Starting phenix.real_space_refine on Fri Oct 23 18:46:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25lv_80193/10_2026/25lv_80193.cif Found real_map, /net/cci-nas-00/data/ceres_data/25lv_80193/10_2026/25lv_80193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25lv_80193/10_2026/25lv_80193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25lv_80193/10_2026/25lv_80193.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25lv_80193/10_2026/25lv_80193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25lv_80193/10_2026/25lv_80193.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.115 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 60 5.16 5 C 6940 2.51 5 N 1692 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10588 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5260 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Chain: "B" Number of atoms: 5260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5260 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 2.34, per 1000 atoms: 0.22 Number of scatterers: 10588 At special positions: 0 Unit cell: (120.657, 91.308, 106.526, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 60 16.00 P 4 15.00 O 1890 8.00 N 1692 7.00 C 6940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 334.9 milliseconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 5 sheets defined 63.5% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.677A pdb=" N LEU A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 78 removed outlier: 3.822A pdb=" N LEU A 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 75 through 78' Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 93 through 109 removed outlier: 3.551A pdb=" N GLY A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 128 through 138 removed outlier: 4.015A pdb=" N LEU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 179 removed outlier: 3.698A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 removed outlier: 3.965A pdb=" N LYS A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 removed outlier: 3.831A pdb=" N SER A 207 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 221 through 229 removed outlier: 3.928A pdb=" N VAL A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY A 227 " --> pdb=" O ASN A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 removed outlier: 3.811A pdb=" N VAL A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.677A pdb=" N PHE A 242 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 272 removed outlier: 3.537A pdb=" N LEU A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 282 removed outlier: 4.126A pdb=" N VAL A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 278 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 296 through 305 removed outlier: 4.514A pdb=" N GLY A 302 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 322 through 349 removed outlier: 3.741A pdb=" N VAL A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TYR A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Proline residue: A 336 - end of helix Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 358 through 364 removed outlier: 3.620A pdb=" N SER A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 364 " --> pdb=" O PHE A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 368 through 402 removed outlier: 3.611A pdb=" N THR A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 438 removed outlier: 4.334A pdb=" N TYR A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.959A pdb=" N ALA A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 452 " --> pdb=" O HIS A 448 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 Processing helix chain 'A' and resid 476 through 500 removed outlier: 4.072A pdb=" N ILE A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 535 removed outlier: 3.943A pdb=" N VAL A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 515 " --> pdb=" O THR A 511 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET A 519 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP A 523 " --> pdb=" O MET A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 582 removed outlier: 4.461A pdb=" N SER A 575 " --> pdb=" O THR A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 653 removed outlier: 3.719A pdb=" N ARG A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 745 through 753 Processing helix chain 'A' and resid 753 through 761 removed outlier: 3.794A pdb=" N PHE A 757 " --> pdb=" O HIS A 753 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 66 removed outlier: 3.674A pdb=" N LEU B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 93 through 109 removed outlier: 3.547A pdb=" N GLY B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 128 through 138 removed outlier: 4.010A pdb=" N LEU B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 removed outlier: 3.653A pdb=" N GLU B 154 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 155 " --> pdb=" O ASP B 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 151 through 155' Processing helix chain 'B' and resid 169 through 179 Processing helix chain 'B' and resid 180 through 201 removed outlier: 3.907A pdb=" N LYS B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 removed outlier: 3.819A pdb=" N SER B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 