Starting phenix.real_space_refine on Thu Jun 4 00:21:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hnw_52316/06_2026/9hnw_52316.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hnw_52316/06_2026/9hnw_52316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hnw_52316/06_2026/9hnw_52316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hnw_52316/06_2026/9hnw_52316.map" model { file = "/net/cci-nas-00/data/ceres_data/9hnw_52316/06_2026/9hnw_52316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hnw_52316/06_2026/9hnw_52316.cif" } resolution = 3.04 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= 0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 46 5.16 5 C 5907 2.51 5 N 1601 2.21 5 O 1794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9349 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3241 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 15, 'TRANS': 390} Chain breaks: 2 Chain: "B" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4904 Classifications: {'peptide': 621} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 597} Chain breaks: 2 Chain: "C" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ABU:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 600 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DAB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1483 SG CYS A 440 60.699 39.254 43.871 1.00 45.12 S ATOM 1506 SG CYS A 443 64.222 40.222 42.938 1.00 45.96 S ATOM 2021 SG CYS A 506 62.330 42.297 45.352 1.00 50.48 S ATOM 2044 SG CYS A 509 61.262 42.433 41.736 1.00 50.30 S Time building chain proxies: 2.34, per 1000 atoms: 0.25 Number of scatterers: 9349 At special positions: 0 Unit cell: (100.32, 108.68, 121.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 46 16.00 O 1794 8.00 N 1601 7.00 C 5907 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 additional links: simple=1, symmetry=0 Simple link: pdb=" C GLY C 75 " - pdb=" N ABU C 76 " Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 256.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 443 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 506 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 440 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 509 " Number of angles added : 6 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 19 sheets defined 24.6% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 89 through 101 removed outlier: 3.760A pdb=" N PHE A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 128 removed outlier: 4.614A pdb=" N ASN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 166 removed outlier: 3.756A pdb=" N ILE A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.712A pdb=" N THR A 171 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 200 through 227 Processing helix chain 'A' and resid 424 through 430 Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 563 through 568 removed outlier: 4.336A pdb=" N GLU A 566 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 744 removed outlier: 3.557A pdb=" N TYR A 743 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 768 Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 328 through 334 Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 445 through 449 Processing helix chain 'B' and resid 462 through 471 removed outlier: 3.540A pdb=" N ALA B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 Processing helix chain 'B' and resid 531 through 535 removed outlier: 3.504A pdb=" N GLY B 534 " --> pdb=" O ARG B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.695A pdb=" N ASN B 543 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU B 544 " --> pdb=" O MET B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 555 removed outlier: 3.671A pdb=" N ILE B 551 " --> pdb=" O PRO B 547 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE B 553 " --> pdb=" O TRP B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 604 Processing helix chain 'B' and resid 631 through 639 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.687A pdb=" N HIS A 198 " --> pdb=" O GLY C 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 446 through 453 removed outlier: 3.706A pdb=" N ALA A 515 " --> pdb=" O ILE A 498 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 455 through 459 removed outlier: 6.114A pdb=" N TYR A 778 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 582 " --> pdb=" O TYR A 778 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU A 780 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA A 580 " --> pdb=" O LEU A 780 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR A 782 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A 578 " --> pdb=" O TYR A 782 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS A 784 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR A 576 " --> pdb=" O LYS A 784 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 459 removed outlier: 6.114A pdb=" N TYR A 778 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 582 " --> pdb=" O TYR A 778 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU A 780 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA A 580 " --> pdb=" O LEU A 780 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR A 782 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A 578 " --> pdb=" O TYR A 782 