Starting phenix.real_space_refine on Wed Mar 4 12:32:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tz0_20585/03_2026/6tz0_20585.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tz0_20585/03_2026/6tz0_20585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6tz0_20585/03_2026/6tz0_20585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tz0_20585/03_2026/6tz0_20585.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tz0_20585/03_2026/6tz0_20585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tz0_20585/03_2026/6tz0_20585.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 8708 2.51 5 N 2333 2.21 5 O 2579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13674 Number of models: 1 Model: "" Number of chains: 2 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 Time building chain proxies: 2.48, per 1000 atoms: 0.18 Number of scatterers: 13674 At special positions: 0 Unit cell: (105.138, 145.494, 84.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2579 8.00 N 2333 7.00 C 8708 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=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 499.6 milliseconds 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 17 sheets defined 50.8% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 6 through 9 Processing helix chain 'A' and resid 10 through 16 removed outlier: 3.702A pdb=" N GLU A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 36 removed outlier: 4.209A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 45 removed outlier: 3.583A pdb=" N ARG A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.745A pdb=" N THR A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.662A pdb=" N TYR A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 135 Processing helix chain 'A' and resid 144 through 161 Processing helix chain 'A' and resid 165 through 176 removed outlier: 4.066A pdb=" N THR A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 223 through 238 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.811A pdb=" N GLY A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 294 through 307 removed outlier: 4.395A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 324 through 340 removed outlier: 3.690A pdb=" N VAL A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 357 removed outlier: 3.534A pdb=" N SER A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 398 removed outlier: 3.865A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 410 removed outlier: 3.880A pdb=" N GLY A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 457 through 460 removed outlier: 3.511A pdb=" N TYR A 460 " --> pdb=" O ALA A 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 460' Processing helix chain 'A' and resid 463 through 470 removed outlier: 4.143A pdb=" N PHE A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.560A pdb=" N SER A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 removed outlier: 3.521A pdb=" N TYR A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 3.813A 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 529 through 536 Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'A' and resid 556 through 574 removed outlier: 3.610A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 Processing helix chain 'A' and resid 643 through 666 removed outlier: 3.779A pdb=" N HIS A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 706 Processing helix chain 'A' and resid 735 through 739 removed outlier: 3.564A pdb=" N ARG A 738 " --> pdb=" O PHE A 735 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 739 " --> pdb=" O ALA A 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 735 through 739' Processing helix chain 'A' and resid 753 through 767 removed outlier: 3.557A pdb=" N MET A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 787 removed outlier: 3.692A pdb=" N LEU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 809 removed outlier: 3.542A pdb=" N THR A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 807 " --> pdb=" O SER A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 839 removed outlier: 3.700A pdb=" N MET A 839 " --> pdb=" O TRP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 879 removed outlier: 4.045A pdb=" N TYR A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 887 Processing helix chain 'A' and resid 893 through 900 Processing helix chain 'A' and resid 901 through 912 removed outlier: 3.666A pdb=" N ALA A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 916 Processing helix chain 'A' and resid 926 through 938 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 944 through 959 removed outlier: 3.824A pdb=" N LYS A 948 " --> pdb=" O GLY A 944 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 949 " --> pdb=" O GLU A 945 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 959 " --> pdb=" O ASP A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 995 through 1005 removed outlier: 4.115A pdb=" N VAL A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1020 removed outlier: 3.947A pdb=" N ALA A1018 " --> pdb=" O PRO A1015 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A1019 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A1020 " --> pdb=" O ASP A1017 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1015 through 1020' Processing helix chain 'A' and resid 1034 through 1038 removed outlier: 3.601A pdb=" N LYS A1038 " --> pdb=" O PRO A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1063 Processing helix chain 'A' and resid 1073 through 1081 removed outlier: 3.802A pdb=" N ILE A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1102 Processing helix chain 'A' and resid 1106 through 1115 Processing helix chain 'A' and resid 1117 through 