Starting phenix.real_space_refine on Sat May 17 13:15:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h77_34519/05_2025/8h77_34519.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h77_34519/05_2025/8h77_34519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h77_34519/05_2025/8h77_34519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h77_34519/05_2025/8h77_34519.map" model { file = "/net/cci-nas-00/data/ceres_data/8h77_34519/05_2025/8h77_34519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h77_34519/05_2025/8h77_34519.cif" } resolution = 3.2 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= 0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 76 5.16 5 Be 2 3.05 5 C 9939 2.51 5 N 2698 2.21 5 O 3001 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15726 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5158 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 17, 'TRANS': 618} Chain breaks: 1 Chain: "B" Number of atoms: 5012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5012 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 17, 'TRANS': 602} Chain breaks: 1 Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 942 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 928 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "E" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1134 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "F" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2490 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 295} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.30, per 1000 atoms: 0.53 Number of scatterers: 15726 At special positions: 0 Unit cell: (113.42, 142.31, 138.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 76 16.00 P 4 15.00 F 6 9.00 O 3001 8.00 N 2698 7.00 C 9939 6.00 Be 2 4.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 2.0 seconds 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3676 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 17 sheets defined 40.5% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 Processing helix chain 'A' and resid 37 through 61 removed outlier: 4.244A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 94 through 103 removed outlier: 3.591A pdb=" N GLY A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.676A pdb=" N ALA A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 138 removed outlier: 3.511A pdb=" N TYR A 137 " --> pdb=" O TYR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 removed outlier: 3.678A pdb=" N VAL A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 310 Processing helix chain 'A' and resid 398 through 420 removed outlier: 4.140A pdb=" N LYS A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 444 removed outlier: 4.218A pdb=" N LYS A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LYS A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 490 through 496 removed outlier: 3.597A pdb=" N ASN A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 548 through 571 removed outlier: 4.447A pdb=" N LYS A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ASN A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU A 563 " --> pdb=" O LYS A 559 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 removed outlier: 3.616A pdb=" N ARG A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.651A pdb=" N MET A 620 " --> pdb=" O THR A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 645 removed outlier: 3.704A pdb=" N GLU A 636 " --> pdb=" O HIS A 632 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 666 removed outlier: 3.817A pdb=" N LYS A 652 " --> pdb=" O ASP A 648 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 665 " --> pdb=" O THR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 688 removed outlier: 4.157A pdb=" N HIS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.962A pdb=" N LEU B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 60 removed outlier: 4.271A pdb=" N ARG B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 67 removed outlier: 3.716A pdb=" N LEU B 65 " --> pdb=" O PRO B 62 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER B 67 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.548A pdb=" N ALA B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 398 through 422 removed outlier: 3.594A pdb=" N LYS B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 444 removed outlier: 4.331A pdb=" N ALA B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 452 Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 490 through 495 Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 515 through 526 removed outlier: 4.125A pdb=" N GLU B 519 " --> pdb=" O GLU B 515 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.617A pdb=" N LYS B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 552 " --> pdb=" O GLU B 548 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 554 " --> pdb=" O LYS B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 572 Processing helix chain 'B' and resid 599 through 607 Processing helix chain 'B' and resid 613 through 621 removed outlier: 3.552A pdb=" N MET B 617 " --> pdb=" O ASN B 614 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY B 618 " --> pdb=" O SER B 615 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR B 619 " --> pdb=" O THR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 645 removed outlier: 3.791A pdb=" N ALA B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 666 Processing helix chain 'B' and resid 672 through 689 removed outlier: 4.087A pdb=" N HIS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 302 removed outlier: 3.690A pdb=" N LEU E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 312 removed outlier: 3.732A pdb=" N LEU E 309 " --> pdb=" O THR E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 325 removed outlier: 3.988A pdb=" N LEU E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 337 removed outlier: 4.119A pdb=" N ARG E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 391 removed outlier: 3.559A pdb=" N GLY E 385 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS E 391 " --> pdb=" O GLU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 395 Processing helix chain 'F' and resid 3 through 10 Processing helix chain 'F' and resid 52 through 56 removed outlier: 3.522A pdb=" N THR F 55 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 80 removed outlier: 4.012A pdb=" N GLU F 74 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET F 80 " --> pdb=" O ILE F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 108 removed