Starting phenix.real_space_refine on Fri Oct 23 18:08:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25jn_80158/10_2026/25jn_80158.cif Found real_map, /net/cci-nas-00/data/ceres_data/25jn_80158/10_2026/25jn_80158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/25jn_80158/10_2026/25jn_80158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25jn_80158/10_2026/25jn_80158.map" model { file = "/net/cci-nas-00/data/ceres_data/25jn_80158/10_2026/25jn_80158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25jn_80158/10_2026/25jn_80158.cif" } resolution = 2.92 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= 0.004 sd= 0.084 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 6946 2.51 5 N 1694 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 67 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: 10596 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5264 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Chain: "B" Number of atoms: 5264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5264 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: 2.49, per 1000 atoms: 0.23 Number of scatterers: 10596 At special positions: 0 Unit cell: (122.36, 90.16, 102.12, 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 1694 7.00 C 6946 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: 0.83 Conformation dependent library (CDL) restraints added in 307.3 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 3 sheets defined 67.9% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.619A pdb=" N LEU A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 91 through 109 removed outlier: 4.157A pdb=" N VAL A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A 96 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 128 through 141 removed outlier: 3.835A pdb=" N TYR A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 179 removed outlier: 3.568A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 removed outlier: 3.559A pdb=" N LYS A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 removed outlier: 3.816A pdb=" N SER A 207 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 222 through 236 removed outlier: 5.539A pdb=" N ILE A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 272 removed outlier: 3.639A pdb=" N LEU A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.541A pdb=" N ASN A 282 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 300 through 305 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 311 through 317 removed outlier: 3.803A pdb=" N PHE A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 352 removed outlier: 4.876A pdb=" N TYR A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Proline residue: A 336 - end of helix removed outlier: 3.506A pdb=" N THR A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 364 through 367 Proline residue: A 367 - end of helix No H-bonds generated for 'chain 'A' and resid 364 through 367' Processing helix chain 'A' and resid 368 through 401 Processing helix chain 'A' and resid 422 through 440 removed outlier: 4.180A pdb=" N TYR A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 472 removed outlier: 3.881A pdb=" N ALA A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 452 " --> pdb=" O HIS A 448 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N THR A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 500 removed outlier: 3.910A pdb=" N GLU A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 537 removed outlier: 5.194A pdb=" N LEU A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ILE A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 549 Processing helix chain 'A' and resid 571 through 582 removed outlier: 4.189A pdb=" N SER A 575 " --> pdb=" O THR A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 654 Processing helix chain 'A' and resid 717 through 727 removed outlier: 3.587A pdb=" N LYS A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 753 Processing helix chain 'A' and resid 753 through 761 removed outlier: 3.693A pdb=" N LEU A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 772 through 774 No H-bonds generated for 'chain 'A' and resid 772 through 774' Processing helix chain 'B' and resid 56 through 66 removed outlier: 3.616A pdb=" N LEU B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 91 through 109 removed outlier: 4.317A pdb=" N VAL B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL B 96 " --> pdb=" O LYS B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 128 through 141 removed outlier: 3.837A pdb=" N TYR B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 179 removed outlier: 3.610A pdb=" N ASN B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 removed outlier: 3.575A pdb=" N LYS B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.509A 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 222 through 236 removed outlier: 5.521A pdb=" N ILE B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 272 removed outlier: 3.641A pdb=" N LEU B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.511A pdb=" N LEU B 278 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN B 282 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 294 through 300 Processing helix chain 'B' and resid 300 through 305 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 311 through 317 removed outlier: 3.801A pdb=" N PHE B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 352 removed outlier: 4.875A pdb=" N TYR B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Proline residue: B 336 - end of helix removed outlier: 3.524A pdb=" N THR B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 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 401 Processing helix chain 'B' and resid 422 through 438 removed outlier: 4.211A pdb=" N TYR B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 473 removed outlier: 3.766A pdb=" N ALA B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 452 " --> pdb=" O HIS B 448 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N THR B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP B 473 " --> pdb=" O MET B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 500 removed outlier: 3.929A pdb=" N GLU B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR B 494 " --> pdb=" O ILE B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 537 removed outlier: 4.342A pdb=" N