1133 Processing helix chain 'A' and resid 1154 through 1159 Processing helix chain 'A' and resid 1165 through 1169 Processing helix chain 'A' and resid 1173 through 1189 removed outlier: 3.843A pdb=" N LEU A1177 " --> pdb=" O GLN A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1212 Processing helix chain 'B' and resid 9 through 16 removed outlier: 3.669A pdb=" N TYR B 13 " --> pdb=" O HIS B 9 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 61 removed outlier: 3.638A pdb=" N LYS B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 79 Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.648A pdb=" N SER B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 removed outlier: 3.766A pdb=" N LEU B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 4.063A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 325 through 341 Processing helix chain 'B' and resid 358 through 375 removed outlier: 3.737A pdb=" N PHE B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.999A 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 428 Processing helix chain 'B' and resid 433 through 439 removed outlier: 3.542A pdb=" N LEU B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 458 removed outlier: 3.655A pdb=" N MET B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 4.045A 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: 3.742A pdb=" N ALA B 496 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 519 removed outlier: 3.613A pdb=" N ARG B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 538 Processing helix chain 'B' and resid 546 through 557 removed outlier: 3.708A pdb=" N ILE B 554 " --> pdb=" O MET B 550 " (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 removed outlier: 3.645A pdb=" N LYS A 191 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.581A pdb=" N GLY A 280 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 380 through 384 removed outlier: 6.758A pdb=" N SER A 380 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER A 374 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS A 382 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 434 through 437 removed outlier: 6.155A pdb=" N GLU A 434 " --> pdb=" O TRP A 445 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TRP A 445 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU A 436 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 491 removed outlier: 5.741A pdb=" N ILE A 474 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLU A 623 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N LEU A 476 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 672 through 677 removed outlier: 7.084A pdb=" N ILE A 685 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE A 675 " --> pdb=" O MET A 683 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET A 683 " --> pdb=" O ILE A 675 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA9, first strand: chain 'A' and resid 720 through 722 removed outlier: 3.985A 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 795 removed outlier: 3.507A pdb=" N ILE A 831 " --> pdb=" O THR A 813 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 867 through 868 Processing sheet with id=AB3, first strand: chain 'A' and resid 919 through 921 Processing sheet with id=AB4, first strand: chain 'A' and resid 1022 through 1030 removed outlier: 4.287A pdb=" N ARG A1197 " --> pdb=" O GLU A1027 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 157 through 159 removed outlier: 6.959A pdb=" N ILE B 158 " --> pdb=" O ILE B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 204 through 208 removed outlier: 6.214A pdb=" N ARG B 204 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE B 229 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE B 206 " --> pdb=" O PHE B 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 297 through 299 removed outlier: 3.503A pdb=" N VAL B 267 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY B 255 " --> pdb=" O PRO B 318 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 257 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE B 316 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR B 259 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 378 through 381 removed outlier: 3.618A pdb=" N GLU B 488 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 353 " --> pdb=" O GLY B 489 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL B 505 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 350 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B 507 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR B 352 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR B 504 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL B 545 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU B 506 " --> pdb=" O VAL B 545 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3588 1.33 - 1.45: 2659 1.45 - 1.57: 7625 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 13968 Sorted by residual: bond pdb=" CB VAL A 589 " pdb=" CG2 VAL A 589 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 3.02e+00 bond pdb=" CB PHE A 206 " pdb=" CG PHE A 206 " ideal model delta sigma weight residual 1.502 1.464 0.038 2.30e-02 1.89e+03 2.80e+00 bond pdb=" N VAL A 891 " pdb=" CA VAL A 891 " ideal model delta sigma weight residual 1.459 1.441 0.018 1.15e-02 7.56e+03 2.53e+00 bond pdb=" CA VAL A 891 " pdb=" C VAL A 891 " ideal model delta sigma weight residual 1.525 1.508 0.017 1.17e-02 7.31e+03 2.17e+00 bond pdb=" CA ASP A 893 " pdb=" C ASP A 893 " ideal model delta sigma weight residual 1.524 1.504 0.020 1.35e-02 5.49e+03 2.11e+00 ... (remaining 13963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 18026 1.93 - 3.86: 756 3.86 - 5.79: 