228 through 237 removed outlier: 3.916A pdb=" N ILE B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ILE B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.673A pdb=" N PHE B 242 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 272 removed outlier: 3.535A pdb=" N LEU B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 282 removed outlier: 4.126A pdb=" N VAL B 277 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 278 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 296 through 305 removed outlier: 4.515A pdb=" N GLY B 302 " --> pdb=" O TRP B 298 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 322 through 349 removed outlier: 3.740A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TYR B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Proline residue: B 336 - end of helix Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.617A pdb=" N SER B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE B 364 " --> pdb=" O PHE B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 368 through 402 removed outlier: 3.612A pdb=" N THR B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 438 removed outlier: 4.296A pdb=" N TYR B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 438 " --> pdb=" O ILE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 457 removed outlier: 4.024A pdb=" N HIS B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 452 " --> pdb=" O HIS B 448 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 454 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 472 Processing helix chain 'B' and resid 476 through 500 removed outlier: 4.062A pdb=" N ILE B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR B 494 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 537 removed outlier: 3.885A pdb=" N VAL B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 515 " --> pdb=" O THR B 511 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU B 516 " --> pdb=" O ILE B 512 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET B 519 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE B 522 " --> pdb=" O ALA B 518 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP B 523 " --> pdb=" O MET B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 549 Processing helix chain 'B' and resid 571 through 582 removed outlier: 4.424A pdb=" N SER B 575 " --> pdb=" O THR B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 653 removed outlier: 3.728A pdb=" N ARG B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 643 " --> pdb=" O GLU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 725 Processing helix chain 'B' and resid 744 through 753 removed outlier: 3.555A pdb=" N LYS B 748 " --> pdb=" O SER B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 761 removed outlier: 3.746A pdb=" N PHE B 757 " --> pdb=" O HIS B 753 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA2, first strand: chain 'A' and resid 554 through 556 Processing sheet with id=AA3, first strand: chain 'A' and resid 608 through 611 removed outlier: 6.443A pdb=" N PHE A 588 " --> pdb=" O PHE A 620 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N CYS A 622 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 590 " --> pdb=" O CYS A 622 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL A 624 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 592 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N TYR A 626 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS A 594 " --> pdb=" O TYR A 626 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY A 560 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE A 591 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE A 562 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE A 593 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLY A 733 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR A 730 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL A 779 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET A 732 " --> pdb=" O VAL A 779 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N MET A 781 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLU A 734 " --> pdb=" O MET A 781 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N TYR A 783 " --> pdb=" O GLU A 734 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU A 736 " --> pdb=" O TYR A 783 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU A 785 " --> pdb=" O GLU A 736 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR A 738 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU A 776 " --> pdb=" O GLY B 780 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LEU B 776 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N TYR B 730 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL B 779 " --> pdb=" O TYR B 730 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N MET B 732 " --> pdb=" O VAL B 779 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N MET B 781 " --> pdb=" O MET B 732 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLU B 734 " --> pdb=" O MET B 781 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N TYR B 783 " --> pdb=" O GLU B 734 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU B 736 " --> pdb=" O TYR B 783 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B 