Starting phenix.real_space_refine on Thu Jul 31 16:47:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tz0_20585/07_2025/6tz0_20585.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tz0_20585/07_2025/6tz0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6tz0_20585/07_2025/6tz0_20585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tz0_20585/07_2025/6tz0_20585.map" model { file = "/net/cci-nas-00/data/ceres_data/6tz0_20585/07_2025/6tz0_20585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tz0_20585/07_2025/6tz0_20585.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.08, per 1000 atoms: 0.59 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: 3.06 Conformation dependent library (CDL) restraints added in 1.8 seconds 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... Secondary structure from input PDB file: 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: 1.86 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: 5.34 Time building geometry restraints manager: 3.71 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.380 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.180 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.065 0.004 TRP A 606 HIS 0.018 0.003 HIS B 59 PHE 0.054 0.004 PHE A 769 TYR 0.040 0.003 TYR A 331 ARG 0.016 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.16318 ( 578) hydrogen bonds : angle 6.94213 ( 1653) covalent geometry : bond 0.00647 (13968) covalent geometry : angle 0.93935 (18918) *********************** 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 : 1.608 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: 0.7362 (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: 0.7235 (mtt90) REVERT: A 1133 LEU cc_start: 0.7447 (mt) cc_final: 0.7197 (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: 1.4720 time to fit residues: 651.2894 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 : 1.597 ------------------------------------------------------------------------------- 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 143 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 81 optimal weight: 0.0980 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 236 HIS A 375 ASN A 378 HIS A 412 HIS A 481 GLN A 514 ASN 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 182 HIS B 212 ASN B 217 GLN B 272 ASN B 436 GLN B 459 GLN B 490 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.130403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.108182 restraints weight = 18474.281| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.65 r_work: 0.3110 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13968 Z= 0.116 Angle : 0.544 7.490 18918 Z= 0.287 Chirality : 0.041 0.173 2112 Planarity : 0.004 0.040 2417 Dihedral : 5.266 53.814 1905 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.88 % Favored : 97.06 % Rotamer: Outliers : 3.36 % Allowed : 11.83 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.18), residues: 1701 helix: -0.54 (0.17), residues: 818 sheet: -0.74 (0.36), residues: 172 loop : -1.33 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 606 HIS 0.007 0.001 HIS B 59 PHE 0.020 0.002 PHE A 769 TYR 0.020 0.001 TYR B 253 ARG 0.006 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 578) hydrogen bonds : angle 4.72705 ( 1653) covalent geometry : bond 0.00261 (13968) covalent geometry : angle 0.54398 (18918) *********************** 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 321 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 271 time to evaluate : 1.539 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8906 (mttp) REVERT: A 25 GLU cc_start: 0.7663 (tt0) cc_final: 0.7389 (tm-30) REVERT: A 46 ASN cc_start: 0.8209 (t0) cc_final: 0.7978 (t0) REVERT: A 100 LYS cc_start: 0.8538 (mppt) cc_final: 0.8327 (mptp) REVERT: A 231 MET cc_start: 0.8637 (mmm) cc_final: 0.8349 (mmp) REVERT: A 302 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8201 (mtmm) REVERT: A 452 MET cc_start: 0.8843 (tpt) cc_final: 0.8620 (ttt) REVERT: A 481 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: A 489 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8399 (tp) REVERT: A 752 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6621 (mpt-90) REVERT: A 942 LYS cc_start: 0.8292 (tptm) cc_final: 0.8007 (tppp) REVERT: A 978 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7346 (tp40) REVERT: A 982 MET cc_start: 0.7653 (mtm) cc_final: 0.7383 (mtp) REVERT: A 988 THR cc_start: 0.7700 (p) cc_final: 0.7382 (m) REVERT: A 1080 ARG cc_start: 0.6689 (tmt90) cc_final: 0.6457 (ttt180) REVERT: A 1098 LYS cc_start: 0.8288 (mttm) cc_final: 0.7739 (pttt) REVERT: A 1107 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7099 (tm) REVERT: A 1126 ARG cc_start: 0.8045 (mtp180) cc_final: 0.7305 (mtt90) REVERT: B 140 GLU cc_start: 0.8707 (tt0) cc_final: 0.8411 (tt0) REVERT: B 254 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8340 (mm-30) REVERT: B 369 GLN cc_start: 0.8672 (mm110) cc_final: 0.8444 (mm110) REVERT: B 419 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: B 450 ASP cc_start: 0.8834 (m-30) cc_final: 0.8516 (m-30) outliers start: 50 outliers final: 19 residues processed: 298 average time/residue: 1.4889 time to fit residues: 479.0778 Evaluate side-chains 239 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 