LEU B 510 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LEU B 516 " --> pdb=" O ILE B 512 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ILE B 522 " --> pdb=" O ALA B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 549 Processing helix chain 'B' and resid 571 through 582 removed outlier: 4.178A pdb=" N SER B 575 " --> pdb=" O THR B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 652 Processing helix chain 'B' and resid 717 through 727 removed outlier: 3.675A pdb=" N LYS B 726 " --> pdb=" O LYS B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 753 Processing helix chain 'B' and resid 753 through 761 removed outlier: 3.710A pdb=" N LEU B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 769 Processing helix chain 'B' and resid 772 through 774 No H-bonds generated for 'chain 'B' and resid 772 through 774' 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 608 through 611 removed outlier: 7.547A pdb=" N PHE A 620 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE A 588 " --> pdb=" O PHE A 620 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N CYS A 622 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU A 590 " --> pdb=" O CYS A 622 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL A 624 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER A 592 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N TYR A 626 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS A 594 " --> pdb=" O TYR A 626 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER A 583 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A 556 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N HIS A 585 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY A 558 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLY A 733 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LEU A 777 " --> pdb=" O MET A 728 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR A 730 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A 779 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N MET A 732 " --> pdb=" O VAL A 779 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N MET A 781 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLU A 734 " --> pdb=" O MET A 781 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR A 783 " --> pdb=" O GLU A 734 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU A 736 " --> pdb=" O TYR A 783 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU A 785 " --> pdb=" O GLU A 736 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR A 738 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU A 776 " --> pdb=" O GLY B 780 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU B 776 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU B 777 " --> pdb=" O MET B 728 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TYR B 730 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL B 779 " --> pdb=" O TYR B 730 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N MET B 732 " --> pdb=" O VAL B 779 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N MET B 781 " --> pdb=" O MET B 732 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU B 734 " --> pdb=" O MET B 781 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N TYR B 783 " --> pdb=" O GLU B 734 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU B 736 " --> pdb=" O TYR B 783 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU B 785 " --> pdb=" O GLU B 736 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR B 738 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY B 733 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER B 583 " --> pdb=" O ASN B 554 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 556 " --> pdb=" O SER B 583 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N HIS B 585 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY B 558 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE B 620 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE B 588 " --> pdb=" O PHE B 620 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N CYS B 622 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU B 590 " --> pdb=" O CYS B 622 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL B 624 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER B 592 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N TYR B 626 " --> pdb=" O SER B 592 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS B 594 " --> pdb=" O TYR B 626 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 410 through 411 608 hydrogen bonds defined for protein. 1755 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: 1.99 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3021 1.33 - 1.45: 1889 1.45 - 1.57: 5812 1.57 - 1.69: 6 1.69 - 1.81: 104 Bond restraints: 10832 Sorted by residual: bond pdb=" CA SER B 250 " pdb=" CB SER B 250 " ideal model delta sigma weight residual 1.532 1.454 0.078 1.79e-02 3.12e+03 1.91e+01 bond pdb=" CA SER A 250 " pdb=" CB SER A 250 " ideal model delta sigma weight residual 1.532 1.467 0.065 1.79e-02 3.12e+03 1.32e+01 bond pdb=" N ASP A 631 " pdb=" CA ASP A 631 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.10e+01 bond pdb=" CA TYR A 628 " pdb=" C TYR A 628 " ideal model delta sigma weight residual 1.523 1.466 0.057 1.80e-02 3.09e+03 1.00e+01 bond pdb=" N ILE B 472 " pdb=" CA ILE B 472 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.08e-02 8.57e+03 9.90e+00 ... (remaining 10827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 14177 2.42 - 4.84: 431 4.84 - 7.26: 85 7.26 - 9.68: 14 9.68 - 12.09: 5 Bond angle restraints: 14712 Sorted by residual: angle pdb=" N THR A 475 " pdb=" CA THR A 475 " pdb=" C THR A 475 " ideal model delta sigma weight residual 110.53 100.33 10.20 1.29e+00 6.01e-01 6.25e+01 angle pdb=" C ASP A 274 " pdb=" CA ASP A 274 " pdb=" CB ASP A 274 " ideal model delta sigma weight residual 111.82 101.54 10.28 1.38e+00 5.25e-01 5.55e+01 angle pdb=" N PHE B 440 " pdb=" CA PHE B 440 " pdb=" C PHE B 440 " ideal model delta sigma weight residual 114.04 105.18 8.86 1.24e+00 6.50e-01 5.10e+01 angle pdb=" CB GLU A 630 " pdb=" CG GLU A 630 " pdb=" CD GLU A 630 " ideal model delta sigma weight residual 112.60 100.51 12.09 1.70e+00 3.46e-01 5.06e+01 angle pdb=" N GLU B 718 " pdb=" CA GLU B 718 " pdb=" C GLU B 718 " ideal model delta sigma weight residual 113.23 104.60 8.63 1.24e+00 6.50e-01 