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS A 784 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR A 576 " --> pdb=" O LYS A 784 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE A 579 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 596 " --> pdb=" O PHE A 750 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 598 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS A 746 " --> pdb=" O VAL A 600 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP A 747 " --> pdb=" O THR A 758 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 504 through 506 Processing sheet with id=AA6, first strand: chain 'A' and resid 535 through 536 Processing sheet with id=AA7, first strand: chain 'B' and resid 421 through 423 removed outlier: 3.546A pdb=" N THR B 430 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU B 429 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU B 519 " --> pdb=" O THR B 524 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N THR B 524 " --> pdb=" O GLU B 519 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 39 removed outlier: 6.536A pdb=" N ALA B 48 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU B 36 " --> pdb=" O PHE B 46 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE B 46 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU B 38 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG B 44 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 54 " --> pdb=" O MET B 71 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 69 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER B 58 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR B 67 " --> pdb=" O SER B 58 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 84 removed outlier: 3.871A pdb=" N LEU B 90 " --> pdb=" O TRP B 102 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 92 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 99 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N THR B 112 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 101 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B 108 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.888A pdb=" N ILE B 141 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 171 through 176 removed outlier: 3.760A pdb=" N ILE B 183 " --> pdb=" O TRP B 195 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU B 192 " --> pdb=" O LYS B 205 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS B 205 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 194 " --> pdb=" O LEU B 203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 213 through 218 removed outlier: 3.991A pdb=" N ALA B 246 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N SER B 238 " --> pdb=" O CYS B 244 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N CYS B 244 " --> pdb=" O SER B 238 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 255 through 260 removed outlier: 3.890A pdb=" N GLY B 271 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 276 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 297 through 302 removed outlier: 6.919A pdb=" N ALA B 315 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N MET B 300 " --> pdb=" O TRP B 313 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP B 313 " --> pdb=" O MET B 300 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU B 302 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA B 311 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.603A pdb=" N ILE B 375 " --> pdb=" O TRP B 387 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TYR B 386 " --> pdb=" O ASP B 397 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASP B 397 " --> pdb=" O TYR B 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 442 through 444 Processing sheet with id=AB9, first strand: chain 'B' and resid 583 through 588 removed outlier: 4.282A pdb=" N ASP B 583 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 569 " --> pdb=" O ASP B 583 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N LEU B 668 " --> pdb=" O LYS B 564 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU B 670 " --> pdb=" O PRO B 566 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR B 568 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N TYR B 672 " --> pdb=" O TYR B 568 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLN B 570 " --> pdb=" O TYR B 672 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 12 through 16 removed outlier: 8.870A pdb=" N LEU C 67 " --> pdb=" O GLN C 2 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE C 4 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU C 69 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS C 6 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 12 through 16 removed outlier: 8.942A pdb=" N LEU D 67 " --> pdb=" O GLN D 2 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N PHE D 4 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU D 69 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LYS D 6 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU D 71 " --> pdb=" O LYS D 6 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 966 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: 1.77 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1622 1.32 - 1.44: 2335 1.44 - 1.57: 5494 1.57 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 9515 