outlier: 3.867A pdb=" N VAL F 101 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 144 removed outlier: 3.581A pdb=" N ASP F 139 " --> pdb=" O HIS F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 193 Proline residue: F 180 - end of helix Processing helix chain 'F' and resid 195 through 214 Processing helix chain 'F' and resid 220 through 245 removed outlier: 3.541A pdb=" N ILE F 224 " --> pdb=" O SER F 220 " (cutoff:3.500A) Proline residue: F 232 - end of helix removed outlier: 3.685A pdb=" N CYS F 240 " --> pdb=" O ASN F 236 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS F 241 " --> pdb=" O TYR F 237 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU F 242 " --> pdb=" O CYS F 238 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL F 243 " --> pdb=" O GLN F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 258 Processing helix chain 'F' and resid 265 through 278 removed outlier: 4.593A pdb=" N ARG F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 295 removed outlier: 3.516A pdb=" N LYS F 290 " --> pdb=" O ALA F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 320 removed outlier: 4.614A pdb=" N VAL F 302 " --> pdb=" O LEU F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 329 removed outlier: 3.772A pdb=" N PHE F 324 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG F 325 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY F 326 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE F 328 " --> pdb=" O ARG F 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.604A pdb=" N GLU A 13 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 179 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 281 removed outlier: 3.777A pdb=" N LEU A 217 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 73 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N TYR A 216 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ILE A 75 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 83 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N HIS A 149 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLU A 153 " --> pdb=" O HIS A 149 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE A 165 " --> pdb=" O PHE B 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA4, first strand: chain 'A' and resid 220 through 223 removed outlier: 3.757A pdb=" N ARG A 221 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU A 274 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS A 223 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE A 272 " --> pdb=" O LYS A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 315 through 322 removed outlier: 6.663A pdb=" N ILE A 335 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL A 318 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A 333 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N HIS A 320 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA A 331 " --> pdb=" O HIS A 320 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER A 322 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE A 329 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET A 363 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 357 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N PHE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 458 through 459 removed outlier: 4.166A pdb=" N HIS A 458 " --> pdb=" O TYR A 512 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N VAL A 511 " --> pdb=" O SER A 482 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N TYR A 484 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N MET A 513 " --> pdb=" O TYR A 484 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE A 486 " --> pdb=" O MET A 513 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA8, first strand: chain 'B' and resid 315 through 323 removed outlier: 4.004A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 335 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 354 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET B 363 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL B 357 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N PHE B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 510 through 513 removed outlier: 5.893A pdb=" N ILE B 483 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 577 through 580 removed outlier: 3.985A pdb=" N LYS B 577 " --> pdb=" O LYS B 624 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS B 590 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 65 through 68 removed outlier: 3.545A pdb=" N LEU C 74 " --> pdb=" O LYS C 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 25 through 31 removed outlier: 4.601A pdb=" N VAL C 27 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N SER C 39 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL C 29 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR C 37 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE C 31 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE C 47 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.250A pdb=" N ALA D 6 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 24 through 31 removed outlier: 5.824A pdb=" N ASP D 26 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU D 41 " --> pdb=" O ASP D 26 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS D 49 " --> pdb=" O CYS D 40 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY D 42 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE D 47 " --> pdb=" O GLY D 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 291 through 294 removed outlier: 3.877A pdb=" N GLY E 293 " --> pdb=" O LYS E 284 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE E 364 " --> pdb=" O ASP E 371 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE E 373 " --> pdb=" O ARG E 362 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG E 362 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA E 375 " --> pdb=" O ASN E 360 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN E 360 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN E 377 " --> pdb=" O GLN E 358 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLN E 358 " --> pdb=" O GLN E 377 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP E 356 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG E 355 " --> pdb=" O LEU E 347 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 34 through 36 removed outlier: 3.646A pdb=" N THR F 35 " --> pdb=" O LYS F 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 40 through 41 615 hydrogen bonds defined for protein. 