4.85e+01 ... (remaining 14707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.15: 5861 24.15 - 48.31: 392 48.31 - 72.46: 72 72.46 - 96.62: 9 96.62 - 120.77: 2 Dihedral angle restraints: 6336 sinusoidal: 2460 harmonic: 3876 Sorted by residual: dihedral pdb=" CD ARG B 441 " pdb=" NE ARG B 441 " pdb=" CZ ARG B 441 " pdb=" NH1 ARG B 441 " ideal model delta sinusoidal sigma weight residual 0.00 89.14 -89.14 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CD ARG B 241 " pdb=" NE ARG B 241 " pdb=" CZ ARG B 241 " pdb=" NH1 ARG B 241 " ideal model delta sinusoidal sigma weight residual 0.00 76.20 -76.20 1 1.00e+01 1.00e-02 7.31e+01 dihedral pdb=" CD ARG B 295 " pdb=" NE ARG B 295 " pdb=" CZ ARG B 295 " pdb=" NH1 ARG B 295 " ideal model delta sinusoidal sigma weight residual 0.00 59.79 -59.79 1 1.00e+01 1.00e-02 4.77e+01 ... (remaining 6333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1241 0.060 - 0.120: 400 0.120 - 0.180: 67 0.180 - 0.240: 16 0.240 - 0.300: 2 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CA PHE B 249 " pdb=" N PHE B 249 " pdb=" C PHE B 249 " pdb=" CB PHE B 249 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA PHE A 249 " pdb=" N PHE A 249 " pdb=" C PHE A 249 " pdb=" CB PHE A 249 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA PHE B 440 " pdb=" N PHE B 440 " pdb=" C PHE B 440 " pdb=" CB PHE B 440 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1723 not shown) Planarity restraints: 1784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 441 " 1.098 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG B 441 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG B 441 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 441 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 441 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 241 " 1.066 9.50e-02 1.11e+02 4.78e-01 1.38e+02 pdb=" NE ARG B 241 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 241 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 241 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 241 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 295 " 0.951 9.50e-02 1.11e+02 4.26e-01 1.10e+02 pdb=" NE ARG B 295 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG B 295 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 295 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 295 " 0.024 2.00e-02 2.50e+03 ... (remaining 1781 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.69: 479 2.69 - 3.30: 12298 3.30 - 3.91: 21524 3.91 - 4.53: 32230 4.53 - 5.14: 48774 Nonbonded interactions: 115305 Sorted by model distance: nonbonded pdb=" ND2 ASN B 269 " pdb=" O SER B 363 " model vdw 2.077 3.120 nonbonded pdb=" ND2 ASN A 269 " pdb=" O SER A 363 " model vdw 2.083 3.120 nonbonded pdb=" OH TYR A 104 " pdb=" O LEU A 281 " model vdw 2.092 3.040 nonbonded pdb=" OH TYR B 104 " pdb=" O LEU B 281 " model vdw 2.092 3.040 nonbonded pdb=" NH1 ARG A 555 " pdb=" O HIS A 585 " model vdw 2.130 3.120 ... (remaining 115300 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: 0.02 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.020 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:9.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.304 10833 Z= 0.579 Angle : 1.046 12.095 14712 Z= 0.615 Chirality : 0.061 0.300 1726 Planarity : 0.021 0.492 1784 Dihedral : 16.379 120.770 3856 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.37 % Favored : 91.87 % Rotamer: Outliers : 6.75 % Allowed : 16.78 % Favored : 76.47 % Cbeta Deviations : 0.16 % 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: -4.35 (0.19), residues: 1316 helix: -2.95 (0.13), residues: 818 sheet: -2.07 (0.44), residues: 102 loop : -2.41 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 606 TYR 0.021 0.003 TYR B 104 PHE 0.023 0.002 PHE B 130 TRP 0.020 0.003 TRP B 479 HIS 0.009 0.002 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.01138 / 0.50 (10832) covalent geometry : angle 1.04589 / 0.61 (14712) hydrogen bonds : bond 0.19411 / 12.68 ( 608) hydrogen bonds : angle 9.30732 / 6.64 ( 1755) Misc. bond : bond 0.30417 / 16.01 ( 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 253 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 175 time to evaluate : 0.348 Fit side-chains REVERT: A 60 SER cc_start: 0.8483 (t) cc_final: 0.7931 (p) REVERT: A 182 PHE cc_start: 0.7452 (t80) cc_final: 0.7134 (t80) REVERT: A 218 LYS cc_start: 0.7961 (ptmt) cc_final: 0.7539 (ptmm) REVERT: A 295 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.6135 (tpt170) REVERT: A 610 ARG cc_start: 0.7945 (ttp-170) cc_final: 0.7715 (ttm170) REVERT: A 651 HIS cc_start: 0.7218 (m-70) cc_final: 0.6977 (m170) REVERT: A 716 GLN cc_start: 0.6199 (OUTLIER) cc_final: 0.4052 (pm20) REVERT: B 60 SER cc_start: 0.8484 (t) cc_final: 0.7923 (p) REVERT: B 182 PHE cc_start: 0.7474 (t80) cc_final: 0.7179 (t80) REVERT: B 218 LYS cc_start: 0.7971 (ptmt) cc_final: 0.7534 (ptmm) REVERT: B 295 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6468 (tpt170) REVERT: B 610 ARG cc_start: 0.7934 (ttp-170) cc_final: 0.7717 (ttm170) REVERT: B 632 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7980 (tt) REVERT: B 651 HIS cc_start: 0.7205 (m-70) cc_final: 0.6926 (m90) REVERT: B 716 GLN cc_start: 0.5875 (OUTLIER) cc_final: 0.3806 (pm20) REVERT: B 718 GLU cc_start: 0.5190 (OUTLIER) cc_final: 0.4449 (pt0) REVERT: B 732 MET cc_start: 0.8693 (ptm) cc_final: 0.8456 (ptm) outliers start: 78 outliers final: 38 residues processed: 235 average time/residue: 0.4718 time to fit residues: 120.6982 Evaluate side-chains 197 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 716 GLN Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 774 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: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN A 223 ASN A 273 HIS A 352 HIS A 385 GLN A 543 ASN A 546 GLN B 64 GLN B 223 ASN B 273 HIS B 352 HIS B 385 GLN B 543 ASN B 716 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.132341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.110910 restraints weight = 11774.729| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.27 r_work: 0.3139 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10833 Z= 0.142 Angle : 0.664 8.905 14712 Z= 0.347 Chirality : 0.044 0.177 1726 Planarity : 0.005 0.058 1784 Dihedral : 9.924 129.330 1546 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.17 % Favored : 94.68 % Rotamer: Outliers : 4.93 % Allowed : 16.52 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % 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: -2.13 (0.22), residues: 1316 helix: -1.13 (0.17), residues: 842 sheet: -2.13 (0.47), residues: 102 loop : -1.38 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 441 TYR 0.017 0.001 TYR A 104 PHE 0.011 0.001 PHE B 130 TRP 0.009 0.001 TRP B 258 HIS 0.007 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (10832) covalent geometry : angle 0.66395 / 0.35 (14712) hydrogen bonds : bond 0.03995 / 2.65 ( 608) hydrogen bonds : angle 5.84889 / 4.23 ( 1755) Misc. bond : bond 0.00025 / 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 241 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 184 time to evaluate : 0.339 Fit side-chains REVERT: A 60 SER cc_start: 0.8004 (t) cc_final: 0.7401 (p) REVERT: A 182 PHE cc_start: 0.7209 (t80) cc_final: 0.6837 (t80) REVERT: A 218 LYS cc_start: 0.7504 (ptmt) cc_final: 0.7050 (ptmm) REVERT: A 287 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7453 (mt) REVERT: A 415 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7792 (tttt) REVERT: A 474 LYS cc_start: 0.5029 (OUTLIER) cc_final: 0.2621 (pptt) REVERT: A 600 ARG cc_start: 0.7720 (mtt-85) cc_final: 0.7436 (mtt180) REVERT: A 610 ARG cc_start: 0.8157 (ttp-170) cc_final: 0.7808 (ttm170) REVERT: A 648 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6478 (tt0) REVERT: A 651 HIS cc_start: 0.7376 (m-70) cc_final: 0.6904 (m90) REVERT: A 718 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7621 (tp30) REVERT: A 741 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.6314 (mppt) REVERT: B 60 SER cc_start: 0.7970 (t) cc_final: 0.7356 (p) REVERT: B 93 ASP cc_start: 0.8233 (m-30) cc_final: 0.8009 (m-30) REVERT: B 157 ASN cc_start: 0.8001 (m-40) cc_final: 0.7670 (m110) REVERT: B 182 PHE cc_start: 0.7231 (t80) cc_final: 0.6877 (t80) REVERT: B 218 LYS cc_start: 0.7486 (ptmt) cc_final: 0.7031 (ptmm) REVERT: B 287 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7448 (mt) REVERT: B 295 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.5786 (tpt170) REVERT: B 610 ARG cc_start: 0.8182 (ttp-170) cc_final: 0.7849 (ttm170) REVERT: B 648 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6417 (tt0) REVERT: B 718 GLU cc_start: 0.5158 (OUTLIER) cc_final: 0.4760 (mm-30) outliers start: 57 outliers final: 21 residues processed: 223 average time/residue: 0.4855 time to fit residues: 117.5426 Evaluate side-chains 191 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [37, 65, 57, 106, 52, 62, 10, 130, 34, 70, 92] chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.0010 chunk 130 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.131256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.108028 restraints weight = 11945.380| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.52 r_work: 0.3101 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10833 Z= 0.158 Angle : 0.643 8.776 14712 Z= 0.331 Chirality : 0.044 0.170 1726 Planarity : 0.004 0.050 1784 Dihedral : 8.705 130.988 1496 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.81 % Allowed : 18.25 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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 (0.23), residues: 1316 helix: -0.44 (0.18), residues: 838 sheet: -2.05 (0.48), residues: 102 loop : -1.31 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 441 TYR 0.013 0.002 TYR A 70 PHE 0.014 0.001 PHE B 130 TRP 0.009 0.001 TRP A 258 HIS 0.007 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (10832) covalent geometry : angle 0.64262 / 0.33 (14712) hydrogen bonds : bond 0.03773 / 2.50 ( 608) hydrogen bonds : angle 5.49972 / 3.99 ( 1755) Misc. bond : bond 0.00055 / 0.03 ( 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 213 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 60 SER cc_start: 0.7951 (t) cc_final: 0.7341 (p) REVERT: A 182 PHE cc_start: 0.7030 (t80) cc_final: 0.6671 (t80) REVERT: A 218 LYS cc_start: 0.7544 (ptmt) cc_final: 0.7083 (ptmm) REVERT: A 287 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7378 (mt) REVERT: A 474 LYS cc_start: 0.4582 (OUTLIER) cc_final: 0.2447 (ptpp) REVERT: A 600 ARG cc_start: 0.7748 (mtt-85) cc_final: 0.7443 (mtt90) REVERT: A 610 ARG cc_start: 0.8197 (ttp-170) cc_final: 0.7903 (ttm170) REVERT: A 648 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6261 (tt0) REVERT: A 651 HIS cc_start: 0.7385 (m-70) cc_final: 0.6941 (m90) REVERT: A 652 HIS cc_start: 0.6976 (m90) cc_final: 0.6510 (m90) REVERT: A 741 LYS cc_start: 0.6659 (OUTLIER) cc_final: 0.6294 (mppt) REVERT: B 60 SER cc_start: 0.7963 (t) cc_final: 0.7351 (p) REVERT: B 93 ASP cc_start: 0.8140 (m-30) cc_final: 0.7931 (m-30) REVERT: B 157 ASN cc_start: 0.7958 (m-40) cc_final: 0.7604 (m110) REVERT: B 175 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.7031 (pm20) REVERT: B 182 PHE cc_start: 0.7180 (t80) cc_final: 0.6870 (t80) REVERT: B 218 LYS cc_start: 0.7550 (ptmt) cc_final: 0.7144 (ptmm) REVERT: B 610 ARG cc_start: 0.8198 (ttp-170) cc_final: 0.7904 (ttm170) REVERT: B 648 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6404 (tt0) REVERT: B 718 GLU cc_start: 0.4926 (OUTLIER) cc_final: 0.4570 (mm-30) outliers start: 44 outliers final: 24 residues processed: 200 average time/residue: 0.4727 time to fit residues: 103.0430 Evaluate side-chains 188 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [76, 120, 16, 122, 82, 62, 94, 56, 6, 61, 23] chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.132416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.109163 restraints weight = 11898.907| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.53 r_work: 0.3114 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10833 Z= 0.145 Angle : 0.617 8.720 14712 Z= 0.316 Chirality : 0.043 0.162 1726 Planarity : 0.004 0.055 1784 Dihedral : 8.409 132.279 1488 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.98 % Allowed : 18.34 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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 (0.18), residues: 850 sheet: -2.05 (0.48), residues: 102 loop : -1.11 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 441 TYR 0.014 0.001 TYR A 450 PHE 0.013 0.001 PHE B 130 TRP 0.009 0.001 TRP B 370 HIS 0.006 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (10832) covalent