90 5.79 - 7.72: 31 7.72 - 9.65: 15 Bond angle restraints: 18918 Sorted by residual: angle pdb=" N CYS A 788 " pdb=" CA CYS A 788 " pdb=" C CYS A 788 " ideal model delta sigma weight residual 111.36 118.61 -7.25 1.09e+00 8.42e-01 4.43e+01 angle pdb=" N ARG A 790 " pdb=" CA ARG A 790 " pdb=" C ARG A 790 " ideal model delta sigma weight residual 113.16 120.08 -6.92 1.24e+00 6.50e-01 3.11e+01 angle pdb=" N ARG A 791 " pdb=" CA ARG A 791 " pdb=" C ARG A 791 " ideal model delta sigma weight residual 109.07 117.13 -8.06 1.61e+00 3.86e-01 2.50e+01 angle pdb=" C GLY A 427 " pdb=" N ARG A 428 " pdb=" CA ARG A 428 " ideal model delta sigma weight residual 121.54 130.62 -9.08 1.91e+00 2.74e-01 2.26e+01 angle pdb=" N LEU A 892 " pdb=" CA LEU A 892 " pdb=" C LEU A 892 " ideal model delta sigma weight residual 110.28 103.27 7.01 1.48e+00 4.57e-01 2.24e+01 ... (remaining 18913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.15: 7822 14.15 - 28.30: 416 28.30 - 42.46: 121 42.46 - 56.61: 15 56.61 - 70.76: 6 Dihedral angle restraints: 8380 sinusoidal: 3348 harmonic: 5032 Sorted by residual: dihedral pdb=" CA GLN A 480 " pdb=" C GLN A 480 " pdb=" N GLN A 481 " pdb=" CA GLN A 481 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA LEU A 753 " pdb=" C LEU A 753 " pdb=" N ASN A 754 " pdb=" CA ASN A 754 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" N GLN A 363 " pdb=" C GLN A 363 " pdb=" CA GLN A 363 " pdb=" CB GLN A 363 " ideal model delta harmonic sigma weight residual 122.80 133.83 -11.03 0 2.50e+00 1.60e-01 1.95e+01 ... (remaining 8377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1903 0.094 - 0.188: 195 0.188 - 0.281: 10 0.281 - 0.375: 3 0.375 - 0.469: 1 Chirality restraints: 2112 Sorted by residual: chirality pdb=" CA GLN A 363 " pdb=" N GLN A 363 " pdb=" C GLN A 363 " pdb=" CB GLN A 363 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" CB VAL A 357 " pdb=" CA VAL A 357 " pdb=" CG1 VAL A 357 " pdb=" CG2 VAL A 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB VAL A 771 " pdb=" CA VAL A 771 " pdb=" CG1 VAL A 771 " pdb=" CG2 VAL A 771 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2109 not shown) Planarity restraints: 2417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 606 " -0.028 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP A 606 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP A 606 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 606 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 606 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 606 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 606 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 606 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 606 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 606 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 769 " -0.018 2.00e-02 2.50e+03 2.37e-02 9.87e+00 pdb=" CG PHE A 769 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 769 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 769 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 769 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 769 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 769 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 203 " -0.048 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO A 204 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.041 5.00e-02 4.00e+02 ... (remaining 2414 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4083 2.82 - 3.34: 11899 3.34 - 3.86: 22703 3.86 - 4.38: 26743 4.38 - 4.90: 45779 Nonbonded interactions: 111207 Sorted by model distance: nonbonded pdb=" OH TYR B 352 " pdb=" OD1 ASP B 495 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR B 386 " pdb=" O HIS B 466 " model vdw 2.301 3.040 nonbonded pdb=" O LYS A 778 " pdb=" OH TYR A 845 " model vdw 2.312 3.040 nonbonded pdb=" OG SER A 716 " pdb=" O SER A 719 " model vdw 2.312 3.040 nonbonded pdb=" OE2 GLU A 612 " pdb=" NH2 ARG A 641 " model vdw 2.318 3.120 ... (remaining 111202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 12.450 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 : 0.006 0.078 13968 Z= 0.277 Angle : 0.939 9.650 18918 Z= 0.509 Chirality : 0.058 0.469 2112 Planarity : 0.007 0.072 2417 Dihedral : 10.042 70.759 5146 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.54 % Allowed : 3.56 % Favored : 95.90 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.16), residues: 1701 helix: -2.41 (0.13), residues: 810 sheet: -1.18 (0.34), residues: 176 loop : -1.97 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 336 TYR 0.040 0.003 TYR A 331 PHE 0.054 0.004 PHE A 769 TRP 0.065 0.004 TRP A 606 HIS 0.018 0.003 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00647 (13968) covalent geometry : angle 0.93935 (18918) hydrogen bonds : bond 0.16318 ( 578) hydrogen bonds : angle 6.94213 ( 1653) *********************** 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 413 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 405 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 203 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8696 (tt) REVERT: A 906 LEU cc_start: 0.8827 (mt) cc_final: 0.8458 (mt) REVERT: A 988 THR cc_start: 0.7797 (p) cc_final: 0.7361 (m) REVERT: A 998 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7935 (mp) REVERT: A 1019 LEU cc_start: 0.8713 (mt) cc_final: 0.8451 (mt) REVERT: A 1022 TYR cc_start: 0.8654 (p90) cc_final: 0.8133 (p90) REVERT: A 1080 ARG cc_start: 0.6767 (tmt90) cc_final: 0.6537 (ttt180) REVERT: A 1098 LYS cc_start: 0.8339 (mttm) cc_final: 0.7797 (pttt) REVERT: A 1126 ARG cc_start: 0.7791 (mtp180) cc_final: 0.7219 (mtt90) REVERT: A 1133 LEU cc_start: 0.7447 (mt) cc_final: 0.7198 (pp) REVERT: B 450 ASP cc_start: 0.8295 (m-30) cc_final: 0.7820 (m-30) outliers start: 8 outliers final: 3 residues processed: 409 average time/residue: 0.6860 time to fit residues: 302.1774 Evaluate side-chains 241 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 236 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain B residue 427 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.0870 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 164 ASN A 236 HIS A 375 ASN A 378 HIS A 412 HIS A 481 GLN A 629 GLN A 717 GLN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 ASN A 931 ASN A 939 GLN A 990 GLN A1044 ASN A1084 HIS A1095 GLN A1121 GLN A1140 HIS A1194 GLN B 180 GLN B 212 ASN B 217 GLN B 272 ASN B 393 ASN B 436 GLN B 459 GLN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.106345 restraints weight = 18393.921| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.62 r_work: 0.3078 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13968 Z= 0.145 Angle : 0.580 7.167 18918 Z= 0.306 Chirality : 0.042 0.186 2112 Planarity : 0.004 0.043 2417 Dihedral : 5.398 52.345 1905 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.71 % Rotamer: Outliers : 3.49 % Allowed : 11.90 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.18), residues: 1701 helix: -0.61 (0.17), residues: 811 sheet: -0.76 (0.36), residues: 170 loop : -1.36 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 336 TYR 0.022 0.002 TYR B 253 PHE 0.022 0.002 PHE A 769 TRP 0.028 0.002 TRP A 606 HIS 0.008 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00335 (13968) covalent geometry : angle 0.57994 (18918) hydrogen bonds : bond 0.04441 ( 578) hydrogen bonds : angle 4.83985 ( 1653) *********************** 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 315 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 263 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8913 (mttp) REVERT: A 25 GLU cc_start: 0.7701 (tt0) cc_final: 0.7404 (tm-30) REVERT: A 100 LYS cc_start: 0.8558 (mppt) cc_final: 0.8291 (mptp) REVERT: A 231 MET cc_start: 0.8641 (mmm) cc_final: 0.8364 (mmp) REVERT: A 302 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8094 (mtmm) REVERT: A 306 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8105 (mt) REVERT: A 452 MET cc_start: 0.8913 (tpt) cc_final: 0.8688 (ttt) REVERT: A 481 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: A 752 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6747 (mpt-90) REVERT: A 760 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8701 (tp) REVERT: A 942 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7991 (tppp) REVERT: A 978 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7329 (tp40) REVERT: A 988 THR cc_start: 0.7708 (p) cc_final: 0.7378 (m) REVERT: A 992 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.6974 (mttp) REVERT: A 1019 LEU cc_start: 0.8647 (mt) cc_final: 0.8261 (mt) REVERT: A 1022 TYR cc_start: 0.9039 (p90) cc_final: 0.8262 (p90) REVERT: A 1080 ARG cc_start: 0.6777 (tmt90) cc_final: 0.6547 (tmt90) REVERT: A 1098 LYS cc_start: 0.8335 (mttm) cc_final: 0.7767 (pttt) REVERT: A 1107 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6867 (tm) REVERT: A 1126 ARG cc_start: 0.8076 (mtp180) cc_final: 0.7344 (mtt90) REVERT: B 72 MET cc_start: 0.9207 (tpp) cc_final: 0.9004 (ttp) REVERT: B 254 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8359 (mm-30) REVERT: B 419 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: B 450 ASP cc_start: 0.8800 (m-30) cc_final: 0.8483 (m-30) outliers start: 52 outliers final: 20 residues processed: 293 average time/residue: 0.7145 time to fit residues: 225.3899 Evaluate side-chains 239 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 7 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 chunk 166 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 164 ASN A 375 ASN A 481 GLN A 629 GLN A 717 GLN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN A1121 GLN B 212 ASN B 429 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.126985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.104529 restraints weight = 18487.623| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.64 r_work: 0.3057 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13968 Z= 0.140 Angle : 0.541 7.207 18918 Z= 0.286 Chirality : 0.041 0.198 2112 Planarity : 0.004 0.034 2417 Dihedral : 4.720 44.449 1899 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.17 % Allowed : 12.84 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.19), residues: 1701 helix: 0.32 (0.18), residues: 805 sheet: -0.66 (0.37), residues: 168 loop : -1.16 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1073 TYR 0.018 0.002 TYR B 253 PHE 0.017 0.002 PHE A 769 TRP 0.021 0.002 TRP A 606 HIS 0.006 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00327 (13968) covalent geometry : angle 0.54096 (18918) hydrogen bonds : bond 0.03965 ( 578) hydrogen bonds : angle 4.52297 ( 1653) *********************** 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 291 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8903 (mttp) REVERT: A 25 GLU cc_start: 0.7711 (tt0) cc_final: 0.7494 (tm-30) REVERT: A 302 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8101 (mtmm) REVERT: A 452 MET cc_start: 0.8917 (tpt) cc_final: 0.8697 (ttt) REVERT: A 481 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: A 752 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6859 (tpt-90) REVERT: A 760 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8672 (tp) REVERT: A 771 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8170 (m) REVERT: A 978 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7288 (tp40) REVERT: A 988 THR cc_start: 0.7623 (p) cc_final: 0.7322 (m) REVERT: A 992 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7401 (mmmm) REVERT: A 993 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.7157 (ttp80) REVERT: A 1019 LEU cc_start: 0.8619 (mt) cc_final: 0.8226 (mt) REVERT: A 1022 TYR cc_start: 0.9049 (p90) cc_final: 0.8232 (p90) REVERT: A 1080 ARG cc_start: 0.6693 (tmt90) cc_final: 0.6362 (ttt180) REVERT: A 1098 LYS cc_start: 0.8262 (mttm) cc_final: 0.7705 (pttt) REVERT: A 1107 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6926 (tm) REVERT: A 1126 ARG cc_start: 0.8167 (mtp180) cc_final: 0.7414 (mtt90) REVERT: B 72 MET cc_start: 0.9178 (tpp) cc_final: 0.8969 (ttp) REVERT: B 254 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8320 (mm-30) REVERT: B 419 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: B 450 ASP cc_start: 0.8840 (m-30) cc_final: 0.8509 (m-30) outliers start: 62 outliers final: 29 residues processed: 274 average time/residue: 0.7255 time to fit residues: 214.0575 Evaluate side-chains 246 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 88 optimal weight: 30.0000 chunk 120 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 481 GLN A 514 ASN A 653 GLN A 687 GLN A 717 GLN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN A1044 ASN A1095 GLN A1121 GLN B 212 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102222 restraints weight = 18311.306| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.62 r_work: 0.3019 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13968 Z= 0.174 Angle : 0.566 8.140 18918 Z= 0.298 Chirality : 0.042 0.206 2112 Planarity : 0.004 0.034 2417 Dihedral : 4.753 47.028 1899 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.50 % Allowed : 13.04 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.20), residues: 1701 helix: 0.67 (0.18), residues: 803 sheet: -0.78 (0.35), residues: 176 loop : -1.03 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 336 TYR 0.021 0.002 TYR A 511 PHE 0.016 0.002 PHE A 769 TRP 0.019 0.002 TRP A 606 HIS 0.009 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00414 (13968) covalent geometry : angle 0.56580 (18918) hydrogen bonds : bond 0.04209 ( 578) hydrogen bonds : angle 4.50509 ( 1653) *********************** 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 291 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 224 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8936 (mttp) REVERT: A 37 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7013 (ptm-80) REVERT: A 452 MET cc_start: 0.8962 (tpt) cc_final: 0.8732 (ttt) REVERT: A 481 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7181 (pm20) REVERT: A 641 ARG cc_start: 0.7874 (ttt-90) cc_final: 0.7492 (ttt-90) REVERT: A 752 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6889 (mpt-90) REVERT: A 760 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8690 (tp) REVERT: A 771 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8264 (m) REVERT: A 916 LEU cc_start: 0.8638 (mt) cc_final: 0.8358 (mp) REVERT: A 978 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7324 (tp40) REVERT: A 988 THR cc_start: 0.7671 (p) cc_final: 0.7349 (m) REVERT: A 992 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7335 (mmtp) REVERT: A 993 ARG cc_start: 0.7688 (mtm-85) cc_final: 0.7294 (ttp80) REVERT: A 1080 ARG cc_start: 0.6822 (tmt90) cc_final: 0.6351 (ttt180) REVERT: A 1098 LYS cc_start: 0.8273 (mttm) cc_final: 0.7670 (pttt) REVERT: A 1107 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6930 (tm) REVERT: A 1126 ARG cc_start: 0.8191 (mtp180) cc_final: 0.7417 (mtt90) REVERT: B 21 ARG cc_start: 0.8743 (mtt-85) cc_final: 0.8460 (mtt180) REVERT: B 254 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8299 (mm-30) REVERT: B 419 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8050 (mt-10) REVERT: B 450 ASP cc_start: 0.8871 (m-30) cc_final: 0.8569 (m-30) outliers start: 67 outliers final: 36 residues processed: 267 average time/residue: 0.7204 time to fit residues: 207.2473 Evaluate side-chains 261 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 62 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 153 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN A 514 ASN A 717 GLN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN A1121 GLN B 212 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.103369 restraints weight = 18214.108| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.61 r_work: 0.3042 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13968 Z= 0.134 Angle : 0.537 8.737 18918 Z= 0.281 Chirality : 0.041 0.192 2112 Planarity : 0.004 0.034 2417 Dihedral : 4.562 48.700 1897 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.37 % Allowed : 13.58 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.20), residues: 1701 helix: 0.96 (0.18), residues: 804 sheet: -0.53 (0.37), residues: 168 loop : -0.88 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 276 TYR 0.014 0.001 TYR B 253 PHE 0.014 0.001 PHE A 206 TRP 0.013 0.001 TRP A 606 HIS 0.006 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00315 (13968) covalent geometry : angle 0.53694 (18918) hydrogen bonds : bond 0.03736 ( 578) hydrogen bonds : angle 4.35658 ( 1653) *********************** 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 286 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 221 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8930 (mttp) REVERT: A 37 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7015 (ptm-80) REVERT: A 452 MET cc_start: 0.9004 (tpt) cc_final: 0.8778 (ttt) REVERT: A 481 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7191 (pm20) REVERT: A 484 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6947 (mpp80) REVERT: A 752 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6896 (mpt-90) REVERT: A 771 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8268 (m) REVERT: A 959 ARG cc_start: 0.7824 (tpp-160) cc_final: 0.7534 (tpp-160) REVERT: A 978 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7285 (tp40) REVERT: A 988 THR cc_start: 0.7744 (p) cc_final: 0.7413 (m) REVERT: A 992 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7400 (mmtp) REVERT: A 993 ARG cc_start: 0.7599 (mtm-85) cc_final: 0.7250 (ttp80) REVERT: A 1098 LYS cc_start: 0.8162 (mttm) cc_final: 0.7634 (pttt) REVERT: A 1107 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.6999 (tm) REVERT: A 1126 ARG cc_start: 0.8189 (mtp180) cc_final: 0.7418 (mtt90) REVERT: B 21 ARG cc_start: 0.8749 (mtt-85) cc_final: 0.8469 (mtt180) REVERT: B 254 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8305 (mm-30) REVERT: B 369 GLN cc_start: 0.8705 (mm110) cc_final: 0.8499 (mm110) REVERT: B 419 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: B 450 ASP cc_start: 0.8856 (m-30) cc_final: 0.8560 (m-30) REVERT: B 465 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8732 (m) outliers start: 65 outliers final: 35 residues processed: 258 average time/residue: 0.7157 time to fit residues: 198.9486 Evaluate side-chains 258 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 7.9990 chunk 19 optimal weight: 0.0010 chunk 106 optimal weight: 30.0000 chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 135 optimal weight: 0.0370 chunk 66 optimal weight: 9.9990 overall best weight: 3.8070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 GLN A 717 GLN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN A1121 GLN B 212 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.126117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.103470 restraints weight = 18290.027| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.61 r_work: 0.3041 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13968 Z= 0.130 Angle : 0.524 9.641 18918 Z= 0.275 Chirality : 0.041 0.197 2112 Planarity : 0.004 0.034 2417 Dihedral : 4.480 49.900 1897 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.17 % Allowed : 14.11 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.20), residues: 1701 helix: 1.20 (0.19), residues: 795 sheet: -0.42 (0.37), residues: 168 loop : -0.77 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 276 TYR 0.016 0.001 TYR B 253 PHE 0.014 0.001 PHE A 206 TRP 0.010 0.001 TRP A 606 HIS 0.006 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00307 (13968) covalent geometry : angle 0.52443 (18918) hydrogen bonds : bond 0.03634 ( 578) hydrogen bonds : angle 4.29780 ( 1653) *********************** 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 277 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 215 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8946 (mttp) REVERT: A 37 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7022 (ptm-80) REVERT: A 100 LYS cc_start: 0.8479 (mppt) cc_final: 0.8149 (mttp) REVERT: A 320 ARG cc_start: 0.8087 (mmp80) cc_final: 0.7857 (mmp80) REVERT: A 752 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6737 (mpt-90) REVERT: A 771 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8270 (m) REVERT: A 906 LEU cc_start: 0.8836 (mp) cc_final: 0.8517 (mt) REVERT: A 912 ASN cc_start: 0.8208 (m-40) cc_final: 0.7946 (m-40) REVERT: A 978 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7299 (tp40) REVERT: A 988 THR cc_start: 0.7734 (p) cc_final: 0.7394 (m) REVERT: A 992 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7421 (mmtp) REVERT: A 993 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7269 (ttp80) REVERT: A 1080 ARG cc_start: 0.6827 (tmt90) cc_final: 0.6467 (tmt90) REVERT: A 1098 LYS cc_start: 0.8165 (mttm) cc_final: 0.7650 (pttt) REVERT: A 1107 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7146 (tm) REVERT: A 1126 ARG cc_start: 0.8270 (mtp180) cc_final: 0.7466 (mtt90) REVERT: B 21 ARG cc_start: 0.8756 (mtt-85) cc_final: 0.8471 (mtt180) REVERT: B 419 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: B 450 ASP cc_start: 0.8801 (m-30) cc_final: 0.8455 (m-30) REVERT: B 465 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8749 (m) outliers start: 62 outliers final: 36 residues processed: 252 average time/residue: 0.7382 time to fit residues: 199.8543 Evaluate side-chains 260 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 86 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 88 optimal weight: 30.0000 chunk 120 optimal weight: 9.9990 chunk 96 optimal weight: 30.0000 chunk 46 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 90 optimal weight: 0.0770 chunk 34 optimal weight: 7.9990 chunk 144 optimal weight: 0.4980 overall best weight: 5.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN A1121 GLN B 212 ASN B 346 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.102214 restraints weight = 18169.227| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.60 r_work: 0.3026 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13968 Z= 0.163 Angle : 0.555 10.354 18918 Z= 0.290 Chirality : 0.042 0.209 2112 Planarity : 0.004 0.036 2417 Dihedral : 4.582 50.841 1897 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.90 % Allowed : 14.31 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1701 helix: 1.21 (0.19), residues: 795 sheet: -0.62 (0.36), residues: 180 loop : -0.75 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 276 TYR 0.016 0.002 TYR B 253 PHE 0.016 0.002 PHE A 206 TRP 0.011 0.002 TRP A 606 HIS 0.008 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00388 (13968) covalent geometry : angle 0.55451 (18918) hydrogen bonds : bond 0.03962 ( 