1737 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: 5.03 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2702 1.32 - 1.44: 4056 1.44 - 1.57: 9132 1.57 - 1.69: 8 1.69 - 1.82: 121 Bond restraints: 16019 Sorted by residual: bond pdb=" CA ASP D 70 " pdb=" C ASP D 70 " ideal model delta sigma weight residual 1.520 1.421 0.099 1.25e-02 6.40e+03 6.29e+01 bond pdb=" CA ASP B 672 " pdb=" C ASP B 672 " ideal model delta sigma weight residual 1.531 1.572 -0.040 7.40e-03 1.83e+04 2.97e+01 bond pdb=" N ARG D 71 " pdb=" CA ARG D 71 " ideal model delta sigma weight residual 1.458 1.389 0.069 1.33e-02 5.65e+03 2.66e+01 bond pdb=" CA THR C 69 " pdb=" C THR C 69 " ideal model delta sigma weight residual 1.526 1.459 0.067 1.37e-02 5.33e+03 2.40e+01 bond pdb=" F2 BEF A 802 " pdb="BE BEF A 802 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.83e+01 ... (remaining 16014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 21262 2.88 - 5.76: 265 5.76 - 8.65: 27 8.65 - 11.53: 6 11.53 - 14.41: 4 Bond angle restraints: 21564 Sorted by residual: angle pdb=" C LYS D 65 " pdb=" CA LYS D 65 " pdb=" CB LYS D 65 " ideal model delta sigma weight residual 110.62 100.83 9.79 1.86e+00 2.89e-01 2.77e+01 angle pdb=" N LEU E 325 " pdb=" CA LEU E 325 " pdb=" C LEU E 325 " ideal model delta sigma weight residual 112.89 106.74 6.15 1.24e+00 6.50e-01 2.46e+01 angle pdb=" C1' ADP B 801 " pdb=" C2' ADP B 801 " pdb=" C3' ADP B 801 " ideal model delta sigma weight residual 111.00 96.59 14.41 3.00e+00 1.11e-01 2.31e+01 angle pdb=" N TYR F 98 " pdb=" CA TYR F 98 " pdb=" C TYR F 98 " ideal model delta sigma weight residual 112.55 118.69 -6.14 1.35e+00 5.49e-01 2.07e+01 angle pdb=" N CYS E 327 " pdb=" CA CYS E 327 " pdb=" C CYS E 327 " ideal model delta sigma weight residual 112.90 107.20 5.70 1.31e+00 5.83e-01 1.90e+01 ... (remaining 21559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.16: 9462 31.16 - 62.33: 325 62.33 - 93.49: 28 93.49 - 124.65: 0 124.65 - 155.82: 3 Dihedral angle restraints: 9818 sinusoidal: 4156 harmonic: 5662 Sorted by residual: dihedral pdb=" O2A ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PA ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sinusoidal sigma weight residual 300.00 144.19 155.82 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' ADP B 801 " pdb=" O5' ADP B 801 " pdb=" PA ADP B 801 " pdb=" O2A ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 94.96 -154.96 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 79.51 -139.51 1 2.00e+01 2.50e-03 4.23e+01 ... (remaining 9815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2208 0.095 - 0.189: 139 0.189 - 0.284: 6 0.284 - 0.378: 1 0.378 - 0.473: 1 Chirality restraints: 2355 Sorted by residual: chirality pdb=" CA ILE E 374 " pdb=" N ILE E 374 " pdb=" C ILE E 374 " pdb=" CB ILE E 374 " both_signs ideal model delta sigma weight residual False 2.43 2.91 -0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" CA THR C 69 " pdb=" N THR C 69 " pdb=" C THR C 69 " pdb=" CB THR C 69 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C2' ADP B 801 " pdb=" C1' ADP B 801 " pdb=" C3' ADP B 801 " pdb=" O2' ADP B 801 " both_signs ideal model delta sigma weight residual False -2.51 -2.79 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 2352 not shown) Planarity restraints: 2764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 78 " 0.047 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO B 79 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 79 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 79 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 396 " 0.033 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO E 397 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 397 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 397 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS E 285 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C HIS E 285 " 0.033 2.00e-02 2.50e+03 pdb=" O HIS E 285 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS E 286 " -0.011 2.00e-02 2.50e+03 ... (remaining 2761 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 3 2.07 - 2.78: 3356 2.78 - 3.49: 21640 3.49 - 4.19: 35176 4.19 - 4.90: 61908 Nonbonded interactions: 122083 Sorted by model distance: nonbonded pdb=" OD1 ASN B 46 " pdb=" F1 BEF B 802 " model vdw 1.365 2.990 nonbonded pdb=" CE LYS E 286 " pdb=" CG2 ILE E 292 " model vdw 1.866 3.860 nonbonded pdb=" OG1 THR E 381 " pdb=" OE1 GLU E 384 " model vdw 2.063 3.040 nonbonded pdb=" NE2 GLN F 315 " pdb=" OE2 GLU F 319 " model vdw 2.096 3.120 nonbonded pdb=" O2' ADP B 801 " pdb=" O3' ADP B 801 " model vdw 2.106 2.432 ... (remaining 122078 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 217 or resid 278 through 690 or resid 801 throu \ gh 802)) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 1 through 111) selection = chain 'D' } 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: 1.070 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: 0.110 Set scattering table: 0.140 Process input model: 34.420 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 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 : 0.012 0.999 16021 Z= 1.096 Angle : 0.839 14.411 21564 Z= 0.473 Chirality : 0.050 0.473 2355 Planarity : 0.004 0.069 2764 Dihedral : 15.363 155.815 6142 Min Nonbonded Distance : 1.365 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.12 % Allowed : 0.87 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.57 (0.18), residues: 1912 helix: -0.22 (0.20), residues: 684 sheet: -0.39 (0.29), residues: 325 loop : -1.94 (0.18), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 109 HIS 0.017 0.002 HIS E 285 PHE 0.032 0.002 PHE E 289 TYR 0.019 0.002 TYR F 163 ARG 0.013 0.001 ARG C 88 Details of bonding type rmsd hydrogen bonds : bond 0.19130 ( 615) hydrogen bonds : angle 7.08276 ( 1737) covalent geometry : bond 0.00508 (16019) covalent geometry : angle 0.83874 (21564) Misc. bond : bond 0.95085 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 420 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.7975 (ptmm) cc_final: 0.6983 (mmtt) REVERT: A 125 MET cc_start: 0.6936 (mtm) cc_final: 0.6710 (mtm) REVERT: A 288 ILE cc_start: 0.8391 (mt) cc_final: 0.8147 (mt) REVERT: A 414 GLU cc_start: 0.7098 (tt0) cc_final: 0.6859 (mt-10) REVERT: A 450 ARG cc_start: 0.7490 (ptp-110) cc_final: 0.7182 (ptp90) REVERT: A 492 GLU cc_start: 0.6980 (tp30) cc_final: 0.6711 (tp30) REVERT: A 515 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7858 (mm-30) REVERT: A 553 MET cc_start: 0.5302 (tpp) cc_final: 0.4963 (tpp) REVERT: A 576 GLU cc_start: 