Sorted by residual: bond pdb=" N HIS B 251 " pdb=" CA HIS B 251 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.32e+00 bond pdb=" N VAL A 435 " pdb=" CA VAL A 435 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.29e-02 6.01e+03 7.06e+00 bond pdb=" N GLU A 448 " pdb=" CA GLU A 448 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.23e-02 6.61e+03 6.81e+00 bond pdb=" N PHE B 439 " pdb=" CA PHE B 439 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.16e-02 7.43e+03 6.70e+00 bond pdb=" N LEU B 164 " pdb=" CA LEU B 164 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.69e+00 ... (remaining 9510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 12533 1.48 - 2.95: 279 2.95 - 4.43: 46 4.43 - 5.91: 7 5.91 - 7.39: 3 Bond angle restraints: 12868 Sorted by residual: angle pdb=" CA THR B 161 " pdb=" C THR B 161 " pdb=" O THR B 161 " ideal model delta sigma weight residual 122.64 118.31 4.33 1.25e+00 6.40e-01 1.20e+01 angle pdb=" CA ASP A 199 " pdb=" CB ASP A 199 " pdb=" CG ASP A 199 " ideal model delta sigma weight residual 112.60 115.84 -3.24 1.00e+00 1.00e+00 1.05e+01 angle pdb=" CB LYS A 570 " pdb=" CG LYS A 570 " pdb=" CD LYS A 570 " ideal model delta sigma weight residual 111.30 118.69 -7.39 2.30e+00 1.89e-01 1.03e+01 angle pdb=" CA LEU A 436 " pdb=" C LEU A 436 " pdb=" O LEU A 436 " ideal model delta sigma weight residual 122.63 118.50 4.13 1.29e+00 6.01e-01 1.03e+01 angle pdb=" CA THR B 377 " pdb=" CB THR B 377 " pdb=" OG1 THR B 377 " ideal model delta sigma weight residual 109.60 104.88 4.72 1.50e+00 4.44e-01 9.89e+00 ... (remaining 12863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 5033 17.41 - 34.82: 589 34.82 - 52.23: 129 52.23 - 69.64: 34 69.64 - 87.06: 10 Dihedral angle restraints: 5795 sinusoidal: 2372 harmonic: 3423 Sorted by residual: dihedral pdb=" CA MET B 652 " pdb=" C MET B 652 " pdb=" N ASP B 653 " pdb=" CA ASP B 653 " ideal model delta harmonic sigma weight residual 180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ASP B 51 " pdb=" CB ASP B 51 " pdb=" CG ASP B 51 " pdb=" OD1 ASP B 51 " ideal model delta sinusoidal sigma weight residual -30.00 -89.47 59.47 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ILE B 565 " pdb=" C ILE B 565 " pdb=" N PRO B 566 " pdb=" CA PRO B 566 " ideal model delta harmonic sigma weight residual 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 5792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1038 0.038 - 0.077: 294 0.077 - 0.115: 128 0.115 - 0.154: 11 0.154 - 0.192: 1 Chirality restraints: 1472 Sorted by residual: chirality pdb=" CA VAL A 435 " pdb=" N VAL A 435 " pdb=" C VAL A 435 " pdb=" CB VAL A 435 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CA ILE B 182 " pdb=" N ILE B 182 " pdb=" C ILE B 182 " pdb=" CB ILE B 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA VAL B 509 " pdb=" N VAL B 509 " pdb=" C VAL B 509 " pdb=" CB VAL B 509 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 1469 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 75 " 0.063 2.00e-02 2.50e+03 1.36e-01 1.85e+02 pdb=" C GLY C 75 " -0.234 2.00e-02 2.50e+03 pdb=" O GLY C 75 " 0.096 2.00e-02 2.50e+03 pdb=" N ABU C 76 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 72 " -0.463 9.50e-02 1.11e+02 2.07e-01 2.64e+01 pdb=" NE ARG C 72 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG C 72 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 72 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 72 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 143 " 0.015 2.00e-02 2.50e+03 1.58e-02 5.01e+00 pdb=" CG TYR A 143 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 143 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 143 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 143 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 143 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 143 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 143 " -0.001 2.00e-02 2.50e+03 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1723 2.77 - 3.30: 8931 3.30 - 3.84: 15533 3.84 - 4.37: 18397 4.37 - 4.90: 31807 Nonbonded interactions: 76391 Sorted by model distance: nonbonded pdb=" OG SER B 92 " pdb=" NE1 TRP B 102 " model vdw 2.240 3.120 nonbonded pdb=" O SER A 766 " pdb=" OG SER A 772 " model vdw 2.246 3.040 nonbonded pdb=" SG CYS A 90 " pdb=" N ABU C 76 " model vdw 2.263 2.784 nonbonded pdb=" OG1 THR C 7 " pdb=" O LYS C 11 " model vdw 2.278 3.040 nonbonded pdb=" O TRP B 77 " pdb=" OG SER B 94 " model vdw 2.291 3.040 ... (remaining 76386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 62 or resid 64 through 75)) selection = (chain 'D' and (resid 1 through 62 or resid 64 through 75)) } 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: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.410 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.386 9522 Z= 0.467 Angle : 0.564 13.758 12876 Z= 0.317 Chirality : 0.042 0.192 1472 Planarity : 0.006 0.207 1645 Dihedral : 15.952 87.055 3574 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.19 % Allowed : 19.47 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1159 helix: 1.39 (0.34), residues: 252 sheet: -0.59 (0.32), residues: 286 loop : -0.62 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 118 TYR 0.039 0.001 TYR A 143 PHE 0.018 0.001 PHE A 113 TRP 0.009 