578) hydrogen bonds : angle 4.37108 ( 1653) *********************** 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 276 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8979 (mttp) REVERT: A 37 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7071 (ptm-80) REVERT: A 450 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9072 (mm) REVERT: A 484 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6955 (mpp80) REVERT: A 752 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6794 (mpt-90) REVERT: A 906 LEU cc_start: 0.8845 (mp) cc_final: 0.8554 (mt) REVERT: A 912 ASN cc_start: 0.8275 (m-40) cc_final: 0.7978 (m-40) REVERT: A 959 ARG cc_start: 0.7967 (tpp-160) cc_final: 0.7729 (tpp-160) REVERT: A 978 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7288 (tp40) REVERT: A 988 THR cc_start: 0.7719 (p) cc_final: 0.7361 (m) REVERT: A 992 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7434 (mmtp) REVERT: A 993 ARG cc_start: 0.7696 (mtm-85) cc_final: 0.7216 (ttp80) REVERT: A 1005 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8219 (mtmm) REVERT: A 1098 LYS cc_start: 0.8160 (mttm) cc_final: 0.7658 (pttt) REVERT: A 1107 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7232 (tm) REVERT: A 1126 ARG cc_start: 0.8298 (mtp180) cc_final: 0.7504 (mtt90) REVERT: B 419 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: B 450 ASP cc_start: 0.8840 (m-30) cc_final: 0.8537 (m-30) REVERT: B 465 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8743 (m) outliers start: 58 outliers final: 39 residues processed: 252 average time/residue: 0.7379 time to fit residues: 199.8818 Evaluate side-chains 257 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 118 optimal weight: 8.9990 chunk 137 optimal weight: 0.0040 chunk 135 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 overall best weight: 6.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 GLN ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 ASN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN A1121 GLN A1140 HIS B 212 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.101101 restraints weight = 18293.155| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.60 r_work: 0.3006 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13968 Z= 0.193 Angle : 0.589 10.455 18918 Z= 0.307 Chirality : 0.043 0.226 2112 Planarity : 0.004 0.039 2417 Dihedral : 4.692 51.702 1897 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.97 % Allowed : 14.85 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.20), residues: 1701 helix: 1.15 (0.18), residues: 794 sheet: -0.52 (0.37), residues: 175 loop : -0.74 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 276 TYR 0.018 0.002 TYR A1130 PHE 0.018 0.002 PHE A 206 TRP 0.011 0.002 TRP A 606 HIS 0.009 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00464 (13968) covalent geometry : angle 0.58853 (18918) hydrogen bonds : bond 0.04264 ( 578) hydrogen bonds : angle 4.44573 ( 1653) *********************** 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 272 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.9010 (mttp) REVERT: A 37 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7107 (ptm-80) REVERT: A 100 LYS cc_start: 0.8490 (mppt) cc_final: 0.8177 (mptp) REVERT: A 319 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8180 (mm) REVERT: A 450 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9074 (mm) REVERT: A 484 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6966 (mpp80) REVERT: A 752 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7166 (tpt-90) REVERT: A 906 LEU cc_start: 0.8826 (mp) cc_final: 0.8526 (mt) REVERT: A 912 ASN cc_start: 0.8316 (m-40) cc_final: 0.8015 (m-40) REVERT: A 959 ARG cc_start: 0.7989 (tpp-160) cc_final: 0.7739 (tpp-160) REVERT: A 978 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7273 (tp40) REVERT: A 988 THR cc_start: 0.7661 (p) cc_final: 0.7277 (m) REVERT: A 992 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7371 (mmtp) REVERT: A 1005 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8213 (mtmm) REVERT: A 1098 LYS cc_start: 0.8164 (mttm) cc_final: 0.7659 (pttt) REVERT: A 1107 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7094 (tm) REVERT: A 1126 ARG cc_start: 0.8255 (mtp180) cc_final: 0.7451 (mtt90) REVERT: B 364 SER cc_start: 0.9031 (p) cc_final: 0.8765 (m) REVERT: B 419 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8054 (mt-10) REVERT: B 465 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8720 (m) outliers start: 59 outliers final: 37 residues processed: 248 average time/residue: 0.7636 time to fit residues: 203.8421 Evaluate side-chains 253 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 13 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN A1121 GLN A1140 HIS B 212 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.101295 restraints weight = 18191.263| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.60 r_work: 0.3013 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13968 Z= 0.184 Angle : 0.592 10.927 18918 Z= 0.310 Chirality : 0.043 0.226 2112 Planarity : 0.004 0.063 2417 Dihedral : 4.712 52.314 1897 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.63 % Allowed : 15.52 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.20), residues: 1701 helix: 1.16 (0.18), residues: 794 sheet: -0.49 (0.37), residues: 175 loop : -0.69 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 487 TYR 0.017 0.002 TYR A 511 PHE 0.018 0.002 PHE A 206 TRP 0.011 0.002 TRP B 260 HIS 0.008 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00443 (13968) covalent geometry : angle 0.59177 (18918) hydrogen bonds : bond 0.04198 ( 578) hydrogen bonds : angle 4.45379 ( 1653) *********************** 