0.6321 (mm-30) cc_final: 0.5909 (tp30) REVERT: A 603 GLU cc_start: 0.6681 (tt0) cc_final: 0.6010 (tp30) REVERT: A 681 TYR cc_start: 0.7317 (m-10) cc_final: 0.7111 (m-10) REVERT: B 18 GLN cc_start: 0.7433 (mt0) cc_final: 0.7136 (tt0) REVERT: B 69 LYS cc_start: 0.7395 (ptpt) cc_final: 0.6692 (mmtt) REVERT: B 88 ASP cc_start: 0.6405 (p0) cc_final: 0.5967 (p0) REVERT: B 100 ASN cc_start: 0.7769 (t0) cc_final: 0.7413 (t0) REVERT: B 123 ILE cc_start: 0.6757 (mm) cc_final: 0.6516 (tt) REVERT: B 174 PRO cc_start: 0.8466 (Cg_endo) cc_final: 0.8244 (Cg_exo) REVERT: B 286 LYS cc_start: 0.8276 (mtmt) cc_final: 0.8022 (mttt) REVERT: B 344 PHE cc_start: 0.6001 (m-10) cc_final: 0.5753 (m-80) REVERT: B 424 GLU cc_start: 0.7270 (tm-30) cc_final: 0.7032 (mp0) REVERT: B 450 ARG cc_start: 0.7248 (ttm-80) cc_final: 0.6843 (ttp-170) REVERT: B 477 LYS cc_start: 0.7482 (mmmm) cc_final: 0.7111 (mtpt) REVERT: B 621 MET cc_start: 0.7528 (mmm) cc_final: 0.6934 (mmt) REVERT: B 637 THR cc_start: 0.7349 (m) cc_final: 0.7030 (t) REVERT: B 665 SER cc_start: 0.6905 (t) cc_final: 0.6618 (m) REVERT: C 7 LYS cc_start: 0.8016 (mttm) cc_final: 0.7552 (mttt) REVERT: C 104 ASN cc_start: 0.8169 (m110) cc_final: 0.7927 (m-40) REVERT: C 107 LYS cc_start: 0.7550 (ttmt) cc_final: 0.7029 (ttpp) REVERT: D 78 ARG cc_start: 0.6182 (ttm-80) cc_final: 0.5893 (ttt180) REVERT: E 270 SER cc_start: 0.8122 (m) cc_final: 0.7719 (p) REVERT: E 320 HIS cc_start: 0.6918 (t-90) cc_final: 0.6307 (t-90) REVERT: E 324 MET cc_start: 0.5796 (ptm) cc_final: 0.4251 (tpt) REVERT: E 334 MET cc_start: 0.6275 (ttp) cc_final: 0.5947 (ptp) REVERT: E 350 LYS cc_start: 0.4927 (pttm) cc_final: 0.3792 (tptp) REVERT: E 355 ARG cc_start: 0.6607 (mmt180) cc_final: 0.5962 (ttm-80) REVERT: E 358 GLN cc_start: 0.6872 (tp40) cc_final: 0.6655 (tt0) REVERT: E 363 LEU cc_start: 0.7260 (pt) cc_final: 0.6660 (tp) REVERT: E 364 ILE cc_start: 0.7010 (mm) cc_final: 0.6660 (mm) REVERT: E 383 GLU cc_start: 0.6846 (mp0) cc_final: 0.6520 (mp0) REVERT: F 153 GLU cc_start: 0.2646 (tt0) cc_final: 0.2202 (mt-10) REVERT: F 184 GLN cc_start: 0.6167 (tm-30) cc_final: 0.5871 (pt0) REVERT: F 203 TYR cc_start: 0.6105 (t80) cc_final: 0.5722 (t80) REVERT: F 214 MET cc_start: 0.7545 (mtm) cc_final: 0.7056 (ptp) REVERT: F 223 TRP cc_start: 0.6647 (t60) cc_final: 0.5843 (t60) outliers start: 2 outliers final: 0 residues processed: 421 average time/residue: 0.3421 time to fit residues: 199.3485 Evaluate side-chains 242 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 0.0870 chunk 98 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 174 optimal weight: 10.0000 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 HIS E 351 HIS ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.198001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.159947 restraints weight = 19273.053| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.79 r_work: 0.3645 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16021 Z= 0.150 Angle : 0.660 8.594 21564 Z= 0.343 Chirality : 0.046 0.177 2355 Planarity : 0.004 0.049 2764 Dihedral : 7.478 135.502 2115 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.79 % Allowed : 9.60 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.19), residues: 1912 helix: 0.12 (0.20), residues: 693 sheet: 0.14 (0.29), residues: 333 loop : -1.70 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 157 HIS 0.015 0.002 HIS E 331 PHE 0.031 0.002 PHE E 345 TYR 0.018 0.002 TYR A 472 ARG 0.005 0.001 ARG C 88 Details of bonding type rmsd hydrogen bonds : bond 0.04673 ( 615) hydrogen bonds : angle 5.27649 ( 1737) covalent geometry : bond 0.00341 (16019) covalent geometry : angle 0.65966 (21564) Misc. bond : bond 0.00077 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 276 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.7525 (ptmm) cc_final: 0.6855 (mmtt) REVERT: A 216 TYR cc_start: 0.6715 (m-80) cc_final: 0.6305 (m-80) REVERT: A 366 CYS cc_start: 0.6960 (t) cc_final: 0.6747 (t) REVERT: A 414 GLU cc_start: 0.7920 (tt0) cc_final: 0.7643 (mt-10) REVERT: A 450 ARG cc_start: 0.8211 (ptp-110) cc_final: 0.7973 (ptp90) REVERT: A 509 GLU cc_start: 0.6541 (pm20) cc_final: 0.6198 (tt0) REVERT: A 515 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7788 (mm-30) REVERT: A 553 MET cc_start: 0.5483 (tpp) cc_final: 0.5206 (tpp) REVERT: A 576 GLU cc_start: 0.6585 (mm-30) cc_final: 0.6055 (tp30) REVERT: A 637 THR cc_start: 0.7849 (m) cc_final: 0.7547 (p) REVERT: A 682 ARG cc_start: 0.7294 (tpt170) cc_final: 0.7085 (tpt170) REVERT: B 100 ASN cc_start: 0.8073 (t0) cc_final: 0.7858 (t0) REVERT: B 123 ILE cc_start: 0.7320 (mm) cc_final: 0.7096 (tt) REVERT: B 174 PRO cc_start: 0.8643 (Cg_endo) cc_final: 0.8439 (Cg_exo) REVERT: B 284 LYS cc_start: 0.7412 (mtpt) cc_final: 0.7119 (mmtm) REVERT: B 368 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6937 (mp0) REVERT: B 424 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7500 (mp0) REVERT: B 450 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7391 (ttp-170) REVERT: B 477 LYS cc_start: 0.7721 (mmmm) cc_final: 0.7442 (mtpt) REVERT: B 621 MET cc_start: 0.7845 (mmm) cc_final: 0.7185 (mmt) REVERT: B 637 THR cc_start: 0.7534 (m) cc_final: 0.7152 (t) REVERT: C 7 LYS cc_start: 0.8533 (mttm) cc_final: 0.8197 (mttt) REVERT: C 104 ASN cc_start: 0.8079 (m110) cc_final: 0.7846 (m-40) REVERT: E 324 MET cc_start: 0.6175 (ptm) cc_final: 0.5034 (tpt) REVERT: E 350 LYS cc_start: 0.4938 (pttm) cc_final: 0.3734 (tptp) REVERT: E 399 MET cc_start: 0.4981 (ptt) cc_final: 0.4359 (ptm) REVERT: F 80 MET cc_start: 0.3535 (mtm) cc_final: 0.2419 (ttm) REVERT: F 153 GLU cc_start: 0.2922 (tt0) cc_final: 0.2593 (mt-10) REVERT: F 154 MET cc_start: 0.2641 (tpt) cc_final: 0.1390 (tpt) REVERT: F 173 GLU cc_start: 0.5152 (mp0) cc_final: 0.4905 (mp0) REVERT: F 187 ASN cc_start: 0.5178 (m-40) cc_final: 0.4870 (m-40) REVERT: F 203 TYR cc_start: 0.6399 (t80) cc_final: 0.5501 (t80) REVERT: F 214 MET cc_start: 0.7638 (mtm) cc_final: 0.7166 (ptp) REVERT: F 252 ASP cc_start: 0.6727 (m-30) cc_final: 0.6387 (m-30) outliers start: 31 outliers final: 17 residues processed: 295 average time/residue: 0.3176 time to fit residues: 133.5083 Evaluate side-chains 241 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 224 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 164 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.198291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.160569 restraints weight = 19270.041| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.89 r_work: 0.3655 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16021 