0.001 TRP B 195 HIS 0.004 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.21 ( 9515) covalent geometry : angle 0.54791 / 0.31 (12868) hydrogen bonds : bond 0.20031 / 13.22 ( 342) hydrogen bonds : angle 8.38840 / 6.02 ( 966) metal coordination : bond 0.00692 / 0.34 ( 4) metal coordination : angle 2.64449 / 2.09 ( 6) Misc. bond : bond 0.28859 / 15.05 ( 2) link_TRANS : bond 0.01832 / 0.96 ( 1) link_TRANS : angle 9.90621 / 5.81 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 540 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6789 (mpp) outliers start: 2 outliers final: 0 residues processed: 82 average time/residue: 0.1168 time to fit residues: 13.2508 Evaluate side-chains 74 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 540 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.0040 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.149155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.106163 restraints weight = 17152.429| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 3.92 r_work: 0.3427 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9522 Z= 0.122 Angle : 0.506 6.022 12876 Z= 0.272 Chirality : 0.042 0.143 1472 Planarity : 0.004 0.039 1645 Dihedral : 4.543 55.095 1261 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.80 % Allowed : 17.76 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1159 helix: 1.27 (0.33), residues: 266 sheet: -0.53 (0.31), residues: 297 loop : -0.65 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 72 TYR 0.022 0.001 TYR A 143 PHE 0.014 0.001 PHE A 113 TRP 0.013 0.001 TRP B 102 HIS 0.003 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9515) covalent geometry : angle 0.50280 / 0.27 (12868) hydrogen bonds : bond 0.03939 / 2.54 ( 342) hydrogen bonds : angle 5.88774 / 4.21 ( 966) metal coordination : bond 0.00416 / 0.20 ( 4) metal coordination : angle 2.74535 / 1.90 ( 6) Misc. bond : bond 0.00051 / 0.03 ( 2) link_TRANS : bond 0.00274 / 0.14 ( 1) link_TRANS : angle 0.08301 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.7439 (tp30) cc_final: 0.7173 (tp30) REVERT: C 51 GLU cc_start: 0.7930 (mp0) cc_final: 0.7478 (mp0) outliers start: 19 outliers final: 12 residues processed: 103 average time/residue: 0.1072 time to fit residues: 15.5174 Evaluate side-chains 92 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 656 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 20 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.147168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.103977 restraints weight = 17175.958| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.88 r_work: 0.3391 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9522 Z= 0.176 Angle : 0.513 6.339 12876 Z= 0.272 Chirality : 0.042 0.158 1472 Planarity : 0.003 0.031 1645 Dihedral : 4.441 42.918 1258 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.94 % Allowed : 17.85 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.25), residues: 1159 helix: 1.27 (0.33), residues: 263 sheet: -0.61 (0.31), residues: 296 loop : -0.65 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 72 TYR 0.015 0.001 TYR B 415 PHE 0.013 0.001 PHE A 113 TRP 0.009 0.001 TRP B 102 HIS 0.003 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 9515) covalent geometry : angle 0.50947 / 0.27 (12868) hydrogen bonds : bond 0.03749 / 2.41 ( 342) hydrogen bonds : angle 5.56689 / 3.98 ( 966) metal coordination : bond 0.00931 / 0.45 ( 4) metal coordination : angle 2.79193 / 1.89 ( 6) Misc. bond : bond 0.00085 / 0.04 ( 2) link_TRANS : bond 0.00023 / 0.01 ( 1) link_TRANS : angle 0.26273 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8665 (tt0) REVERT: B 24 GLU cc_start: 0.8097 (tp30) cc_final: 0.7832 (mp0) REVERT: B 406 GLU cc_start: 0.7487 (tp30) cc_final: 0.7153 (tp30) REVERT: C 51 GLU cc_start: 0.7943 (mp0) cc_final: 0.7465 (mp0) outliers start: 31 outliers final: 18 residues processed: 106 average time/residue: 0.0927 time to fit residues: 14.3201 Evaluate side-chains 95 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 656 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 0.0050 chunk 115 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.149107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.106033 restraints weight = 17313.280| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.94 r_work: 0.3414 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9522 Z= 0.122 Angle : 0.479 5.137 12876 Z= 0.257 Chirality : 0.042 0.140 1472 Planarity : 0.003 0.031 1645 Dihedral : 4.444 50.646 1258 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.94 % Allowed : 17.47 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.25), residues: 1159 helix: 1.30 (0.33), residues: 266 sheet: -0.57 (0.31), residues: 296 loop : -0.67 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 72 TYR 0.015 0.001 TYR B 415 PHE 0.013 0.001 PHE B 439 TRP 0.010 0.001 TRP B 102 HIS 0.003 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9515) covalent geometry : angle 0.47598 / 0.26 (12868) hydrogen bonds : bond 0.03181 / 2.05 ( 342) hydrogen bonds : angle 5.28068 / 3.77 ( 966) metal coordination : bond 0.00638 / 0.31 ( 4) metal coordination : angle 2.56753 / 1.76 ( 6) Misc. bond : bond 0.00055 / 0.03 ( 2) link_TRANS : bond 0.00101 / 0.05 ( 1) link_TRANS : angle 0.29163 / 0.17 