geometry : angle 0.61672 / 0.32 (14712) hydrogen bonds : bond 0.03520 / 2.32 ( 608) hydrogen bonds : angle 5.25846 / 3.83 ( 1755) Misc. bond : bond 0.00035 / 0.02 ( 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 210 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 60 SER cc_start: 0.7976 (t) cc_final: 0.7375 (p) REVERT: A 182 PHE cc_start: 0.7052 (t80) cc_final: 0.6707 (t80) REVERT: A 218 LYS cc_start: 0.7615 (ptmt) cc_final: 0.7168 (ptmm) REVERT: A 287 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7375 (mt) REVERT: A 415 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7860 (tttt) REVERT: A 474 LYS cc_start: 0.4109 (OUTLIER) cc_final: 0.2280 (ptpp) REVERT: A 600 ARG cc_start: 0.7753 (mtt-85) cc_final: 0.7424 (mtt180) REVERT: A 610 ARG cc_start: 0.8175 (ttp-170) cc_final: 0.7927 (ttm170) REVERT: A 648 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6661 (tt0) REVERT: A 651 HIS cc_start: 0.7313 (m-70) cc_final: 0.6881 (m90) REVERT: A 652 HIS cc_start: 0.7198 (m90) cc_final: 0.6026 (t-90) REVERT: A 741 LYS cc_start: 0.6597 (OUTLIER) cc_final: 0.6251 (mppt) REVERT: A 774 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8264 (p) REVERT: B 60 SER cc_start: 0.8005 (t) cc_final: 0.7400 (p) REVERT: B 157 ASN cc_start: 0.7982 (m-40) cc_final: 0.7646 (m110) REVERT: B 175 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6904 (pm20) REVERT: B 218 LYS cc_start: 0.7587 (ptmt) cc_final: 0.7201 (ptmm) REVERT: B 295 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.5770 (tpt170) REVERT: B 610 ARG cc_start: 0.8224 (ttp-170) cc_final: 0.7978 (ttm170) REVERT: B 648 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6490 (tt0) REVERT: B 718 GLU cc_start: 0.4863 (OUTLIER) cc_final: 0.4466 (mm-30) REVERT: B 774 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8304 (p) outliers start: 46 outliers final: 23 residues processed: 199 average time/residue: 0.4841 time to fit residues: 104.9075 Evaluate side-chains 188 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [63, 41, 13, 42, 70, 96, 120, 74, 87, 86, 71] chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 120 optimal weight: 0.0980 chunk 74 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.135062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.113479 restraints weight = 12052.041| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.32 r_work: 0.3101 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10833 Z= 0.117 Angle : 0.590 8.375 14712 Z= 0.301 Chirality : 0.042 0.150 1726 Planarity : 0.004 0.050 1784 Dihedral : 8.127 129.494 1486 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.03 % Allowed : 19.64 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -0.53 (0.24), residues: 1316 helix: 0.24 (0.18), residues: 850 sheet: -2.10 (0.48), residues: 102 loop : -0.93 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 441 TYR 0.015 0.001 TYR B 533 PHE 0.019 0.001 PHE B 182 TRP 0.007 0.001 TRP B 258 HIS 0.005 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (10832) covalent geometry : angle 0.58965 / 0.30 (14712) hydrogen bonds : bond 0.03258 / 2.14 ( 608) hydrogen bonds : angle 5.02202 / 3.67 ( 1755) Misc. bond : bond 0.00027 / 0.01 ( 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 219 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 60 SER cc_start: 0.7829 (t) cc_final: 0.7461 (p) REVERT: A 182 PHE cc_start: 0.7037 (t80) cc_final: 0.6692 (t80) REVERT: A 218 LYS cc_start: 0.7434 (ptmt) cc_final: 0.7041 (ptmm) REVERT: A 246 LYS cc_start: 0.6662 (mmtt) cc_final: 0.5726 (pttt) REVERT: A 282 ASN cc_start: 0.7477 (t0) cc_final: 0.7204 (t0) REVERT: A 324 ARG cc_start: 0.7843 (tpp-160) cc_final: 0.7533 (tpp80) REVERT: A 415 LYS cc_start: 0.8030 (mtpt) cc_final: 0.7791 (tttt) REVERT: A 600 ARG cc_start: 0.7609 (mtt-85) cc_final: 0.7267 (mtt180) REVERT: A 610 ARG cc_start: 0.8075 (ttp-170) cc_final: 0.7813 (ttm170) REVERT: A 648 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6606 (tt0) REVERT: A 651 HIS cc_start: 0.7235 (m-70) cc_final: 0.6798 (m90) REVERT: A 652 HIS cc_start: 0.7102 (m90) cc_final: 0.5907 (t-90) REVERT: A 718 GLU cc_start: 0.8264 (tp30) cc_final: 0.8044 (tp30) REVERT: A 726 LYS cc_start: 0.7638 (tmtt) cc_final: 0.7430 (tmtt) REVERT: A 774 SER cc_start: 0.8548 (m) cc_final: 0.8213 (p) REVERT: B 60 SER cc_start: 0.7842 (t) cc_final: 0.7224 (p) REVERT: B 93 ASP cc_start: 0.7789 (m-30) cc_final: 0.7398 (m-30) REVERT: B 175 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6739 (pm20) REVERT: B 218 LYS cc_start: 0.7277 (ptmt) cc_final: 0.7048 (ptmm) REVERT: B 246 LYS cc_start: 0.6638 (mmtt) cc_final: 0.5608 (pttt) REVERT: B 287 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7292 (mt) REVERT: B 295 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.5600 (tpt170) REVERT: B 324 ARG cc_start: 0.7922 (tpp-160) cc_final: 0.7602 (tpp80) REVERT: B 358 ASN cc_start: 0.7722 (t0) cc_final: 0.7182 (m-40) REVERT: B 424 GLU cc_start: 0.8252 (mp0) cc_final: 0.7482 (mt-10) REVERT: B 610 ARG cc_start: 0.8104 (ttp-170) cc_final: 0.7751 (ttm170) REVERT: B 648 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6318 (tt0) REVERT: B 718 GLU cc_start: 0.4771 (OUTLIER) cc_final: 0.4451 (tp30) REVERT: B 774 SER cc_start: 0.8725 (m) cc_final: 0.8374 (p) outliers start: 35 outliers final: 17 residues processed: 211 average time/residue: 0.4560 time to fit residues: 105.0622 Evaluate side-chains 188 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 764 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [2, 61, 70, 73, 130, 82, 78, 109, 24, 77, 63] chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.133865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.112260 restraints weight = 12158.412| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.32 r_work: 0.3086 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10833 Z= 0.133 Angle : 0.600 8.592 14712 Z= 0.307 Chirality : 0.043 0.147 1726 Planarity : 0.004 0.051 1784 Dihedral : 7.942 129.490 1481 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.15 % Allowed : 18.51 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.44 (0.24), residues: 1316 helix: 0.30 (0.18), residues: 852 sheet: -2.09 (0.47), residues: 102 loop : -0.88 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 640 TYR 0.014 0.001 TYR B 70 PHE 0.013 0.001 PHE B 130 TRP 0.008 0.001 