Z= 0.128 Angle : 0.597 7.886 21564 Z= 0.308 Chirality : 0.043 0.242 2355 Planarity : 0.004 0.049 2764 Dihedral : 6.577 119.186 2115 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.60 % Allowed : 11.85 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1912 helix: 0.29 (0.20), residues: 697 sheet: 0.22 (0.29), residues: 335 loop : -1.62 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 157 HIS 0.005 0.001 HIS E 331 PHE 0.026 0.001 PHE E 345 TYR 0.013 0.001 TYR A 472 ARG 0.006 0.000 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 615) hydrogen bonds : angle 4.94642 ( 1737) covalent geometry : bond 0.00286 (16019) covalent geometry : angle 0.59668 (21564) Misc. bond : bond 0.00081 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 257 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.7617 (ptmm) cc_final: 0.6896 (mmtt) REVERT: A 204 LYS cc_start: 0.9036 (ttpt) cc_final: 0.8794 (tttp) REVERT: A 414 GLU cc_start: 0.7894 (tt0) cc_final: 0.7629 (mt-10) REVERT: A 509 GLU cc_start: 0.6510 (pm20) cc_final: 0.6070 (tt0) REVERT: A 515 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 576 GLU cc_start: 0.6551 (mm-30) cc_final: 0.5988 (tp30) REVERT: A 637 THR cc_start: 0.7916 (m) cc_final: 0.7586 (p) REVERT: A 670 LEU cc_start: 0.5432 (OUTLIER) cc_final: 0.5029 (tp) REVERT: A 682 ARG cc_start: 0.7251 (tpt170) cc_final: 0.7046 (tpt170) REVERT: B 25 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7755 (tpp) REVERT: B 123 ILE cc_start: 0.7229 (mm) cc_final: 0.6968 (tt) REVERT: B 144 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7733 (t) REVERT: B 284 LYS cc_start: 0.7453 (mtpt) cc_final: 0.7130 (mmtm) REVERT: B 368 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6681 (mp0) REVERT: B 450 ARG cc_start: 0.7843 (ttm-80) cc_final: 0.7484 (ttp-170) REVERT: B 477 LYS cc_start: 0.7668 (mmmm) cc_final: 0.7411 (mtpt) REVERT: B 503 VAL cc_start: 0.8616 (t) cc_final: 0.8202 (p) REVERT: B 637 THR cc_start: 0.7489 (m) cc_final: 0.7286 (t) REVERT: B 665 SER cc_start: 0.7615 (t) cc_final: 0.7304 (m) REVERT: C 104 ASN cc_start: 0.8107 (m110) cc_final: 0.7892 (m-40) REVERT: E 324 MET cc_start: 0.5975 (ptm) cc_final: 0.4767 (mmt) REVERT: E 350 LYS cc_start: 0.4799 (pttm) cc_final: 0.3718 (tptp) REVERT: E 383 GLU cc_start: 0.7482 (mp0) cc_final: 0.7248 (mp0) REVERT: F 187 ASN cc_start: 0.5084 (m-40) cc_final: 0.4801 (m-40) REVERT: F 214 MET cc_start: 0.7719 (mtm) cc_final: 0.7234 (ptp) REVERT: F 251 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8592 (mm) outliers start: 45 outliers final: 31 residues processed: 286 average time/residue: 0.3183 time to fit residues: 127.6119 Evaluate side-chains 262 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 294 CYS Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 345 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 CYS Chi-restraints excluded: chain F residue 251 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 90 optimal weight: 0.0670 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.196723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.158376 restraints weight = 19119.870| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.75 r_work: 0.3641 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16021 Z= 0.144 Angle : 0.597 7.663 21564 Z= 0.308 Chirality : 0.044 0.210 2355 Planarity : 0.004 0.049 2764 Dihedral : 6.511 122.502 2115 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.29 % Allowed : 13.99 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1912 helix: 0.38 (0.20), residues: 698 sheet: 0.17 (0.29), residues: 331 loop : -1.51 (0.19), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 157 HIS 0.006 0.001 HIS E 326 PHE 0.029 0.002 PHE E 345 TYR 0.014 0.002 TYR A 472 ARG 0.004 0.000 ARG E 333 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 615) hydrogen bonds : angle 4.85668 ( 1737) covalent geometry : bond 0.00333 (16019) covalent geometry : angle 0.59723 (21564) Misc. bond : bond 0.00151 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.7560 (ptmm) cc_final: 0.6835 (mmtt) REVERT: A 204 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8707 (tttp) REVERT: A 414 GLU cc_start: 0.7880 (tt0) cc_final: 0.7629 (mt-10) REVERT: A 515 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7777 (mm-30) REVERT: A 533 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6983 (mp) REVERT: A 567 MET cc_start: 0.6439 (mmm) cc_final: 0.6197 (mmp) REVERT: A 637 THR cc_start: 0.7933 (m) cc_final: 0.7594 (p) REVERT: B 25 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7698 (tpp) REVERT: B 168 ARG cc_start: 0.8122 (mtp85) cc_final: 0.7647 (mtt-85) REVERT: B 284 LYS cc_start: 0.7467 (mtpt) cc_final: 0.7103 (mmtm) REVERT: B 368 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6666 (mp0) REVERT: B 450 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7416 (ttp-170) REVERT: B 477 LYS cc_start: 0.7639 (mmmm) cc_final: 0.7368 (mtpt) REVERT: B 503 VAL cc_start: 0.8598 (t) cc_final: 0.8189 (p) REVERT: B 620 MET cc_start: 0.7717 (mpp) cc_final: 0.6704 (mpp) REVERT: B 621 MET cc_start: 0.7765 (tpp) cc_final: 0.6928 (mmt) REVERT: B 637 THR cc_start: 0.7374 (m) cc_final: 0.7170 (t) REVERT: C 104 ASN cc_start: 0.8083 (m110) cc_final: 0.7863 (m-40) REVERT: E 304 TYR cc_start: 0.5085 (OUTLIER) cc_final: 0.3656 (t80) REVERT: E 324 MET cc_start: 0.5952 (ptm) cc_final: 0.4968 (tpt) REVERT: E 333 ARG cc_start: 0.7423 (ttp-170) cc_final: 0.7211 (mtm110) REVERT: E 334 MET cc_start: 0.7210 (tmm) cc_final: 0.6405 (ptp) REVERT: E 350 LYS cc_start: 0.4882 (pttm) cc_final: 0.3792 (tptp) REVERT: E 383 GLU cc_start: 0.7428 (mp0) cc_final: 0.7227 (mp0) REVERT: F 203 TYR cc_start: 0.6446 (t80) cc_final: 0.5904 (t80) REVERT: F 214 MET cc_start: 0.7702 (mtm) cc_final: 0.7198 (ptp) outliers start: 57 outliers final: 37 residues processed: 276 average time/residue: 0.3156 time to fit residues: 122.6203 Evaluate side-chains 257 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 294 CYS Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 345 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 103 optimal weight: 0.0670 chunk 15 optimal weight: 4.9990 chunk 166 optimal weight: 0.0970 chunk 46 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 chunk 170 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 overall best weight: 1.