785 " --> pdb=" O GLU B 736 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR B 738 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLY B 733 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY B 560 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 591 " --> pdb=" O GLY B 560 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N PHE B 562 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE B 593 " --> pdb=" O PHE B 562 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE B 588 " --> pdb=" O PHE B 620 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N CYS B 622 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU B 590 " --> pdb=" O CYS B 622 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL B 624 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER B 592 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TYR B 626 " --> pdb=" O SER B 592 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS B 594 " --> pdb=" O TYR B 626 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 410 through 411 Processing sheet with id=AA5, first strand: chain 'B' and resid 554 through 556 509 hydrogen bonds defined for protein. 1470 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: 1.57 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1601 1.30 - 1.43: 2958 1.43 - 1.55: 6154 1.55 - 1.68: 7 1.68 - 1.81: 104 Bond restraints: 10824 Sorted by residual: bond pdb=" CA TYR A 533 " pdb=" C TYR A 533 " ideal model delta sigma weight residual 1.524 1.456 0.068 1.29e-02 6.01e+03 2.79e+01 bond pdb=" C LEU A 262 " pdb=" O LEU A 262 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.26e-02 6.30e+03 2.06e+01 bond pdb=" CA SER A 76 " pdb=" CB SER A 76 " ideal model delta sigma weight residual 1.530 1.460 0.069 1.58e-02 4.01e+03 1.93e+01 bond pdb=" CA PHE A 261 " pdb=" C PHE A 261 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.34e-02 5.57e+03 1.58e+01 bond pdb=" N MET A 499 " pdb=" CA MET A 499 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.20e-02 6.94e+03 1.40e+01 ... (remaining 10819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 14485 3.37 - 6.75: 189 6.75 - 10.12: 25 10.12 - 13.50: 4 13.50 - 16.87: 1 Bond angle restraints: 14704 Sorted by residual: angle pdb=" N VAL B 226 " pdb=" CA VAL B 226 " pdb=" C VAL B 226 " ideal model delta sigma weight residual 113.10 102.82 10.28 9.70e-01 1.06e+00 1.12e+02 angle pdb=" C ARG A 295 " pdb=" CA ARG A 295 " pdb=" CB ARG A 295 " ideal model delta sigma weight residual 109.99 93.12 16.87 1.74e+00 3.30e-01 9.40e+01 angle pdb=" N VAL A 459 " pdb=" CA VAL A 459 " pdb=" C VAL A 459 " ideal model delta sigma weight residual 113.39 101.90 11.49 1.47e+00 4.63e-01 6.11e+01 angle pdb=" N ALA B 231 " pdb=" CA ALA B 231 " pdb=" C ALA B 231 " ideal model delta sigma weight residual 114.75 104.92 9.83 1.26e+00 6.30e-01 6.08e+01 angle pdb=" N ALA A 231 " pdb=" CA ALA A 231 " pdb=" C ALA A 231 " ideal model delta sigma weight residual 114.75 104.95 9.80 1.26e+00 6.30e-01 6.05e+01 ... (remaining 14699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.24: 5800 24.24 - 48.49: 456 48.49 - 72.73: 65 72.73 - 96.98: 6 96.98 - 121.22: 1 Dihedral angle restraints: 6328 sinusoidal: 2452 harmonic: 3876 Sorted by residual: dihedral pdb=" C ARG A 295 " pdb=" N ARG A 295 " pdb=" CA ARG A 295 " pdb=" CB ARG A 295 " ideal model delta harmonic sigma weight residual -122.60 -100.37 -22.23 0 2.50e+00 1.60e-01 7.91e+01 dihedral pdb=" CD ARG A 541 " pdb=" NE ARG A 541 " pdb=" CZ ARG A 541 " pdb=" NH1 ARG A 541 " ideal model delta sinusoidal sigma weight residual 0.00 65.53 -65.53 1 1.00e+01 1.00e-02 5.62e+01 dihedral pdb=" O2A ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PA ADP B 901 " pdb=" PB ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 61.22 -121.22 1 2.00e+01 2.50e-03 3.64e+01 ... (remaining 6325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1535 0.081 - 0.162: 170 0.162 - 0.243: 13 0.243 - 0.324: 3 0.324 - 0.405: 5 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CA ARG A 295 " pdb=" N ARG A 295 " pdb=" C ARG A 295 " pdb=" CB ARG A 295 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA LYS A 474 " pdb=" N LYS A 474 " pdb=" C LYS A 474 " pdb=" CB LYS A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CB VAL A 457 " pdb=" CA VAL A 457 " pdb=" CG1 VAL A 457 " pdb=" CG2 VAL A 457 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 1723 not shown) Planarity restraints: 1784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 541 " 0.999 9.50e-02 1.11e+02 4.48e-01 1.21e+02 pdb=" NE ARG A 541 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG A 541 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 541 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 541 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 295 " -0.233 9.50e-02 1.11e+02 1.04e-01 6.69e+00 pdb=" NE ARG A 295 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 295 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 295 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 295 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 295 " -0.012 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C ARG A 295 " 0.044 2.00e-02 2.50e+03 pdb=" O ARG A 295 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 296 " -0.015 2.00e-02 2.50e+03 ... (remaining 1781 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.69: 400 2.69 - 3.31: 11848 3.31 - 3.92: 19566 3.92 - 4.53: 28629 4.53 - 5.14: 45603 Nonbonded interactions: 106046 Sorted by model distance: nonbonded pdb=" OG SER A 76 " pdb=" K K A 902 " model vdw 2.082 2.850 nonbonded pdb=" O TYR A 563 " pdb=" O2' ADP A 901 " model vdw 2.116 3.040 nonbonded pdb=" OG1 THR B 735 " pdb=" O1A ADP B 901 " model vdw 2.119 3.040 nonbonded pdb=" O TYR A 289 " pdb=" OG1 THR A 293 " model vdw 2.137 3.040 nonbonded pdb=" O TYR B 289 " pdb=" OG1 THR B 293 " model vdw 2.138 3.040 ... (remaining 106041 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.440 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 0.011 0.898 10825 Z= 0.928 Angle : 0.965 16.872 14704 Z= 0.588 Chirality : 0.055 0.405 1726 Planarity : 0.013 0.448 1784 Dihedral : 16.629 121.224 3848 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.76 % Allowed : 10.18 % Favored : 89.06 % Rotamer: Outliers : 4.94 % Allowed : 17.68 % Favored : 77.38 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.77 (0.18), residues: 1316 helix: -3.09 (0.14), residues: 802 sheet: -2.36 (0.46), residues: 104 loop : -3.05 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 168 TYR 0.019 0.002 TYR B 289 PHE 0.023 0.002 PHE A 261 TRP 0.019 0.003 TRP A 370 HIS 0.004 0.001 HIS B 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.34 (10824) covalent geometry : angle 0.96489 / 0.59 (14704) hydrogen bonds : bond 0.15177 / 10.59 ( 509) hydrogen bonds : angle 7.74482 / 5.33 ( 1470) Misc. bond : bond 0.89806 / 47.27 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.6448 (ttmt) cc_final: 0.6162 (ttpp) REVERT: A 119 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8023 (mp) REVERT: A 142 MET cc_start: 0.7792 (mtp) cc_final: 0.7356 (mtm) REVERT: A 211 LEU cc_start: 0.8587 (tp) cc_final: 0.8328 (mt) REVERT: A 295 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.5691 (mmp-170) REVERT: A 458 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8226 (mtm) REVERT: A 493 LEU cc_start: 0.7933 (tp) cc_final: 0.7286 (mt) REVERT: A 530 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7933 (mtpp) REVERT: A 610 ARG cc_start: 0.7413 (ttp-170) cc_final: 0.6989 (ttp80) REVERT: B 92 LYS cc_start: 0.6447 (ttmt) cc_final: 0.6179 (ttpp) REVERT: B 142 MET cc_start: 0.7883 (mtp) cc_final: 0.7443 (mtm) REVERT: B 211 LEU cc_start: 0.8527 (tp) cc_final: 0.8295 (mt) REVERT: B 353 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8386 (p) REVERT: B 430 MET cc_start: 0.8225 (ttp) cc_final: 0.8008 (ttp) REVERT: B 474 LYS cc_start: 0.3837 (OUTLIER) cc_final: 0.3501 (pttp) REVERT: B 491 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6343 (mp0) REVERT: B 493 LEU cc_start: 0.7877 (tp) cc_final: 0.7243 (mt) outliers start: 57 outliers final: 39 residues processed: 211 average time/residue: 0.1131 time to fit residues: 33.1081 Evaluate side-chains 185 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 744 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN A 179 ASN A 273 HIS A 282 ASN A 385 GLN A 397 GLN A 543 ASN A 641 HIS A 716 GLN B 64 GLN B 273 HIS B 282 ASN B 385 GLN B 543 ASN B 641 HIS B 716 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.192086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.184250 restraints weight = 11475.704| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 0.40 r_work: 0.3903 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10825 Z= 0.159 Angle : 0.654 7.409 14704 Z= 0.341 Chirality : 0.044 0.269 1726 Planarity : 0.005 0.052 1784 Dihedral : 10.426 129.021 1568 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 5.20 % Allowed : 17.07 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.21), residues: 1316 helix: -1.41 (0.18), residues: 800 sheet: -2.19 (0.45), residues: 104 loop : -2.41 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 292 TYR 0.016 0.002 TYR A 285 PHE 0.010 0.002 PHE B 130 TRP 0.014 0.002 TRP A 258 HIS 0.003 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (10824) covalent geometry : angle 0.65403 / 0.34 (14704) hydrogen bonds : bond 0.04244 / 2.82 ( 509) hydrogen bonds : angle 4.96782 / 3.46 ( 1470) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 159 time to evaluate : 0.431 Fit side-chains REVERT: A 92 LYS cc_start: 0.6602 (ttmt) cc_final: 0.6359 (ttpp) REVERT: A 119 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7659 (mp) REVERT: A 141 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7199 (mmmt) REVERT: A 151 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.5884 (tm-30) REVERT: A 211 LEU cc_start: 0.8632 (tp) cc_final: 0.8411 (mt) REVERT: A 295 ARG cc_start: 0.7768 (ttp80) cc_final: 0.6161 (ttm-80) REVERT: A 328 ILE cc_start: 0.8649 (mt) cc_final: 0.8127 (pt) REVERT: A 491 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: A 493 LEU cc_start: 0.7969 (tp) cc_final: 0.7497 (mt) REVERT: A 530 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8072 (mtpp) REVERT: A 541 ARG cc_start: 0.7891 (ptp-110) cc_final: 0.7462 (ptp-170) REVERT: B 92 LYS cc_start: 0.6640 (ttmt) cc_final: 0.6397 (ttpp) REVERT: B 141 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7153 (mmmt) REVERT: B 211 LEU cc_start: 0.8563 (tp) cc_final: 