TRP B 258 HIS 0.005 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10832) covalent geometry : angle 0.59966 / 0.31 (14712) hydrogen bonds : bond 0.03339 / 2.20 ( 608) hydrogen bonds : angle 5.00813 / 3.66 ( 1755) Misc. bond : bond 0.00037 / 0.02 ( 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 218 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 60 SER cc_start: 0.7854 (t) cc_final: 0.7484 (p) REVERT: A 182 PHE cc_start: 0.7137 (t80) cc_final: 0.6798 (t80) REVERT: A 218 LYS cc_start: 0.7453 (ptmt) cc_final: 0.7026 (ptmm) REVERT: A 246 LYS cc_start: 0.6751 (mmtt) cc_final: 0.5702 (pttt) REVERT: A 282 ASN cc_start: 0.7437 (t0) cc_final: 0.7190 (t0) REVERT: A 324 ARG cc_start: 0.7846 (tpp-160) cc_final: 0.7544 (tpp80) REVERT: A 415 LYS cc_start: 0.8049 (mtpt) cc_final: 0.7772 (tttt) REVERT: A 474 LYS cc_start: 0.3580 (OUTLIER) cc_final: 0.2473 (mttm) REVERT: A 586 SER cc_start: 0.7973 (OUTLIER) cc_final: 0.7498 (m) REVERT: A 590 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8524 (mt) REVERT: A 600 ARG cc_start: 0.7626 (mtt-85) cc_final: 0.7293 (mtt180) REVERT: A 610 ARG cc_start: 0.8074 (ttp-170) cc_final: 0.7824 (ttm170) REVERT: A 648 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6599 (tt0) REVERT: A 652 HIS cc_start: 0.7210 (m90) cc_final: 0.5933 (t-90) REVERT: A 741 LYS cc_start: 0.6451 (OUTLIER) cc_final: 0.6090 (mppt) REVERT: A 774 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8242 (p) REVERT: B 60 SER cc_start: 0.7865 (t) cc_final: 0.7254 (p) REVERT: B 93 ASP cc_start: 0.7802 (m-30) cc_final: 0.7414 (m-30) REVERT: B 175 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6701 (pm20) REVERT: B 218 LYS cc_start: 0.7460 (ptmt) cc_final: 0.7097 (ptmm) REVERT: B 245 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7849 (m-30) REVERT: B 246 LYS cc_start: 0.6758 (mmtt) cc_final: 0.5703 (pttt) REVERT: B 295 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.5614 (tpt170) REVERT: B 324 ARG cc_start: 0.7855 (tpp-160) cc_final: 0.7578 (tpp80) REVERT: B 424 GLU cc_start: 0.8223 (mp0) cc_final: 0.7444 (mt-10) REVERT: B 610 ARG cc_start: 0.8114 (ttp-170) cc_final: 0.7846 (ttm170) REVERT: B 648 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6323 (tt0) REVERT: B 718 GLU cc_start: 0.4716 (OUTLIER) cc_final: 0.4373 (tp30) REVERT: B 774 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8385 (p) outliers start: 48 outliers final: 23 residues processed: 207 average time/residue: 0.4421 time to fit residues: 100.2684 Evaluate side-chains 197 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [20, 117, 21, 126, 7, 64, 17, 55, 83, 58, 40] chunk 20 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.134865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.113108 restraints weight = 12013.934| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.32 r_work: 0.3098 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10833 Z= 0.126 Angle : 0.596 8.481 14712 Z= 0.305 Chirality : 0.043 0.149 1726 Planarity : 0.004 0.051 1784 Dihedral : 7.881 129.023 1480 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.81 % Allowed : 18.86 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.30 (0.24), residues: 1316 helix: 0.40 (0.18), residues: 852 sheet: -2.11 (0.47), residues: 102 loop : -0.78 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 640 TYR 0.014 0.001 TYR B 70 PHE 0.013 0.001 PHE B 182 TRP 0.007 0.001 TRP A 370 HIS 0.005 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (10832) covalent geometry : angle 0.59556 / 0.31 (14712) hydrogen bonds : bond 0.03259 / 2.14 ( 608) hydrogen bonds : angle 4.94326 / 3.61 ( 1755) Misc. bond : bond 0.00030 / 0.02 ( 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 213 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 60 SER cc_start: 0.7815 (t) cc_final: 0.7458 (p) REVERT: A 63 PHE cc_start: 0.8356 (t80) cc_final: 0.7895 (t80) REVERT: A 182 PHE cc_start: 0.7116 (t80) cc_final: 0.6781 (t80) REVERT: A 218 LYS cc_start: 0.7378 (ptmt) cc_final: 0.7095 (ptmm) REVERT: A 246 LYS cc_start: 0.6694 (mmtt) cc_final: 0.5689 (pttt) REVERT: A 282 ASN cc_start: 0.7397 (t0) cc_final: 0.7146 (t0) REVERT: A 324 ARG cc_start: 0.7826 (tpp-160) cc_final: 0.7548 (tpp80) REVERT: A 358 ASN cc_start: 0.7746 (t0) cc_final: 0.7195 (m-40) REVERT: A 381 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7682 (mm) REVERT: A 415 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7768 (tttt) REVERT: A 474 LYS cc_start: 0.3447 (OUTLIER) cc_final: 0.2467 (mttm) REVERT: A 519 MET cc_start: 0.8878 (ttp) cc_final: 0.8556 (ptm) REVERT: A 586 SER cc_start: 0.7926 (OUTLIER) cc_final: 0.7460 (m) REVERT: A 590 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8490 (mt) REVERT: A 600 ARG cc_start: 0.7607 (mtt-85) cc_final: 0.7319 (ptp-110) REVERT: A 610 ARG cc_start: 0.8070 (ttp-170) cc_final: 0.7835 (ttm170) REVERT: A 648 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6603 (tt0) REVERT: A 652 HIS cc_start: 0.7108 (m90) cc_final: 0.5907 (t-90) REVERT: A 732 MET cc_start: 0.9033 (ptm) cc_final: 0.8754 (ptp) REVERT: A 741 LYS cc_start: 0.6451 (OUTLIER) cc_final: 0.6096 (mppt) REVERT: A 774 SER cc_start: 0.8589 (m) cc_final: 0.8249 (p) REVERT: B 60 SER cc_start: 0.7835 (t) cc_final: 0.7225 (p) REVERT: B 93 ASP cc_start: 0.7772 (m-30) cc_final: 0.7378 (m-30) REVERT: B 175 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6586 (pm20) REVERT: B 218 LYS cc_start: 0.7382 (ptmt) cc_final: 0.7107 (ptmm) REVERT: B 246 LYS cc_start: 0.6707 (mmtt) cc_final: 0.5693 (pttt) REVERT: B 295 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.5635 (tpt170) REVERT: B 324 ARG cc_start: 0.7819 (tpp-160) cc_final: 0.7543 (tpp80) REVERT: B 358 ASN cc_start: 0.7688 (t0) cc_final: 0.7151 (m-40) REVERT: B 424 GLU cc_start: 0.8222 (mp0) cc_final: 0.7465 (mt-10) REVERT: B 610 ARG cc_start: 0.8111 (ttp-170) cc_final: 0.7895 (ttm170) REVERT: B 648 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6323 (tt0) REVERT: B 718 GLU cc_start: 0.4746 (OUTLIER) cc_final: 0.4388 (tp30) REVERT: B 774 SER cc_start: 0.8721 (m) cc_final: 0.8375 (p) outliers start: 44 outliers final: 21 residues processed: 205 average time/residue: 0.4521 time to fit residues: 101.3905 Evaluate side-chains 197 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [77, 116, 33, 6, 5, 120, 96, 69, 54, 11, 94] chunk 77 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 