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN D 97 ASN ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 GLN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.195310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.157125 restraints weight = 19522.003| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.82 r_work: 0.3612 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16021 Z= 0.162 Angle : 0.616 10.289 21564 Z= 0.316 Chirality : 0.045 0.321 2355 Planarity : 0.004 0.048 2764 Dihedral : 6.525 123.197 2115 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.29 % Allowed : 15.43 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 1912 helix: 0.34 (0.20), residues: 704 sheet: 0.20 (0.29), residues: 316 loop : -1.51 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 157 HIS 0.008 0.001 HIS E 285 PHE 0.028 0.002 PHE E 345 TYR 0.014 0.002 TYR A 472 ARG 0.004 0.000 ARG E 392 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 615) hydrogen bonds : angle 4.87858 ( 1737) covalent geometry : bond 0.00383 (16019) covalent geometry : angle 0.61572 (21564) Misc. bond : bond 0.00147 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 228 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.7515 (ptmm) cc_final: 0.6881 (mmtt) REVERT: A 204 LYS cc_start: 0.9009 (ttpt) cc_final: 0.8734 (tttp) REVERT: A 414 GLU cc_start: 0.7875 (tt0) cc_final: 0.7605 (mt-10) REVERT: A 515 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7714 (mm-30) REVERT: A 533 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6921 (tp) REVERT: A 576 GLU cc_start: 0.6333 (mt-10) cc_final: 0.5961 (tt0) REVERT: A 612 ARG cc_start: 0.7393 (ttt-90) cc_final: 0.7067 (ttm-80) REVERT: A 637 THR cc_start: 0.7940 (m) cc_final: 0.7609 (p) REVERT: A 660 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6973 (mm-30) REVERT: B 25 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7724 (tpp) REVERT: B 168 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7590 (mtt-85) REVERT: B 209 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7965 (mm) REVERT: B 368 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6532 (mp0) REVERT: B 450 ARG cc_start: 0.7782 (ttm-80) cc_final: 0.7452 (ttp-170) REVERT: B 477 LYS cc_start: 0.7558 (mmmm) cc_final: 0.7298 (mtpt) REVERT: B 529 ASP cc_start: 0.7469 (t0) cc_final: 0.7260 (t0) REVERT: B 620 MET cc_start: 0.7781 (mpp) cc_final: 0.6791 (mpp) REVERT: B 658 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8116 (mt) REVERT: D 70 ASP cc_start: 0.8018 (t0) cc_final: 0.7378 (t0) REVERT: E 282 ARG cc_start: 0.6350 (mtm-85) cc_final: 0.5541 (mtm180) REVERT: E 304 TYR cc_start: 0.5063 (OUTLIER) cc_final: 0.3548 (t80) REVERT: E 324 MET cc_start: 0.6011 (ptm) cc_final: 0.5263 (tpt) REVERT: E 350 LYS cc_start: 0.4606 (pttm) cc_final: 0.3601 (tptp) REVERT: F 184 GLN cc_start: 0.6411 (tm-30) cc_final: 0.5929 (pt0) REVERT: F 203 TYR cc_start: 0.6452 (t80) cc_final: 0.5847 (t80) REVERT: F 214 MET cc_start: 0.7717 (mtm) cc_final: 0.7211 (ptp) REVERT: F 246 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: F 259 ASN cc_start: 0.6990 (m-40) cc_final: 0.6641 (m-40) REVERT: F 294 LEU cc_start: 0.6987 (mm) cc_final: 0.6306 (mm) outliers start: 57 outliers final: 43 residues processed: 266 average time/residue: 0.3153 time to fit residues: 118.2933 Evaluate side-chains 265 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 294 CYS Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 345 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 CYS Chi-restraints excluded: chain F residue 246 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 190 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 47 optimal weight: 0.0060 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN D 97 ASN ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.195724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.157759 restraints weight = 19463.059| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.97 r_work: 0.3607 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16021 Z= 0.145 Angle : 0.597 8.410 21564 Z= 0.307 Chirality : 0.044 0.254 2355 Planarity : 0.004 0.048 2764 Dihedral : 6.396 118.662 2115 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.41 % Allowed : 15.84 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.19), residues: 1912 helix: 0.36 (0.20), residues: 706 sheet: 0.17 (0.29), residues: 317 loop : -1.47 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 157 HIS 0.008 0.001 HIS E 285 PHE 0.026 0.001 PHE E 345 TYR 0.013 0.002 TYR A 472 ARG 0.005 0.000 ARG E 392 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 615) hydrogen bonds : angle 4.81607 ( 1737) covalent geometry : bond 0.00340 (16019) covalent geometry : angle 0.59724 (21564) Misc. bond : bond 0.00121 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 222 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.7526 (ptmm) cc_final: 0.6921 (mmtt) REVERT: A 204 LYS cc_start: 0.9005 (ttpt) cc_final: 0.8725 (tttp) REVERT: A 414 GLU cc_start: 0.7909 (tt0) cc_final: 0.7609 (mt-10) REVERT: A 515 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7636 (mm-30) REVERT: A 612 ARG cc_start: 0.7385 (ttt-90) cc_final: 0.7063 (ttm-80) REVERT: B 25 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7737 (tpp) REVERT: B 168 ARG cc_start: 0.8154 (mtp85) cc_final: 0.7697 (mtt-85) REVERT: B 209 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7958 (mm) REVERT: B 368 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6506 (mp0) REVERT: B 450 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.7470 (ttp-170) REVERT: B 477 LYS cc_start: 0.7545 (mmmm) cc_final: 0.7274 (mtpt) REVERT: B 620 MET cc_start: 0.7763 (mpp) cc_final: 0.6740 (mpp) REVERT: B 621 MET cc_start: 0.7760 (tpp) cc_final: 0.6899 (mmt) REVERT: B 658 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8077 (mt) REVERT: D 22 GLU cc_start: 0.7550 (mp0) cc_final: 0.7283 (mm-30) REVERT: D 70 ASP cc_start: 0.8111 (t0) cc_final: 0.7690 (m-30) REVERT: E 304 TYR cc_start: 0.5024 (OUTLIER) cc_final: 0.3511 (t80) REVERT: E 324 MET cc_start: 0.6022 (ptm) cc_final: 0.5198 (tpt) REVERT: E 334 MET cc_start: 0.7053 (tmm) cc_final: 0.6356 (ptp) REVERT: E 350 LYS cc_start: 0.4554 (pttm) cc_final: 0.3595 (tptp) REVERT: E 383 GLU cc_start: 0.7341 (mp0) cc_final: 0.7078 (mp0) REVERT: F 184 GLN cc_start: 0.6436 (tm-30) cc_final: 0.5941 (pt0) REVERT: F 214 MET cc_start: 0.7723 (mtm) cc_final: 0.7221 (ptp) REVERT: F 259 ASN cc_start: 0.6948 (m-40) cc_final: 0.6595 (m-40) REVERT: F 294 LEU cc_start: 0.7072 (mm) cc_final: 0.6401 (mm) outliers start: 59 outliers final: 43 residues processed: 265 average time/residue: 0.3152 time to fit residues: 119.7927 Evaluate side-chains 256 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 