0.8260 (mt) REVERT: B 328 ILE cc_start: 0.8644 (mt) cc_final: 0.8106 (pt) REVERT: B 430 MET cc_start: 0.8747 (ttp) cc_final: 0.8538 (ttp) REVERT: B 474 LYS cc_start: 0.4221 (OUTLIER) cc_final: 0.3947 (pttp) REVERT: B 491 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: B 493 LEU cc_start: 0.7983 (tp) cc_final: 0.7470 (mt) outliers start: 60 outliers final: 32 residues processed: 213 average time/residue: 0.0914 time to fit residues: 28.2895 Evaluate side-chains 183 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 729 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [54, 66, 117, 75, 71, 37, 65, 57, 106, 52, 62] chunk 54 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 117 optimal weight: 0.0040 chunk 75 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 62 optimal weight: 0.0050 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.194780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.186823 restraints weight = 11535.375| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 0.40 r_work: 0.3929 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10825 Z= 0.107 Angle : 0.571 6.118 14704 Z= 0.296 Chirality : 0.042 0.283 1726 Planarity : 0.004 0.051 1784 Dihedral : 9.251 125.691 1529 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 4.59 % Allowed : 17.59 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.23), residues: 1316 helix: -0.67 (0.19), residues: 808 sheet: -1.94 (0.46), residues: 104 loop : -2.04 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 400 TYR 0.010 0.001 TYR A 70 PHE 0.014 0.001 PHE B 642 TRP 0.012 0.001 TRP B 258 HIS 0.002 0.000 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (10824) covalent geometry : angle 0.57055 / 0.30 (14704) hydrogen bonds : bond 0.03375 / 2.26 ( 509) hydrogen bonds : angle 4.46031 / 3.14 ( 1470) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 166 time to evaluate : 0.284 Fit side-chains REVERT: A 119 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7715 (mp) REVERT: A 295 ARG cc_start: 0.7464 (ttp80) cc_final: 0.5968 (ttm-80) REVERT: A 328 ILE cc_start: 0.8412 (mt) cc_final: 0.8070 (pt) REVERT: A 491 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: A 493 LEU cc_start: 0.7745 (tp) cc_final: 0.7374 (mt) REVERT: A 530 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7975 (mtpp) REVERT: A 541 ARG cc_start: 0.7633 (ptp-110) cc_final: 0.6894 (mtp85) REVERT: B 136 ILE cc_start: 0.8200 (mm) cc_final: 0.7968 (mt) REVERT: B 211 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8138 (mt) REVERT: B 328 ILE cc_start: 0.8431 (mt) cc_final: 0.8046 (pt) REVERT: B 430 MET cc_start: 0.8487 (ttp) cc_final: 0.8245 (ttp) REVERT: B 491 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6508 (mp0) REVERT: B 493 LEU cc_start: 0.7720 (tp) cc_final: 0.7363 (mt) outliers start: 53 outliers final: 31 residues processed: 211 average time/residue: 0.0859 time to fit residues: 27.1418 Evaluate side-chains 181 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 633 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [99, 45, 5, 62, 104, 86, 80, 72, 53, 54, 96] chunk 99 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 104 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.196847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.190051 restraints weight = 11419.085| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 0.37 r_work: 0.3650 rms_B_bonded: 0.85 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 1.79 restraints_weight: 0.2500 r_work: 0.3394 rms_B_bonded: 4.80 restraints_weight: 0.1250 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10825 Z= 0.144 Angle : 0.607 6.567 14704 Z= 0.311 Chirality : 0.044 0.347 1726 Planarity : 0.005 0.049 1784 Dihedral : 8.845 124.284 1514 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 3.47 % Allowed : 20.10 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.24), residues: 1316 helix: -0.57 (0.19), residues: 806 sheet: -1.73 (0.46), residues: 104 loop : -1.75 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 400 TYR 0.016 0.001 TYR B 285 PHE 0.009 0.001 PHE A 130 TRP 0.012 0.002 TRP A 258 HIS 0.003 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (10824) covalent geometry : angle 0.60688 / 0.31 (14704) hydrogen bonds : bond 0.03821 / 2.54 ( 509) hydrogen bonds : angle 4.47169 / 3.15 ( 1470) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.373 Fit side-chains REVERT: A 119 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7592 (mp) REVERT: A 295 ARG cc_start: 0.7710 (ttp80) cc_final: 0.5896 (ttm-80) REVERT: A 328 ILE cc_start: 0.8528 (mt) cc_final: 0.8029 (pt) REVERT: A 491 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: A 493 LEU cc_start: 0.7993 (tp) cc_final: 0.7503 (mt) REVERT: A 530 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8095 (mtpp) REVERT: A 541 ARG cc_start: 0.7656 (ptp-110) cc_final: 0.6985 (mtp85) REVERT: A 546 GLN cc_start: 0.7773 (tp40) cc_final: 0.7559 (mm-40) REVERT: B 211 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8381 (mt) REVERT: B 328 ILE cc_start: 0.8611 (mt) cc_final: 0.8056 (pt) REVERT: B 430 MET cc_start: 0.8742 (ttp) cc_final: 0.8442 (ttp) REVERT: B 491 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: B 493 LEU cc_start: 0.7969 (tp) cc_final: 0.7439 (mt) outliers start: 40 outliers final: 34 residues processed: 183 average time/residue: 0.0832 time to fit residues: 23.3911 Evaluate side-chains 180 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 729 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [85, 44, 66, 31, 19, 59, 1, 113, 65, 50, 55] chunk 85 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.0670 chunk 59 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.199754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.191308 restraints weight = 11297.032| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 0.44 r_work: 0.3658 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10825 Z= 0.115 Angle : 0.573 6.496 14704 Z= 0.292 Chirality : 0.042 0.272 1726 Planarity : 0.004 0.051 1784 Dihedral : 8.493 120.766 1509 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.99 % Allowed : 20.45 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.24), residues: 1316 helix: -0.36 (0.19), residues: 806 sheet: -1.61 (0.47), residues: 104 loop : -1.59 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 400 TYR 0.017 0.001 TYR B 500 PHE 0.014 0.001 PHE A 642 TRP 0.011 0.001 TRP B 258 HIS 0.002 0.000 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (10824) covalent geometry : angle 0.57322 / 0.29 (14704) hydrogen bonds : bond 0.03385 / 2.26 ( 509) hydrogen bonds : angle 4.29497 / 3.04 ( 1470) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 0.413 Fit side-chains REVERT: A 119 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7557 (mp) REVERT: A 295 ARG cc_start: 0.7637 (ttp80) cc_final: 0.5912 (ttm-80) REVERT: A 328 ILE cc_start: 0.8375 (mt) cc_final: 0.7970 (pt) REVERT: A 491 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6430 (mp0) REVERT: A 493 LEU cc_start: 0.7784 (tp) cc_final: 0.7323 (mt) REVERT: A 530 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7852 (mtpp) REVERT: A 541 ARG cc_start: 0.7505 (ptp-110) cc_final: 0.6734 (mtp85) REVERT: B 328 ILE cc_start: 0.8396 (mt) cc_final: 0.7964 (pt) REVERT: B 491 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6384 (mp0) REVERT: B 493 LEU cc_start: 0.7734 (tp) cc_final: 0.7321 (mt) REVERT: B 565 GLU cc_start: 0.8058 (pt0) cc_final: 0.7804 (pt0) outliers start: 46 outliers final: 33 residues processed: 185 average time/residue: 0.0851 time to fit residues: 23.9977 Evaluate side-chains 168 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 729 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [78, 111, 80, 95, 25, 62, 84, 44, 71, 88, 7] chunk 78 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.173124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.158015 restraints weight = 12255.912| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 0.89 r_work: 0.3537 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10825 Z= 0.123 Angle : 0.582 6.674 14704 Z= 0.296 Chirality : 0.044 0.469 1726 Planarity : 0.004 0.048 1784 Dihedral : 8.439 119.474 1509 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.25 % Allowed : 20.88 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.24), residues: 1316 helix: -0.35 (0.19), residues: 806 sheet: -1.43 (0.48), residues: 104 loop : -1.50 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 400 TYR 0.013 0.001 TYR A 285 PHE 0.013 0.001 PHE B 757 TRP 0.011 0.001 TRP B 258 HIS 0.002 0.000 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (10824) covalent geometry : angle 0.58239 / 0.30 (14704) hydrogen bonds : bond 0.03489 / 2.34 ( 509) hydrogen bonds : angle 4.28500 / 3.04 ( 1470) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 0.456 Fit side-chains REVERT: A 119 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7465 (mp) REVERT: A 158 TYR cc_start: 0.5333 (OUTLIER) cc_final: 0.4144 (m-80) REVERT: A 295 ARG cc_start: 0.7810 (ttp80) cc_final: 0.5900 (ttm-80) REVERT: A 328 ILE cc_start: 0.8355 (mt) cc_final: 0.7872 (pt) REVERT: A 464 MET cc_start: 0.8079 (mmm) cc_final: 0.7851 (mtp) REVERT: A 491 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: A 493 LEU cc_start: 0.7991 (tp) cc_final: 0.7500 (mt) REVERT: A 530 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8017 (mtpp) REVERT: A 541 ARG cc_start: 0.7657 (ptp-110) cc_final: 0.6826 (mtp85) REVERT: B 119 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7516 (mp) REVERT: B 158 TYR cc_start: 0.5395 (OUTLIER) cc_final: 0.4405 (m-80) REVERT: B 328 ILE cc_start: 0.8410 (mt) cc_final: 0.7898 (pt) REVERT: B 491 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6498 (mp0) REVERT: B 493 LEU cc_start: 0.7999 (tp) cc_final: 0.7487 (mt) REVERT: B 565 GLU cc_start: 0.8208 (pt0) cc_final: 0.7956 (pt0) outliers start: 49 outliers final: 38 residues processed: 188 average time/residue: 0.0806 time to fit residues: 23.5315 Evaluate side-chains 182 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 729 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [126, 32, 62, 96, 84, 124, 50, 13, 34, 120, 15] chunk 126 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 448 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.199067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.192063 restraints weight = 11435.482| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 0.37 r_work: 0.3675 rms_B_bonded: 0.84 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 