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 274 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.9027 (mttp) REVERT: A 21 GLU cc_start: 0.8255 (pp20) cc_final: 0.7671 (pm20) REVERT: A 37 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7102 (ptm-80) REVERT: A 100 LYS cc_start: 0.8547 (mppt) cc_final: 0.8190 (mttp) REVERT: A 319 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8178 (mm) REVERT: A 450 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9071 (mm) REVERT: A 484 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6947 (mpp80) REVERT: A 752 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7106 (tpt-90) REVERT: A 906 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8524 (mt) REVERT: A 912 ASN cc_start: 0.8320 (m-40) cc_final: 0.8014 (m-40) REVERT: A 959 ARG cc_start: 0.7982 (tpp-160) cc_final: 0.7722 (tpp-160) REVERT: A 978 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7249 (tp40) REVERT: A 988 THR cc_start: 0.7654 (p) cc_final: 0.7248 (m) REVERT: A 992 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7401 (mmtp) REVERT: A 1005 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8225 (mtmm) REVERT: A 1095 GLN cc_start: 0.7097 (mt0) cc_final: 0.6893 (mt0) REVERT: A 1098 LYS cc_start: 0.8138 (mttm) cc_final: 0.7698 (pttt) REVERT: A 1107 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7114 (tm) REVERT: A 1126 ARG cc_start: 0.8276 (mtp180) cc_final: 0.7450 (mtt90) REVERT: B 364 SER cc_start: 0.9027 (p) cc_final: 0.8776 (m) REVERT: B 419 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: B 465 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8710 (m) outliers start: 54 outliers final: 37 residues processed: 254 average time/residue: 0.7481 time to fit residues: 204.3881 Evaluate side-chains 260 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 GLN A 717 GLN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1121 GLN A1140 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102421 restraints weight = 18120.084| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.60 r_work: 0.3029 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13968 Z= 0.146 Angle : 0.563 12.131 18918 Z= 0.294 Chirality : 0.041 0.208 2112 Planarity : 0.004 0.065 2417 Dihedral : 4.617 53.189 1897 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.36 % Allowed : 15.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.20), residues: 1701 helix: 1.28 (0.19), residues: 794 sheet: -0.51 (0.36), residues: 176 loop : -0.64 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 487 TYR 0.016 0.002 TYR A 101 PHE 0.015 0.001 PHE A 206 TRP 0.010 0.001 TRP B 260 HIS 0.006 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00346 (13968) covalent geometry : angle 0.56259 (18918) hydrogen bonds : bond 0.03797 ( 578) hydrogen bonds : angle 4.35493 ( 1653) ********************** 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 265 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.9003 (mttp) REVERT: A 21 GLU cc_start: 0.8242 (pp20) cc_final: 0.7569 (pm20) REVERT: A 37 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7050 (ptm-80) REVERT: A 100 LYS cc_start: 0.8482 (mppt) cc_final: 0.8173 (mptp) REVERT: A 450 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9065 (mm) REVERT: A 752 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7098 (tpt-90) REVERT: A 886 GLN cc_start: 0.7952 (tt0) cc_final: 0.7534 (pt0) REVERT: A 906 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8526 (mt) REVERT: A 912 ASN cc_start: 0.8297 (m-40) cc_final: 0.8010 (m-40) REVERT: A 959 ARG cc_start: 0.8007 (tpp-160) cc_final: 0.7754 (tpp-160) REVERT: A 988 THR cc_start: 0.7658 (p) cc_final: 0.7250 (m) REVERT: A 992 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7486 (mmtp) REVERT: A 1005 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8226 (mtmm) REVERT: A 1095 GLN cc_start: 0.6966 (mt0) cc_final: 0.6728 (mt0) REVERT: A 1098 LYS cc_start: 0.8136 (mttm) cc_final: 0.7694 (pttt) REVERT: A 1126 ARG cc_start: 0.8266 (mtp180) cc_final: 0.7468 (mtt90) REVERT: B 364 SER cc_start: 0.9028 (p) cc_final: 0.8774 (m) REVERT: B 419 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: B 465 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8710 (m) outliers start: 50 outliers final: 37 residues processed: 248 average time/residue: 0.7422 time to fit residues: 197.7372 Evaluate side-chains 255 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 210 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 109 optimal weight: 10.0000 chunk 98 optimal weight: 40.0000 chunk 131 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1121 GLN A1140 HIS B 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.101747 restraints weight = 18259.011| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.60 r_work: 0.3014 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13968 Z= 0.171 Angle : 0.581 11.850 18918 Z= 0.303 Chirality : 0.042 0.219 2112 Planarity : 0.004 0.059 2417 Dihedral : 4.695 57.812 1897 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.36 % Allowed : 15.66 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.20), residues: 1701 helix: 1.23 (0.19), residues: 794 sheet: -0.45 (0.36), residues: 178 loop : -0.66 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 487 TYR 0.017 0.002 TYR A 101 PHE 0.017 0.002 PHE A 206 TRP 0.010 0.002 TRP B 260 HIS 0.008 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00410 (13968) covalent geometry : angle 0.58082 (18918) hydrogen bonds : bond 0.04045 ( 578) hydrogen bonds : angle 4.40766 ( 1653) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5185.70 seconds wall clock time: 88 minutes 47.65 seconds (5327.65 seconds total)