345 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 54 optimal weight: 0.0770 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 0.3980 chunk 167 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 166 optimal weight: 0.0970 chunk 16 optimal weight: 0.0060 chunk 102 optimal weight: 6.9990 overall best weight: 0.5154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.197939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.159713 restraints weight = 19245.439| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.75 r_work: 0.3667 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16021 Z= 0.108 Angle : 0.561 8.422 21564 Z= 0.287 Chirality : 0.042 0.210 2355 Planarity : 0.003 0.049 2764 Dihedral : 6.076 110.883 2115 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.95 % Allowed : 17.17 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 1912 helix: 0.42 (0.20), residues: 713 sheet: 0.20 (0.29), residues: 317 loop : -1.37 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 157 HIS 0.008 0.001 HIS E 285 PHE 0.023 0.001 PHE E 345 TYR 0.010 0.001 TYR F 202 ARG 0.003 0.000 ARG F 304 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 615) hydrogen bonds : angle 4.66597 ( 1737) covalent geometry : bond 0.00239 (16019) covalent geometry : angle 0.56060 (21564) Misc. bond : bond 0.00074 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 224 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.7491 (ptmm) cc_final: 0.6929 (mmtt) REVERT: A 204 LYS cc_start: 0.8951 (ttpt) cc_final: 0.8681 (tttp) REVERT: A 342 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6937 (p0) REVERT: A 414 GLU cc_start: 0.7847 (tt0) cc_final: 0.7537 (mt-10) REVERT: B 25 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7754 (tpp) REVERT: B 168 ARG cc_start: 0.8043 (mtp85) cc_final: 0.7635 (mtt-85) REVERT: B 368 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6452 (mp0) REVERT: B 450 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.7420 (ttp-170) REVERT: B 477 LYS cc_start: 0.7507 (mmmm) cc_final: 0.7259 (mtpt) REVERT: B 620 MET cc_start: 0.7700 (mpp) cc_final: 0.6682 (mpp) REVERT: B 621 MET cc_start: 0.7615 (tpp) cc_final: 0.6734 (mmt) REVERT: B 658 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8111 (mt) REVERT: D 70 ASP cc_start: 0.7941 (t0) cc_final: 0.7538 (m-30) REVERT: E 304 TYR cc_start: 0.5029 (OUTLIER) cc_final: 0.3568 (t80) REVERT: E 324 MET cc_start: 0.6084 (ptm) cc_final: 0.5172 (tpt) REVERT: E 334 MET cc_start: 0.7008 (tmm) cc_final: 0.6236 (ptp) REVERT: E 350 LYS cc_start: 0.4641 (pttm) cc_final: 0.3677 (tptp) REVERT: E 383 GLU cc_start: 0.7310 (mp0) cc_final: 0.6928 (mp0) REVERT: F 187 ASN cc_start: 0.4277 (m110) cc_final: 0.3954 (m-40) REVERT: F 203 TYR cc_start: 0.6405 (t80) cc_final: 0.5943 (t80) REVERT: F 214 MET cc_start: 0.7584 (mtm) cc_final: 0.7106 (ptp) REVERT: F 259 ASN cc_start: 0.7127 (m-40) cc_final: 0.6711 (m-40) REVERT: F 294 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6423 (mm) outliers start: 51 outliers final: 33 residues processed: 257 average time/residue: 0.3130 time to fit residues: 114.1584 Evaluate side-chains 250 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 345 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 106 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.194751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.157200 restraints weight = 19232.289| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.90 r_work: 0.3582 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16021 Z= 0.169 Angle : 0.629 13.112 21564 Z= 0.322 Chirality : 0.045 0.345 2355 Planarity : 0.004 0.049 2764 Dihedral : 6.417 122.841 2115 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.01 % Allowed : 17.28 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.19), residues: 1912 helix: 0.38 (0.20), residues: 707 sheet: 0.18 (0.29), residues: 325 loop : -1.38 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 157 HIS 0.009 0.001 HIS E 285 PHE 0.027 0.002 PHE E 345 TYR 0.014 0.002 TYR A 472 ARG 0.003 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 615) hydrogen bonds : angle 4.87464 ( 1737) covalent geometry : bond 0.00402 (16019) covalent geometry : angle 0.62859 (21564) Misc. bond : bond 0.00111 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 221 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 LYS cc_start: 0.8899 (ttpt) cc_final: 0.8634 (tttp) REVERT: A 523 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.6950 (mt0) REVERT: B 25 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7506 (tpp) REVERT: B 168 ARG cc_start: 0.7833 (mtp85) cc_final: 0.7580 (mtp85) REVERT: B 209 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7946 (mm) REVERT: B 368 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6425 (mp0) REVERT: B 620 MET cc_start: 0.7666 (mpp) cc_final: 0.6643 (mpp) REVERT: B 658 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8004 (mt) REVERT: D 22 GLU cc_start: 0.7553 (mp0) cc_final: 0.7254 (mm-30) REVERT: D 70 ASP cc_start: 0.7952 (t0) cc_final: 0.7618 (m-30) REVERT: E 282 ARG cc_start: 0.6129 (mtm-85) cc_final: 0.5342 (mtm180) REVERT: E 304 TYR cc_start: 0.5000 (OUTLIER) cc_final: 0.3495 (t80) REVERT: E 324 MET cc_start: 0.6045 (ptm) cc_final: 0.5297 (tpt) REVERT: E 350 LYS cc_start: 0.4502 (pttm) cc_final: 0.3563 (tptp) REVERT: F 187 ASN cc_start: 0.4353 (m110) cc_final: 0.4119 (m-40) REVERT: F 194 GLN cc_start: 0.4681 (mm110) cc_final: 0.4253 (mm110) REVERT: F 214 MET cc_start: 0.7564 (mtm) cc_final: 0.7086 (ptp) REVERT: F 294 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6416 (mm) outliers start: 52 outliers final: 41 residues processed: 255 average time/residue: 0.2918 time to fit residues: 106.2250 Evaluate side-chains 257 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 345 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 CYS Chi-restraints excluded: chain F residue 294 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.193428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.154746 restraints weight = 19164.631| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.85 r_work: 0.3599 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16021 Z= 0.192 Angle : 0.665 12.655 21564 Z= 0.340 Chirality : 0.046 0.372 2355 Planarity : 0.004 0.054 2764 Dihedral : 6.609 127.282 2115 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.12 % Allowed : 17.51 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 1912 helix: 0.26 (0.20), residues: 707 sheet: 0.23 (0.29), residues: 316 loop : -1.47 