1.79 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10825 Z= 0.126 Angle : 0.579 6.742 14704 Z= 0.294 Chirality : 0.044 0.466 1726 Planarity : 0.004 0.050 1784 Dihedral : 8.347 118.430 1508 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.51 % Allowed : 20.54 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.24), residues: 1316 helix: -0.40 (0.19), residues: 818 sheet: -1.33 (0.48), residues: 104 loop : -1.35 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 400 TYR 0.020 0.001 TYR B 500 PHE 0.011 0.001 PHE A 757 TRP 0.012 0.001 TRP A 258 HIS 0.003 0.000 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10824) covalent geometry : angle 0.57898 / 0.29 (14704) hydrogen bonds : bond 0.03502 / 2.34 ( 509) hydrogen bonds : angle 4.24976 / 3.02 ( 1470) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7458 (mp) REVERT: A 158 TYR cc_start: 0.5498 (OUTLIER) cc_final: 0.4220 (m-80) REVERT: A 328 ILE cc_start: 0.8389 (mt) cc_final: 0.7964 (pt) REVERT: A 491 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: A 493 LEU cc_start: 0.7768 (tp) cc_final: 0.7326 (mt) REVERT: A 530 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7776 (mtpp) REVERT: A 541 ARG cc_start: 0.7436 (ptp-110) cc_final: 0.6618 (mtp85) REVERT: B 119 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7578 (mp) REVERT: B 158 TYR cc_start: 0.5544 (OUTLIER) cc_final: 0.4367 (m-80) REVERT: B 328 ILE cc_start: 0.8415 (mt) cc_final: 0.7963 (pt) REVERT: B 493 LEU cc_start: 0.7772 (tp) cc_final: 0.7315 (mt) outliers start: 52 outliers final: 41 residues processed: 180 average time/residue: 0.0807 time to fit residues: 22.6164 Evaluate side-chains 179 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 731 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [24, 16, 53, 1, 103, 4, 96, 122, 62, 115, 50] chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.0060 chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 115 optimal weight: 0.0980 chunk 50 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.198450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.190787 restraints weight = 11540.312| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 0.39 r_work: 0.3699 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10825 Z= 0.099 Angle : 0.549 6.226 14704 Z= 0.279 Chirality : 0.043 0.483 1726 Planarity : 0.004 0.049 1784 Dihedral : 8.030 116.087 1506 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.16 % Allowed : 20.54 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.24), residues: 1316 helix: -0.08 (0.19), residues: 810 sheet: -1.17 (0.49), residues: 104 loop : -1.28 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 400 TYR 0.009 0.001 TYR A 70 PHE 0.012 0.001 PHE A 757 TRP 0.011 0.001 TRP A 258 HIS 0.001 0.000 HIS B 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (10824) covalent geometry : angle 0.54905 / 0.28 (14704) hydrogen bonds : bond 0.03071 / 2.06 ( 509) hydrogen bonds : angle 4.07780 / 2.91 ( 1470) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.424 Fit side-chains REVERT: A 119 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7505 (mp) REVERT: A 158 TYR cc_start: 0.5351 (OUTLIER) cc_final: 0.4148 (m-80) REVERT: A 328 ILE cc_start: 0.8362 (mt) cc_final: 0.8002 (pt) REVERT: A 491 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: A 493 LEU cc_start: 0.7681 (tp) cc_final: 0.7345 (mt) REVERT: A 530 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7749 (mtpp) REVERT: A 541 ARG cc_start: 0.7382 (ptp-110) cc_final: 0.6685 (mtp85) REVERT: B 119 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7567 (mp) REVERT: B 158 TYR cc_start: 0.5651 (OUTLIER) cc_final: 0.4462 (m-80) REVERT: B 328 ILE cc_start: 0.8391 (mt) cc_final: 0.8012 (pt) REVERT: B 491 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6282 (mp0) REVERT: B 493 LEU cc_start: 0.7717 (tp) cc_final: 0.7312 (mt) outliers start: 48 outliers final: 34 residues processed: 189 average time/residue: 0.0758 time to fit residues: 22.3374 Evaluate side-chains 178 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 729 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [67, 32, 117, 55, 38, 96, 107, 92, 60, 23, 119] chunk 67 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 96 optimal weight: 0.0370 chunk 107 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.0070 chunk 119 optimal weight: 0.9980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 448 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.176104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.160802 restraints weight = 12096.608| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 0.83 r_work: 0.3591 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10825 Z= 0.105 Angle : 0.553 6.259 14704 Z= 0.281 Chirality : 0.044 0.490 1726 Planarity : 0.004 0.048 1784 Dihedral : 7.834 115.982 1497 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.90 % Allowed : 21.75 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.24), residues: 1316 helix: -0.02 (0.19), residues: 810 sheet: -1.08 (0.49), residues: 104 loop : -1.26 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 400 TYR 0.023 0.001 TYR B 533 PHE 0.020 0.001 PHE A 502 TRP 0.011 0.001 TRP A 258 HIS 0.002 0.000 HIS B 