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 481 GLN Chi-restraints excluded: chain A residue 489 ILE 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 827 LEU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 978 GLN 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 1136 ASN 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 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 144 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 375 ASN A 481 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.101616 restraints weight = 18371.086| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.62 r_work: 0.3009 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13968 Z= 0.221 Angle : 0.623 7.304 18918 Z= 0.329 Chirality : 0.045 0.224 2112 Planarity : 0.005 0.053 2417 Dihedral : 5.032 46.295 1899 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.70 % Allowed : 12.57 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.19), residues: 1701 helix: 0.22 (0.18), residues: 803 sheet: -0.79 (0.36), residues: 182 loop : -1.16 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 606 HIS 0.013 0.002 HIS B 59 PHE 0.025 0.002 PHE A 769 TYR 0.028 0.002 TYR A 511 ARG 0.009 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.04894 ( 578) hydrogen bonds : angle 4.70702 ( 1653) covalent geometry : bond 0.00531 (13968) covalent geometry : angle 0.62305 (18918) *********************** 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 295 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 225 time to evaluate : 1.608 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8955 (mttp) REVERT: A 25 GLU cc_start: 0.7672 (tt0) cc_final: 0.7464 (tm-30) REVERT: A 452 MET cc_start: 0.8900 (tpt) cc_final: 0.8697 (ttt) REVERT: A 481 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7364 (pm20) REVERT: A 752 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6934 (tpt-90) REVERT: A 906 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8546 (mp) REVERT: A 957 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8192 (tptm) REVERT: A 978 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7314 (tp40) REVERT: A 988 THR cc_start: 0.7613 (p) cc_final: 0.7301 (m) REVERT: A 1080 ARG cc_start: 0.6773 (tmt90) cc_final: 0.6401 (ttt180) REVERT: A 1095 GLN cc_start: 0.7230 (mt0) cc_final: 0.6994 (mt0) REVERT: A 1098 LYS cc_start: 0.8336 (mttm) cc_final: 0.7755 (pttt) REVERT: A 1107 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6840 (tm) REVERT: A 1126 ARG cc_start: 0.8159 (mtp180) cc_final: 0.7388 (mtt90) REVERT: B 21 ARG cc_start: 0.8817 (mtt-85) cc_final: 0.8546 (mtt180) REVERT: B 254 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8334 (mm-30) REVERT: B 419 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: B 450 ASP cc_start: 0.8798 (m-30) cc_final: 0.8492 (m-30) outliers start: 70 outliers final: 34 residues processed: 268 average time/residue: 1.5380 time to fit residues: 444.3146 Evaluate side-chains 251 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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 144 ASP 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 533 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP 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 789 LEU Chi-restraints excluded: chain A residue 809 SER 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 906 LEU Chi-restraints excluded: chain A residue 957 LYS Chi-restraints excluded: chain A residue 978 GLN 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 1137 VAL 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 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 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 122 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN A 653 GLN A 717 GLN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN A1044 ASN A1121 GLN A1140 HIS B 59 HIS B 429 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102361 restraints weight = 18190.289| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.61 r_work: 0.3032 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3059 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= 0.162 Angle : 0.559 8.190 18918 Z= 0.295 Chirality : 0.042 0.203 2112 Planarity : 0.004 0.035 2417 Dihedral : 4.765 47.767 1897 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.17 % Allowed : 13.71 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1701 helix: 0.70 (0.18), residues: 795 sheet: -0.83 (0.36), residues: 182 loop : -0.96 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 606 HIS 0.008 0.001 HIS B 59 PHE 0.015 0.002 PHE A 206 TYR 0.018 0.002 TYR A 511 ARG 0.006 0.001 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 578) hydrogen bonds : angle 4.49242 ( 1653) covalent geometry : bond 0.00383 (13968) covalent geometry : angle 0.55923 (18918) *********************** 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 286 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 224 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8939 (mttp) REVERT: A 37 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7103 (ptm-80) REVERT: A 481 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7376 (pm20) REVERT: A 752 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6990 (mpt-90) REVERT: A 978 