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 157 HIS 0.010 0.001 HIS C 57 PHE 0.028 0.002 PHE E 345 TYR 0.017 0.002 TYR A 472 ARG 0.008 0.001 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 615) hydrogen bonds : angle 4.98239 ( 1737) covalent geometry : bond 0.00461 (16019) covalent geometry : angle 0.66526 (21564) Misc. bond : bond 0.00160 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 222 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 LYS cc_start: 0.8987 (ttpt) cc_final: 0.8706 (tttp) REVERT: A 523 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.6833 (mt0) REVERT: A 678 ASN cc_start: 0.6798 (t0) cc_final: 0.6458 (m-40) REVERT: B 25 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7703 (tpp) REVERT: B 168 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7706 (mtt-85) REVERT: B 209 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7923 (mm) REVERT: B 368 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6484 (mp0) REVERT: B 620 MET cc_start: 0.7758 (mpp) cc_final: 0.6745 (mpp) REVERT: B 658 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7994 (mt) REVERT: C 57 HIS cc_start: 0.7968 (m-70) cc_final: 0.7762 (m-70) REVERT: D 12 ARG cc_start: 0.7562 (ttm-80) cc_final: 0.7354 (ttm110) REVERT: D 22 GLU cc_start: 0.7583 (mp0) cc_final: 0.7328 (mm-30) REVERT: D 70 ASP cc_start: 0.8208 (t0) cc_final: 0.7814 (m-30) REVERT: E 282 ARG cc_start: 0.6394 (mtm-85) cc_final: 0.5582 (mtm180) REVERT: E 304 TYR cc_start: 0.5054 (OUTLIER) cc_final: 0.3492 (t80) REVERT: E 324 MET cc_start: 0.6208 (ptm) cc_final: 0.5276 (mmt) REVERT: E 350 LYS cc_start: 0.4465 (pttm) cc_final: 0.3566 (tptp) REVERT: F 184 GLN cc_start: 0.6431 (tm-30) cc_final: 0.5821 (pt0) REVERT: F 194 GLN cc_start: 0.4757 (mm110) cc_final: 0.4266 (mm110) REVERT: F 214 MET cc_start: 0.7457 (mtm) cc_final: 0.7027 (ptp) REVERT: F 283 GLU cc_start: 0.7129 (mp0) cc_final: 0.6872 (mm-30) REVERT: F 294 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6529 (tt) outliers start: 54 outliers final: 43 residues processed: 257 average time/residue: 0.3046 time to fit residues: 111.9505 Evaluate side-chains 264 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 345 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 CYS Chi-restraints excluded: chain F residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 38 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 189 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 165 optimal weight: 20.0000 chunk 117 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN E 299 GLN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.196293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.157383 restraints weight = 19567.484| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.85 r_work: 0.3635 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16021 Z= 0.128 Angle : 0.610 12.393 21564 Z= 0.311 Chirality : 0.044 0.346 2355 Planarity : 0.004 0.051 2764 Dihedral : 6.270 120.398 2115 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.37 % Allowed : 18.21 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.19), residues: 1912 helix: 0.37 (0.20), residues: 711 sheet: 0.31 (0.29), residues: 322 loop : -1.36 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 157 HIS 0.009 0.001 HIS C 57 PHE 0.024 0.001 PHE E 345 TYR 0.024 0.001 TYR D 9 ARG 0.004 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 615) hydrogen bonds : angle 4.80062 ( 1737) covalent geometry : bond 0.00296 (16019) covalent geometry : angle 0.61017 (21564) Misc. bond : bond 0.00061 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.7587 (ptmm) cc_final: 0.6929 (mmtt) REVERT: A 204 LYS cc_start: 0.8990 (ttpt) cc_final: 0.8708 (tttp) REVERT: A 523 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6720 (mt0) REVERT: A 606 MET cc_start: 0.8072 (mmm) cc_final: 0.7793 (mmp) REVERT: B 25 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7687 (tpp) REVERT: B 168 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7714 (mtt-85) REVERT: B 368 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6418 (mp0) REVERT: B 620 MET cc_start: 0.7813 (mpp) cc_final: 0.6900 (mpp) REVERT: B 658 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7996 (mt) REVERT: C 57 HIS cc_start: 0.7866 (m-70) cc_final: 0.7643 (m-70) REVERT: D 22 GLU cc_start: 0.7619 (mp0) cc_final: 0.7360 (mm-30) REVERT: D 70 ASP cc_start: 0.8162 (t0) cc_final: 0.7742 (m-30) REVERT: E 282 ARG cc_start: 0.6253 (mtm-85) cc_final: 0.5501 (mtm180) REVERT: E 304 TYR cc_start: 0.5083 (OUTLIER) cc_final: 0.3531 (t80) REVERT: E 324 MET cc_start: 0.6151 (ptm) cc_final: 0.5220 (mmt) REVERT: E 350 LYS cc_start: 0.4565 (pttm) cc_final: 0.3642 (tptp) REVERT: F 184 GLN cc_start: 0.6587 (tm-30) cc_final: 0.5820 (pt0) REVERT: F 187 ASN cc_start: 0.4564 (m110) cc_final: 0.4220 (m-40) REVERT: F 194 GLN cc_start: 0.4654 (mm110) cc_final: 0.4222 (mm110) REVERT: F 214 MET cc_start: 0.7556 (mtm) cc_final: 0.7123 (ptp) REVERT: F 283 GLU cc_start: 0.7011 (mp0) cc_final: 0.6786 (mm-30) REVERT: F 294 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6527 (tt) outliers start: 41 outliers final: 34 residues processed: 241 average time/residue: 0.3214 time to fit residues: 109.2318 Evaluate side-chains 245 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 294 CYS Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 345 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 82 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.196721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.157173 restraints weight = 19342.492| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.83 r_work: 0.3647 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16021 Z= 0.126 Angle : 0.600 12.009 21564 Z= 0.305 Chirality : 0.044 0.343 2355 Planarity : 0.003 0.048 2764 Dihedral : 6.154 119.722 2115 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.77 % Allowed : 17.92 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.19), residues: 1912 helix: 0.49 (0.20), residues: 711 sheet: 0.37 (0.29), residues: 314 loop : -1.34 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 157 HIS 0.009 0.001 HIS E 285 PHE 0.022 0.001 PHE E 345 TYR 0.020 0.001 TYR A 681 ARG 0.010 0.000 ARG E 333 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 615) hydrogen bonds : angle 4.68622 ( 1737) covalent geometry : bond 0.00293 (16019) covalent geometry : angle 0.60022 (21564) Misc. bond : bond 0.00073 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8996.11 seconds wall clock time: 155 minutes 58.89 seconds (9358.89 seconds total)