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (10824) covalent geometry : angle 0.55261 / 0.28 (14704) hydrogen bonds : bond 0.03179 / 2.13 ( 509) hydrogen bonds : angle 4.07453 / 2.91 ( 1470) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.315 Fit side-chains REVERT: A 119 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7486 (mp) REVERT: A 158 TYR cc_start: 0.5130 (OUTLIER) cc_final: 0.4013 (m-80) REVERT: A 328 ILE cc_start: 0.8357 (mt) cc_final: 0.7900 (pt) REVERT: A 491 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: A 493 LEU cc_start: 0.7877 (tp) cc_final: 0.7484 (mt) REVERT: A 530 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7946 (mtpp) REVERT: A 541 ARG cc_start: 0.7532 (ptp-110) cc_final: 0.6790 (mtp85) REVERT: A 719 LEU cc_start: 0.6888 (mt) cc_final: 0.6616 (mp) REVERT: B 119 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7469 (mp) REVERT: B 158 TYR cc_start: 0.5499 (OUTLIER) cc_final: 0.4245 (m-80) REVERT: B 328 ILE cc_start: 0.8405 (mt) cc_final: 0.7939 (pt) REVERT: B 491 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6399 (mp0) REVERT: B 493 LEU cc_start: 0.7927 (tp) cc_final: 0.7493 (mt) REVERT: B 719 LEU cc_start: 0.6850 (mt) cc_final: 0.6593 (mp) outliers start: 45 outliers final: 37 residues processed: 186 average time/residue: 0.0743 time to fit residues: 21.5454 Evaluate side-chains 182 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 731 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [7, 33, 83, 10, 16, 59, 30, 119, 3, 79, 88] chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 59 optimal weight: 0.0570 chunk 30 optimal weight: 0.0040 chunk 119 optimal weight: 0.0870 chunk 3 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.3888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.203890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.196257 restraints weight = 11411.032| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 0.38 r_work: 0.4041 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10825 Z= 0.100 Angle : 0.546 6.382 14704 Z= 0.278 Chirality : 0.043 0.489 1726 Planarity : 0.004 0.049 1784 Dihedral : 7.712 113.926 1497 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.73 % Allowed : 22.18 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.24), residues: 1316 helix: 0.12 (0.19), residues: 810 sheet: -0.99 (0.49), residues: 104 loop : -1.23 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 400 TYR 0.012 0.001 TYR B 533 PHE 0.013 0.001 PHE A 757 TRP 0.011 0.001 TRP A 258 HIS 0.002 0.000 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (10824) covalent geometry : angle 0.54572 / 0.28 (14704) hydrogen bonds : bond 0.03053 / 2.05 ( 509) hydrogen bonds : angle 4.01644 / 2.86 ( 1470) Misc. bond : bond 0.00021 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 0.299 Fit side-chains REVERT: A 119 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7623 (mp) REVERT: A 158 TYR cc_start: 0.5669 (OUTLIER) cc_final: 0.4527 (m-80) REVERT: A 328 ILE cc_start: 0.8531 (mt) cc_final: 0.8142 (pt) REVERT: A 491 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: A 493 LEU cc_start: 0.7832 (tp) cc_final: 0.7492 (mt) REVERT: A 541 ARG cc_start: 0.7432 (ptp-110) cc_final: 0.6822 (mtp85) REVERT: A 719 LEU cc_start: 0.7171 (mt) cc_final: 0.6932 (mp) REVERT: B 119 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7648 (mp) REVERT: B 136 ILE cc_start: 0.8245 (mm) cc_final: 0.7967 (mt) REVERT: B 158 TYR cc_start: 0.5828 (OUTLIER) cc_final: 0.4436 (m-80) REVERT: B 328 ILE cc_start: 0.8541 (mt) cc_final: 0.8151 (pt) REVERT: B 491 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: B 493 LEU cc_start: 0.7873 (tp) cc_final: 0.7482 (mt) REVERT: B 719 LEU cc_start: 0.7131 (mt) cc_final: 0.6922 (mp) outliers start: 43 outliers final: 32 residues processed: 182 average time/residue: 0.0785 time to fit residues: 22.0878 Evaluate side-chains 184 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 731 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [80, 105, 25, 118, 36, 68, 120, 32, 49, 89, 96] chunk 80 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 96 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.202454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.194585 restraints weight = 11429.120| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 0.40 r_work: 0.3698 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10825 Z= 0.111 Angle : 0.562 6.359 14704 Z= 0.285 Chirality : 0.044 0.482 1726 Planarity : 0.004 0.047 1784 Dihedral : 7.437 113.884 1487 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.38 % Allowed : 22.62 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.24), residues: 1316 helix: 0.09 (0.19), residues: 810 sheet: -0.98 (0.49), residues: 104 loop : -1.20 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 400 TYR 0.021 0.001 TYR B 500 PHE 0.036 0.001 PHE A 502 TRP 0.011 0.001 TRP A 258 HIS 0.002 0.000 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (10824) covalent geometry : angle 0.56169 / 0.28 (14704) hydrogen bonds : bond 0.03247 / 2.18 ( 509) hydrogen bonds : angle 4.06937 / 2.90 ( 1470) Misc. bond : bond 0.00020 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2410.17 seconds wall clock time: 42 minutes 1.40 seconds (2521.40 seconds total)