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7310 (tp40) REVERT: A 988 THR cc_start: 0.7661 (p) cc_final: 0.7351 (m) REVERT: A 992 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7333 (mmtp) REVERT: A 1098 LYS cc_start: 0.8230 (mttm) cc_final: 0.7688 (pttt) REVERT: A 1107 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6931 (tm) REVERT: A 1126 ARG cc_start: 0.8209 (mtp180) cc_final: 0.7423 (mtt90) REVERT: B 21 ARG cc_start: 0.8751 (mtt-85) cc_final: 0.8487 (mtt180) REVERT: B 254 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8342 (mm-30) REVERT: B 369 GLN cc_start: 0.8709 (mm110) cc_final: 0.8477 (mm110) REVERT: B 419 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: B 450 ASP cc_start: 0.8837 (m-30) cc_final: 0.8535 (m-30) outliers start: 62 outliers final: 35 residues processed: 265 average time/residue: 1.5868 time to fit residues: 453.3063 Evaluate side-chains 252 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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 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 809 SER 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 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 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 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 126 optimal weight: 9.9990 chunk 92 optimal weight: 0.3980 chunk 50 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 127 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN A1121 GLN A1140 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.129331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106772 restraints weight = 18175.875| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.62 r_work: 0.3091 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.002 0.027 13968 Z= 0.090 Angle : 0.489 9.369 18918 Z= 0.257 Chirality : 0.039 0.159 2112 Planarity : 0.003 0.033 2417 Dihedral : 4.312 49.115 1897 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.76 % Allowed : 14.31 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1701 helix: 1.23 (0.19), residues: 797 sheet: -0.55 (0.37), residues: 164 loop : -0.82 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 606 HIS 0.003 0.001 HIS A1036 PHE 0.009 0.001 PHE A 783 TYR 0.012 0.001 TYR A1042 ARG 0.006 0.000 ARG A 791 Details of bonding type rmsd hydrogen bonds : bond 0.03012 ( 578) hydrogen bonds : angle 4.14610 ( 1653) covalent geometry : bond 0.00197 (13968) covalent geometry : angle 0.48939 (18918) *********************** 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 271 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 215 time to evaluate : 1.447 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8883 (mttp) REVERT: A 37 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7027 (ptm-80) REVERT: A 100 LYS cc_start: 0.8464 (mppt) cc_final: 0.8183 (mttp) REVERT: A 481 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7233 (pm20) REVERT: A 752 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6759 (mpt-90) REVERT: A 906 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8471 (mt) REVERT: A 915 ASP cc_start: 0.8029 (m-30) cc_final: 0.7598 (m-30) REVERT: A 959 ARG cc_start: 0.7787 (tpp-160) cc_final: 0.7460 (tpp-160) REVERT: A 978 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7200 (tp40) REVERT: A 988 THR cc_start: 0.7705 (p) cc_final: 0.7404 (m) REVERT: A 992 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7144 (mmmt) REVERT: A 1098 LYS cc_start: 0.8163 (mttm) cc_final: 0.7602 (pttt) REVERT: A 1107 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7043 (tm) REVERT: A 1126 ARG cc_start: 0.8221 (mtp180) cc_final: 0.7421 (mtt180) REVERT: B 21 ARG cc_start: 0.8691 (mtt-85) cc_final: 0.8449 (mtt180) outliers start: 56 outliers final: 28 residues processed: 252 average time/residue: 1.5759 time to fit residues: 428.0086 Evaluate side-chains 232 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 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 809 SER Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 906 LEU 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 1107 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 372 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 110 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 617 GLN A 717 GLN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN A1121 GLN A1140 HIS B 346 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.129504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.106841 restraints weight = 18246.230| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.62 r_work: 0.3093 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13968 Z= 0.092 Angle : 0.491 9.764 18918 Z= 0.256 Chirality : 0.039 0.160 2112 Planarity : 0.003 0.032 2417 Dihedral : 4.189 50.357 1897 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.49 % Allowed : 14.85 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1701 helix: 1.48 (0.19), residues: 795 sheet: -0.39 (0.37), residues: 168 loop : -0.69 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 256 HIS 0.004 0.001 HIS A1036 PHE 0.009 0.001 PHE A 206 TYR 0.011 0.001 TYR B 253 ARG 0.007 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.02958 ( 578) hydrogen bonds : angle 4.07473 ( 1653) covalent geometry : bond 0.00206 (13968) covalent geometry : angle 0.49149 (18918) *********************** 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 264 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 212 time to evaluate : 1.441 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8869 (mttp) REVERT: A 37 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7082 (ptm-80) REVERT: A 116 TYR cc_start: 0.8262 (m-80) cc_final: 0.7988 (m-80) REVERT: A 131 LYS cc_start: 0.8417 (mtpp) cc_final: 0.8096 (tttt) REVERT: A 481 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7277 (pm20) REVERT: A 484 ARG cc_start: 0.7512 (tpp80) cc_final: 0.6850 (mtp180) REVERT: A 812 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7558 (ptm) REVERT: A 906 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8494 (mt) REVERT: A 959 ARG cc_start: 0.7724 (tpp-160) cc_final: 0.7480 (tpp-160) REVERT: A 985 LYS cc_start: 0.8462 (pmmt) cc_final: 0.7716 (tppp) REVERT: A 988 THR cc_start: 0.7703 (p) cc_final: 0.7423 (m) REVERT: A 1098 LYS cc_start: 0.8198 (mttm) cc_final: 0.7620 (pttt) REVERT: A 1107 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7080 (tm) REVERT: A 1126 ARG cc_start: 0.8241 (mtp180) cc_final: 0.7493 (mtt180) REVERT: B 21 ARG cc_start: 0.8722 (mtt-85) cc_final: 0.8482 (mtt180) REVERT: B 254 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8253 (mm-30) REVERT: B 419 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8053 (mt-10) outliers start: 52 outliers final: 30 residues processed: 247 average time/residue: 1.5776 time to fit residues: 419.9424 Evaluate side-chains 237 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 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 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 771 VAL Chi-restraints excluded: chain A residue 809 SER 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 906 LEU Chi-restraints excluded: chain A residue 913 ILE 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 321 MET 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 442 VAL Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 123 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 81 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN A 687 GLN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN A1121 GLN A1140 HIS ** B 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.102172 restraints weight = 18404.867| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.62 r_work: 0.3025 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3374 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= 0.177 Angle : 0.577 10.442 18918 Z= 0.299 Chirality : 0.043 0.202 2112 Planarity : 0.004 0.036 2417 Dihedral : 4.551 51.138 1897 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.83 % Allowed : 15.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1701 helix: 1.32 (0.19), residues: 795 sheet: -0.51 (0.36), residues: 192 loop : -0.65 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 606 HIS 0.008 0.001 HIS A1036 PHE 0.018 0.002 PHE A 206 TYR 0.017 0.002 TYR A 511 ARG 0.006 0.001 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 578) hydrogen bonds : angle 4.35463 ( 1653) covalent geometry : bond 0.00424 (13968) covalent geometry : angle 0.57694 (18918) *********************** 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 267 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 210 time to evaluate : 1.530 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7500 (mp0) REVERT: A 17 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8956 (mttp) REVERT: A 37 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7166 (ptm-80) REVERT: A 100 LYS cc_start: 0.8466 (mppt) cc_final: 0.8163 (mptp) REVERT: A 479 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7396 (mmm-85) REVERT: A 481 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7288 (pm20) REVERT: A 484 ARG cc_start: 0.7501 (tpp80) cc_final: 0.6824 (mtp180) REVERT: A 906 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8511 (mt) REVERT: A 959 ARG cc_start: 0.7755 (tpp-160) cc_final: 0.7510 (tpp-160) REVERT: A 988 THR cc_start: 0.7679 (p) cc_final: 0.7364 (m) REVERT: A 1080 ARG cc_start: 0.6466 (ttt-90) cc_final: 0.6168 (tmt90) REVERT: A 1095 GLN cc_start: 0.7211 (mt0) cc_final: 0.6985 (mt0) REVERT: A 1098 LYS cc_start: 0.8150 (mttm) cc_final: 0.7666 (pttt) REVERT: A 1107 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7234 (tm) REVERT: A 1126 ARG cc_start: 0.8254 (mtp180) cc_final: 0.7512 (mtt90) REVERT: B 21 ARG cc_start: 0.8774 (mtt-85) cc_final: 0.8509 (mtt180) REVERT: B 254 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8265 (mm-30) REVERT: B 364 SER cc_start: 0.9024 (p) cc_final: 0.8759 (m) REVERT: B 419 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8033 (mt-10) outliers start: 57 outliers final: 33 residues processed: 245 average time/residue: 1.5391 time to fit residues: 407.2617 Evaluate side-chains 243 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 1.965 ------------------------------------------------------------------------------- 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 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 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 771 VAL Chi-restraints excluded: chain A residue 809 SER 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 906 LEU 