96 optimal weight: 0.0570 chunk 69 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.112222 restraints weight = 12026.130| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.31 r_work: 0.3086 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10833 Z= 0.137 Angle : 0.604 8.663 14712 Z= 0.309 Chirality : 0.044 0.157 1726 Planarity : 0.004 0.050 1784 Dihedral : 7.842 129.217 1477 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.00 % Favored : 93.92 % Rotamer: Outliers : 3.55 % Allowed : 19.12 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.27 (0.24), residues: 1316 helix: 0.43 (0.18), residues: 852 sheet: -2.10 (0.47), residues: 102 loop : -0.77 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 640 TYR 0.017 0.001 TYR A 70 PHE 0.014 0.001 PHE B 130 TRP 0.008 0.001 TRP B 370 HIS 0.005 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (10832) covalent geometry : angle 0.60360 / 0.31 (14712) hydrogen bonds : bond 0.03352 / 2.19 ( 608) hydrogen bonds : angle 4.95435 / 3.62 ( 1755) Misc. bond : bond 0.00038 / 0.02 ( 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 211 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 60 SER cc_start: 0.7869 (t) cc_final: 0.7494 (p) REVERT: A 182 PHE cc_start: 0.7038 (t80) cc_final: 0.6710 (t80) REVERT: A 218 LYS cc_start: 0.7370 (ptmt) cc_final: 0.7119 (ptmm) REVERT: A 246 LYS cc_start: 0.6705 (mmtt) cc_final: 0.5654 (pttt) REVERT: A 324 ARG cc_start: 0.7831 (tpp-160) cc_final: 0.7553 (tpp80) REVERT: A 358 ASN cc_start: 0.7746 (t0) cc_final: 0.7203 (m-40) REVERT: A 381 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7698 (mm) REVERT: A 415 LYS cc_start: 0.8043 (mtpt) cc_final: 0.7779 (tttt) REVERT: A 474 LYS cc_start: 0.3477 (OUTLIER) cc_final: 0.2472 (mttm) REVERT: A 519 MET cc_start: 0.8858 (ttp) cc_final: 0.8567 (ptm) REVERT: A 586 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7481 (m) REVERT: A 590 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8497 (mt) REVERT: A 600 ARG cc_start: 0.7637 (mtt-85) cc_final: 0.7349 (ptp-110) REVERT: A 610 ARG cc_start: 0.8071 (ttp-170) cc_final: 0.7838 (ttm170) REVERT: A 647 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.6970 (mttp) REVERT: A 648 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6670 (tt0) REVERT: A 651 HIS cc_start: 0.7407 (OUTLIER) cc_final: 0.6661 (m90) REVERT: A 652 HIS cc_start: 0.7240 (m90) cc_final: 0.5996 (t-90) REVERT: A 732 MET cc_start: 0.9027 (ptm) cc_final: 0.8751 (ptp) REVERT: A 741 LYS cc_start: 0.6417 (OUTLIER) cc_final: 0.6076 (mppt) REVERT: A 774 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8256 (p) REVERT: B 60 SER cc_start: 0.7884 (t) cc_final: 0.7272 (p) REVERT: B 93 ASP cc_start: 0.7798 (m-30) cc_final: 0.7403 (m-30) REVERT: B 175 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6592 (pm20) REVERT: B 218 LYS cc_start: 0.7409 (ptmt) cc_final: 0.7134 (ptmm) REVERT: B 246 LYS cc_start: 0.6735 (mmtt) cc_final: 0.5679 (pttt) REVERT: B 295 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.5639 (tpt170) REVERT: B 324 ARG cc_start: 0.7842 (tpp-160) cc_final: 0.7540 (tpp80) REVERT: B 358 ASN cc_start: 0.7693 (t0) cc_final: 0.7161 (m-40) REVERT: B 424 GLU cc_start: 0.8238 (mp0) cc_final: 0.7482 (mt-10) REVERT: B 610 ARG cc_start: 0.8100 (ttp-170) cc_final: 0.7886 (ttm170) REVERT: B 648 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6350 (tt0) REVERT: B 718 GLU cc_start: 0.4803 (OUTLIER) cc_final: 0.4429 (tp30) REVERT: B 774 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8419 (p) outliers start: 41 outliers final: 21 residues processed: 200 average time/residue: 0.4537 time to fit residues: 98.9964 Evaluate side-chains 198 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [13, 90, 99, 89, 34, 129, 57, 9, 67, 103, 1] chunk 13 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 0.0040 chunk 67 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN B 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.136240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.114568 restraints weight = 12034.548| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.32 r_work: 0.3118 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10833 Z= 0.117 Angle : 0.587 8.518 14712 Z= 0.301 Chirality : 0.043 0.162 1726 Planarity : 0.004 0.050 1784 Dihedral : 7.689 128.258 1477 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 94.00 % Rotamer: Outliers : 3.03 % Allowed : 20.16 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -0.10 (0.24), residues: 1316 helix: 0.56 (0.18), residues: 858 sheet: -2.16 (0.47), residues: 102 loop : -0.69 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 640 TYR 0.013 0.001 TYR A 70 PHE 0.012 0.001 PHE B 182 TRP 0.007 0.001 TRP B 258 HIS 0.005 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (10832) covalent geometry : angle 0.58683 / 0.30 (14712) hydrogen bonds : bond 0.03183 / 2.09 ( 608) hydrogen bonds : angle 4.84910 / 3.55 ( 1755) Misc. bond : bond 0.00023 / 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 208 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 60 SER cc_start: 0.7847 (t) cc_final: 0.7490 (p) REVERT: A 63 PHE cc_start: 0.8323 (t80) cc_final: 0.7848 (t80) REVERT: A 175 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6571 (pm20) REVERT: A 182 PHE cc_start: 0.7010 (t80) cc_final: 0.6700 (t80) REVERT: A 218 LYS cc_start: 0.7399 (ptmt) cc_final: 0.7136 (ptmm) REVERT: A 246 LYS cc_start: 0.6558 (mmtt) cc_final: 0.5554 (pttt) REVERT: A 324 ARG cc_start: 0.7827 (tpp-160) cc_final: 0.7554 (tpp80) REVERT: A 358 ASN cc_start: 0.7692 (t0) cc_final: 0.7151 (m-40) REVERT: A 381 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7684 (mm) REVERT: A 415 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7783 (tttt) REVERT: A 474 LYS cc_start: 0.3379 (OUTLIER) cc_final: 0.2465 (mttm) REVERT: A 590 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8475 (mt) REVERT: A 600 ARG cc_start: 0.7598 (mtt-85) cc_final: 0.7342 (ptp-110) REVERT: A 647 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.6987 (mttp) REVERT: A 648 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6684 (tt0) REVERT: A 651 HIS cc_start: 0.7420 (OUTLIER) cc_final: 0.6690 (m90) REVERT: A 652 HIS cc_start: 0.7186 (m90) cc_final: 0.5933 (t-90) REVERT: A 774 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8288 (p) REVERT: B 60 SER cc_start: 0.7853 (t) cc_final: 0.7470 (p) REVERT: B 63 PHE cc_start: 0.8352 (t80) cc_final: 0.7870 (t80) REVERT: B 93 ASP cc_start: 0.7785 (m-30) cc_final: 0.7389 (m-30) REVERT: B 103 ILE cc_start: 0.7535 (mt) cc_final: 0.7296 (mm) REVERT: B 175 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6582 (pm20) REVERT: B 218 LYS cc_start: 0.7385 (ptmt) cc_final: 0.7113 (ptmm) REVERT: B 246 LYS cc_start: 0.6577 (mmtt) cc_final: 0.5555 (pttt) REVERT: B 295 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.5639 (tpt170) REVERT: B 324 ARG cc_start: 0.7833 (tpp-160) cc_final: 0.7556 (tpp80) REVERT: B 358 ASN cc_start: 0.7668 (t0) cc_final: 0.7144 (m-40) REVERT: B 424 GLU cc_start: 0.8172 (mp0) cc_final: 0.7512 (mt-10) REVERT: B 519 MET cc_start: 0.8884 (ttp) cc_final: 0.8674 (ptm) REVERT: B 648 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6358 (tt0) REVERT: B 718 GLU cc_start: 0.4741 (OUTLIER) cc_final: 0.4402 (tp30) REVERT: B 774 SER cc_start: 0.8740 (m) cc_final: 0.8392 (p) outliers start: 35 outliers final: 19 residues processed: 200 average time/residue: 0.4709 time to fit residues: 102.5460 Evaluate side-chains 195 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [80, 112, 49, 57, 20, 127, 97, 54, 104, 4, 50] chunk 80 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN B 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.135212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.113536 restraints weight = 11962.906| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.32 r_work: 0.3104 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10833 Z= 0.127 Angle : 0.594 8.652 14712 Z= 0.304 Chirality : 0.043 0.171 1726 Planarity : 0.004 0.046 1784 Dihedral : 7.627 128.666 1477 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.94 % Allowed : 20.59 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.04 (0.24), residues: 1316 helix: 0.63 (0.18), residues: 852 sheet: -2.25 (0.47), residues: 104 loop : -0.65 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 640 TYR 0.014 0.001 TYR A 70 PHE 0.012 0.001 PHE B 130 TRP 0.007 0.001 TRP B 370 HIS 0.005 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10832) covalent geometry : angle 0.59412 / 0.30 (14712) hydrogen bonds : bond 0.03260 / 2.14 ( 608) hydrogen bonds : angle 4.87402 / 3.56 ( 1755) Misc. bond : bond 0.00035 / 0.02 ( 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 199 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 60 SER cc_start: 0.7859 (t) cc_final: 0.7508 (p) REVERT: A 63 PHE cc_start: 0.8347 (t80) cc_final: 0.7882 (t80) REVERT: A 175 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6665 (pm20) REVERT: A 182 PHE cc_start: 0.7018 (t80) cc_final: 0.6721 (t80) REVERT: A 218 LYS cc_start: 0.7431 (ptmt) cc_final: 0.7157 (ptmm) REVERT: A 246 LYS cc_start: 0.6741 (mmtt) cc_final: 0.5715 (pttt) REVERT: A 324 ARG cc_start: 0.7824 (tpp-160) cc_final: 0.7557 (tpp80) REVERT: A 358 ASN cc_start: 0.7696 (t0) cc_final: 0.7156 (m-40) REVERT: A 381 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7693 (mm) REVERT: A 415 LYS cc_start: 0.8019 (mtpt) cc_final: 0.7771 (tttt) REVERT: A 474 LYS cc_start: 0.3363 (OUTLIER) cc_final: 0.2460 (mttm) REVERT: A 590 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8507 (mt) REVERT: A 600 ARG cc_start: 0.7631 (mtt-85) cc_final: 0.7360 (ptp-110) REVERT: A 647 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7006 (mttp) REVERT: A 648 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6586 (tt0) REVERT: A 651 HIS cc_start: 0.7481 (OUTLIER) cc_final: 0.6758 (m90) REVERT: A 652 HIS cc_start: 0.7224 (m90) cc_final: 0.5960 (t-90) REVERT: A 774 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.8290 (p) REVERT: B 60 SER cc_start: 0.7863 (t) cc_final: 0.7485 (p) REVERT: B 63 PHE cc_start: 0.8382 (t80) cc_final: 0.7901 (t80) REVERT: B 93 ASP cc_start: 0.7777 (m-30) cc_final: 0.7378 (m-30) REVERT: B 103 ILE cc_start: 0.7522 (mt) cc_final: 0.7283 (mm) REVERT: B 175 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6593 (pm20) REVERT: B 218 LYS cc_start: 0.7421 (ptmt) cc_final: 0.7107 (ptmm) REVERT: B 246 LYS cc_start: 0.6775 (mmtt) cc_final: 0.5741 (pttt) REVERT: B 295 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.5639 (tpt170) REVERT: B 324 ARG cc_start: 0.7825 (tpp-160) cc_final: 0.7548 (tpp80) REVERT: B 358 ASN cc_start: 0.7702 (t0) cc_final: 0.7160 (m-40) REVERT: B 424 GLU cc_start: 0.8217 (mp0) cc_final: 0.7522 (mt-10) REVERT: B 648 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6396 (tt0) REVERT: B 651 HIS cc_start: 0.7244 (OUTLIER) cc_final: 0.6383 (m90) REVERT: B 718 GLU cc_start: 0.4763 (OUTLIER) cc_final: 0.4398 (tp30) REVERT: B 774 SER cc_start: 0.8753 (OUTLIER) cc_final: 0.8404 (p) outliers start: 34 outliers final: 20 residues processed: 190 average time/residue: 0.4804 time to fit residues: 99.5533 Evaluate side-chains 196 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 774 SER Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [98, 28, 111, 22, 122, 99, 94, 73, 27, 0, 92] chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 122 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 73 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN B 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.137107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115336 restraints weight = 12057.987| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.33 r_work: 0.3128 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10833 Z= 0.115 Angle : 0.582 8.540 14712 Z= 0.297 Chirality : 0.042 0.179 1726 Planarity : 0.004 0.059 1784 Dihedral : 7.571 128.090 1477 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.11 % Allowed : 20.67 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: 0.07 (0.24), residues: 1316 helix: 0.71 (0.18), residues: 858 sheet: -2.29 (0.47), residues: 104 loop : -0.57 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 640 TYR 0.012 0.001 TYR A 70 PHE 0.011 0.001 PHE B 182 TRP 0.008 0.001 TRP B 258 HIS 0.005 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (10832) covalent geometry : angle 0.58224 / 0.30 (14712) hydrogen bonds : bond 0.03137 / 2.06 ( 608) hydrogen bonds : angle 4.79856 / 3.51 ( 1755) Misc. bond : bond 0.00025 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3414.10 seconds wall clock time: 59 minutes 6.47 seconds (3546.47 seconds total)