: A 484 ARG cc_start: 0.8024 (mtt180) cc_final: 0.7021 (ttt-90) REVERT: A 681 ASP cc_start: 0.9068 (OUTLIER) cc_final: 0.8853 (t0) REVERT: A 714 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7376 (pt0) REVERT: A 812 MET cc_start: 0.7863 (ptm) cc_final: 0.7640 (ptm) REVERT: A 918 ASP cc_start: 0.8594 (m-30) cc_final: 0.8177 (m-30) REVERT: A 951 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7716 (ptm160) REVERT: A 956 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8570 (mp) REVERT: A 999 HIS cc_start: 0.8774 (t-170) cc_final: 0.8423 (t-90) REVERT: A 1025 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8028 (mm-30) REVERT: A 1109 ASP cc_start: 0.8170 (t70) cc_final: 0.7506 (t0) REVERT: A 1138 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: A 1175 ARG cc_start: 0.8300 (ttm170) cc_final: 0.8049 (ttt180) REVERT: B 212 ASN cc_start: 0.8397 (t0) cc_final: 0.8068 (t160) REVERT: B 276 ARG cc_start: 0.8514 (ttp-170) cc_final: 0.8261 (ttm170) REVERT: B 359 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8029 (ptpt) outliers start: 60 outliers final: 36 residues processed: 240 average time/residue: 1.7251 time to fit residues: 455.1050 Evaluate side-chains 231 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 2.092 ------------------------------------------------------------------------------- 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 431 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 471 LYS 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 714 GLU 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 196 THR 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 359 LYS Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 424 GLU 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 169 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 GLN A 481 GLN A 724 GLN A 807 ASN B 64 ASN B 459 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.127414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.092136 restraints weight = 17423.775| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.45 r_work: 0.2801 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14950 Z= 0.170 Angle : 0.538 9.234 20437 Z= 0.273 Chirality : 0.041 0.165 2314 Planarity : 0.004 0.037 2458 Dihedral : 11.617 148.328 2498 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.56 % Allowed : 16.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1701 helix: 0.62 (0.18), residues: 829 sheet: -0.45 (0.40), residues: 162 loop : -0.63 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 260 HIS 0.005 0.001 HIS A1036 PHE 0.017 0.001 PHE A 902 TYR 0.012 0.001 TYR A1083 ARG 0.007 0.000 ARG A 841 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 594) hydrogen bonds : angle 4.16901 ( 1653) covalent geometry : bond 0.00408 (14949) covalent geometry : angle 0.53795 (20437) Misc. bond : bond 0.00051 ( 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 252 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 199 time to evaluate : 1.712 Fit side-chains REVERT: A 8 TYR cc_start: 0.8801 (p90) cc_final: 0.8156 (p90) REVERT: A 54 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.8031 (m-30) REVERT: A 92 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8583 (mt-10) REVERT: A 263 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8687 (m110) REVERT: A 313 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7740 (mm-30) REVERT: A 468 LYS cc_start: 0.8729 (mtpm) cc_final: 0.8306 (mtmm) REVERT: A 484 ARG cc_start: 0.7979 (mtt180) cc_final: 0.7016 (ttt-90) REVERT: A 899 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8077 (tm-30) REVERT: A 918 ASP cc_start: 0.8550 (m-30) cc_final: 0.8106 (m-30) REVERT: A 951 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7691 (ptm160) REVERT: A 956 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8509 (mp) REVERT: A 999 HIS cc_start: 0.8789 (t-170) cc_final: 0.8428 (t-90) REVERT: A 1009 TYR cc_start: 0.8056 (t80) cc_final: 0.7233 (t80) REVERT: A 1109 ASP cc_start: 0.8220 (t70) cc_final: 0.7524 (t0) REVERT: A 1138 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7474 (tt0) REVERT: A 1159 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: A 1175 ARG cc_start: 0.8218 (ttm170) cc_final: 0.7994 (ttt180) REVERT: B 212 ASN cc_start: 0.8330 (t0) cc_final: 0.7926 (t0) REVERT: B 276 ARG cc_start: 0.8552 (ttp-170) cc_final: 0.8311 (ttm170) REVERT: B 359 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7802 (ptpt) REVERT: B 488 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8486 (mt-10) outliers start: 53 outliers final: 36 residues processed: 238 average time/residue: 1.7707 time to fit residues: 462.3635 Evaluate side-chains 236 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 1.704 ------------------------------------------------------------------------------- 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 431 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 471 LYS 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 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 411 THR Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 427 ILE 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 51 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 135 optimal weight: 0.0670 chunk 130 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 111 optimal weight: 0.1980 chunk 168 optimal weight: 0.6980 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN A 807 ASN A1070 ASN B 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.098509 restraints weight = 17619.238| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.36 r_work: 0.2880 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14950 Z= 0.090 Angle : 0.475 9.153 20437 Z= 0.241 Chirality : 0.038 0.147 2314 Planarity : 0.003 0.037 2458 Dihedral : 11.116 135.771 2498 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.15 % Allowed : 18.01 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1701 helix: 0.97 (0.18), residues: 838 sheet: -0.38 (0.41), residues: 158 loop : -0.53 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 260 HIS 0.004 0.001 HIS A1203 PHE 0.016 0.001 PHE A 902 TYR 0.010 0.001 TYR A 563 ARG 0.007 0.000 ARG A 841 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 594) hydrogen bonds : angle 3.92868 ( 1653) covalent geometry : bond 0.00196 (14949) covalent geometry : angle 0.47483 (20437) Misc. bond : bond 0.00025 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11838.27 seconds wall clock time: 207 minutes 49.75 seconds (12469.75 seconds total)