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 254 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 442 VAL Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 93 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 127 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 ASN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1121 GLN A1140 HIS ** B 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.101550 restraints weight = 18333.519| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.61 r_work: 0.3011 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3430 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= 0.189 Angle : 0.595 11.329 18918 Z= 0.309 Chirality : 0.043 0.216 2112 Planarity : 0.004 0.039 2417 Dihedral : 4.652 51.976 1897 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.49 % Allowed : 15.99 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.20), residues: 1701 helix: 1.23 (0.19), residues: 795 sheet: -0.55 (0.36), residues: 194 loop : -0.64 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 606 HIS 0.008 0.001 HIS A1036 PHE 0.018 0.002 PHE A 206 TYR 0.019 0.002 TYR B 253 ARG 0.007 0.001 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 578) hydrogen bonds : angle 4.42924 ( 1653) covalent geometry : bond 0.00453 (13968) covalent geometry : angle 0.59525 (18918) *********************** 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 262 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 210 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7492 (mp0) REVERT: A 17 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9007 (mttp) REVERT: A 37 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7365 (ptm-80) REVERT: A 100 LYS cc_start: 0.8535 (mppt) cc_final: 0.8196 (mttp) REVERT: A 450 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9065 (mm) REVERT: A 484 ARG cc_start: 0.7512 (tpp80) cc_final: 0.6813 (mtp180) REVERT: A 906 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8495 (mt) REVERT: A 959 ARG cc_start: 0.7724 (tpp-160) cc_final: 0.7465 (tpp-160) REVERT: A 978 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7261 (tp40) REVERT: A 988 THR cc_start: 0.7681 (p) cc_final: 0.7357 (m) REVERT: A 1080 ARG cc_start: 0.6528 (ttt-90) cc_final: 0.6261 (tmt90) REVERT: A 1095 GLN cc_start: 0.7096 (mt0) cc_final: 0.6873 (mt0) REVERT: A 1098 LYS cc_start: 0.8152 (mttm) cc_final: 0.7660 (pttt) REVERT: A 1107 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7216 (tm) REVERT: A 1126 ARG cc_start: 0.8264 (mtp180) cc_final: 0.7480 (mtt90) REVERT: B 21 ARG cc_start: 0.8763 (mtt-85) cc_final: 0.8492 (mtt180) REVERT: B 254 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8345 (mm-30) REVERT: B 364 SER cc_start: 0.9022 (p) cc_final: 0.8770 (m) REVERT: B 419 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8025 (mt-10) outliers start: 52 outliers final: 33 residues processed: 241 average time/residue: 1.5225 time to fit residues: 395.5334 Evaluate side-chains 241 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 1.615 ------------------------------------------------------------------------------- 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 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 771 VAL Chi-restraints excluded: chain A residue 809 SER 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 906 LEU Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 978 GLN 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 254 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 442 VAL Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 160 optimal weight: 0.0980 chunk 8 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 63 optimal weight: 0.0970 chunk 43 optimal weight: 0.7980 chunk 100 optimal weight: 20.0000 chunk 141 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1121 GLN A1140 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.105067 restraints weight = 18096.241| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.61 r_work: 0.3065 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13968 Z= 0.102 Angle : 0.523 11.978 18918 Z= 0.270 Chirality : 0.040 0.171 2112 Planarity : 0.004 0.062 2417 Dihedral : 4.335 53.061 1897 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.82 % Allowed : 16.60 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1701 helix: 1.50 (0.19), residues: 794 sheet: -0.29 (0.39), residues: 166 loop : -0.58 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 260 HIS 0.004 0.001 HIS A1036 PHE 0.010 0.001 PHE A 206 TYR 0.015 0.001 TYR B 253 ARG 0.013 0.001 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 578) hydrogen bonds : angle 4.18743 ( 1653) covalent geometry : bond 0.00233 (13968) covalent geometry : angle 0.52321 (18918) *********************** 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 243 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 1.640 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8950 (mttp) REVERT: A 37 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7130 (ptm-80) REVERT: A 100 LYS cc_start: 0.8472 (mppt) cc_final: 0.8143 (mttp) REVERT: A 116 TYR cc_start: 0.8250 (m-80) cc_final: 0.7975 (m-80) REVERT: A 481 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7305 (pm20) REVERT: A 812 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7628 (ptm) REVERT: A 906 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8485 (mt) REVERT: A 959 ARG cc_start: 0.7709 (tpp-160) cc_final: 0.7428 (tpp-160) REVERT: A 988 THR cc_start: 0.7680 (p) cc_final: 0.7346 (m) REVERT: A 1080 ARG cc_start: 0.6485 (ttt-90) cc_final: 0.6240 (tmt90) REVERT: A 1098 LYS cc_start: 0.8173 (mttm) cc_final: 0.7637 (pttt) REVERT: A 1126 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7480 (mtt180) REVERT: B 21 ARG cc_start: 0.8710 (mtt-85) cc_final: 0.8449 (mtt180) REVERT: B 254 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8302 (mm-30) REVERT: B 419 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8058 (mt-10) outliers start: 42 outliers final: 32 residues processed: 230 average time/residue: 1.5843 time to fit residues: 391.7592 Evaluate side-chains 232 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 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 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 771 VAL Chi-restraints excluded: chain A residue 809 SER 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 906 LEU 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 254 GLU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN A 687 GLN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN A1121 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.101841 restraints weight = 18191.942| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.60 r_work: 0.3021 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3513 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= 0.179 Angle : 0.585 10.184 18918 Z= 0.305 Chirality : 0.043 0.218 2112 Planarity : 0.004 0.056 2417 Dihedral : 4.606 59.949 1897 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.62 % Allowed : 16.94 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1701 helix: 1.34 (0.19), residues: 796 sheet: -0.46 (0.36), residues: 190 loop : -0.53 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 606 HIS 0.008 0.001 HIS A1036 PHE 0.017 0.002 PHE A 206 TYR 0.018 0.002 TYR B 253 ARG 0.014 0.001 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 578) hydrogen bonds : angle 4.37978 ( 1653) covalent geometry : bond 0.00430 (13968) covalent geometry : angle 0.58525 (18918) ********************** 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 241 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.9002 (mttp) REVERT: A 37 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7363 (ptm-80) REVERT: A 100 LYS cc_start: 0.8541 (mppt) cc_final: 0.8136 (mttp) REVERT: A 481 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7318 (pm20) REVERT: A 906 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8506 (mt) REVERT: A 959 ARG cc_start: 0.7773 (tpp-160) cc_final: 0.7493 (tpp-160) REVERT: A 988 THR cc_start: 0.7555 (p) cc_final: 0.7231 (m) REVERT: A 1045 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8082 (pt) REVERT: A 1080 ARG cc_start: 0.6518 (ttt-90) cc_final: 0.6267 (tmt90) REVERT: A 1098 LYS cc_start: 0.8195 (mttm) cc_final: 0.7667 (pttt) REVERT: A 1126 ARG cc_start: 0.8236 (mtp180) cc_final: 0.7465 (mtt90) REVERT: B 21 ARG cc_start: 0.8749 (mtt-85) cc_final: 0.8474 (mtt180) REVERT: B 254 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8384 (mm-30) REVERT: B 364 SER cc_start: 0.9029 (p) cc_final: 0.8769 (m) REVERT: B 419 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8024 (mt-10) outliers start: 39 outliers final: 31 residues processed: 228 average time/residue: 1.6190 time to fit residues: 399.5848 Evaluate side-chains 237 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 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 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 771 VAL Chi-restraints excluded: chain A residue 809 SER 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 906 LEU 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 254 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 442 VAL Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 105 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 119 optimal weight: 30.0000 chunk 23 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 ASN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN 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 = 0.3435 r_free = 0.3435 target = 0.125336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.102505 restraints weight = 18315.896| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.63 r_work: 0.3020 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13968 Z= 0.148 Angle : 0.564 12.239 18918 Z= 0.292 Chirality : 0.042 0.200 2112 Planarity : 0.004 0.060 2417 Dihedral : 4.517 52.695 1897 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.82 % Allowed : 16.87 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1701 helix: 1.36 (0.19), residues: 796 sheet: -0.45 (0.37), residues: 178 loop : -0.57 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 260 HIS 0.007 0.001 HIS A 126 PHE 0.015 0.001 PHE A 206 TYR 0.016 0.002 TYR B 253 ARG 0.013 0.001 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 578) hydrogen bonds : angle 4.33086 ( 1653) covalent geometry : bond 0.00354 (13968) covalent geometry : angle 0.56360 (18918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11013.05 seconds wall clock time: 187 minutes 46.59 seconds (11266.59 seconds total)