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 481 GLU cc_start: 0.1880 (OUTLIER) cc_final: 0.1401 (tm-30) REVERT: A 566 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8665 (tt0) REVERT: B 24 GLU cc_start: 0.8115 (tp30) cc_final: 0.7859 (mp0) REVERT: B 110 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7306 (ptp) REVERT: B 396 GLU cc_start: 0.8666 (mp0) cc_final: 0.8331 (mp0) REVERT: B 644 GLN cc_start: 0.6650 (OUTLIER) cc_final: 0.6210 (mt0) REVERT: C 51 GLU cc_start: 0.7984 (mp0) cc_final: 0.7500 (mp0) outliers start: 31 outliers final: 19 residues processed: 106 average time/residue: 0.1030 time to fit residues: 15.6041 Evaluate side-chains 100 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 113 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 75 optimal weight: 0.0970 chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.148867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.104971 restraints weight = 17093.552| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 4.02 r_work: 0.3404 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9522 Z= 0.140 Angle : 0.489 5.977 12876 Z= 0.259 Chirality : 0.042 0.138 1472 Planarity : 0.003 0.030 1645 Dihedral : 4.418 40.814 1258 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.23 % Allowed : 17.85 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.25), residues: 1159 helix: 1.40 (0.33), residues: 263 sheet: -0.54 (0.31), residues: 296 loop : -0.66 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.017 0.001 TYR B 415 PHE 0.011 0.001 PHE A 113 TRP 0.010 0.001 TRP B 102 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9515) covalent geometry : angle 0.48602 / 0.26 (12868) hydrogen bonds : bond 0.03159 / 2.03 ( 342) hydrogen bonds : angle 5.18017 / 3.70 ( 966) metal coordination : bond 0.00770 / 0.38 ( 4) metal coordination : angle 2.33828 / 1.57 ( 6) Misc. bond : bond 0.00055 / 0.03 ( 2) link_TRANS : bond 0.00077 / 0.04 ( 1) link_TRANS : angle 0.45951 / 0.27 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.397 Fit side-chains REVERT: A 181 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8306 (tt) REVERT: A 481 GLU cc_start: 0.1722 (OUTLIER) cc_final: 0.1235 (tm-30) REVERT: A 482 MET cc_start: 0.4242 (tpt) cc_final: 0.3788 (tpt) REVERT: A 566 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8686 (tt0) REVERT: B 396 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8366 (mp0) REVERT: B 644 GLN cc_start: 0.6611 (OUTLIER) cc_final: 0.6188 (mt0) REVERT: C 41 GLN cc_start: 0.9047 (pt0) cc_final: 0.8781 (pt0) REVERT: C 51 GLU cc_start: 0.8026 (mp0) cc_final: 0.7516 (mp0) outliers start: 34 outliers final: 25 residues processed: 108 average time/residue: 0.0930 time to fit residues: 14.7072 Evaluate side-chains 107 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 99 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.147782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.103595 restraints weight = 17167.703| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 4.12 r_work: 0.3379 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9522 Z= 0.171 Angle : 0.512 6.658 12876 Z= 0.272 Chirality : 0.042 0.142 1472 Planarity : 0.003 0.031 1645 Dihedral : 4.421 36.291 1258 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.80 % Allowed : 18.14 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.25), residues: 1159 helix: 1.34 (0.33), residues: 263 sheet: -0.57 (0.30), residues: 301 loop : -0.68 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 655 TYR 0.019 0.001 TYR B 415 PHE 0.011 0.001 PHE A 535 TRP 0.011 0.001 TRP B 102 HIS 0.002 0.001 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 9515) covalent geometry : angle 0.50944 / 0.27 (12868) hydrogen bonds : bond 0.03263 / 2.10 ( 342) hydrogen bonds : angle 5.19064 / 3.69 ( 966) metal coordination : bond 0.01033 / 0.51 ( 4) metal coordination : angle 2.38101 / 1.63 ( 6) Misc. bond : bond 0.00087 / 0.04 ( 2) link_TRANS : bond 0.00083 / 0.04 ( 1) link_TRANS : angle 0.35884 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 78 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8374 (tt) REVERT: A 481 GLU cc_start: 0.1733 (OUTLIER) cc_final: 0.1246 (tm-30) REVERT: A 482 MET cc_start: 0.4226 (tpt) cc_final: 0.3759 (tpp) REVERT: A 566 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8862 (tt0) REVERT: B 396 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: B 644 GLN cc_start: 0.6614 (OUTLIER) cc_final: 0.6136 (mt0) REVERT: C 41 GLN cc_start: 0.9079 (pt0) cc_final: 0.8820 (pt0) REVERT: C 51 GLU cc_start: 0.8092 (mp0) cc_final: 0.7577 (mp0) outliers start: 40 outliers final: 30 residues processed: 111 average time/residue: 0.1122 time to fit residues: 17.4684 Evaluate side-chains 109 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.148138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.104398 restraints weight = 16981.860| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 4.00 r_work: 0.3391 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9522 Z= 0.143 Angle : 0.500 6.394 12876 Z= 0.265 Chirality : 0.042 0.173 1472 Planarity : 0.003 0.033 1645 Dihedral : 4.413 42.059 1258 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.61 % Allowed : 17.76 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1159 helix: 1.38 (0.33), residues: 263 sheet: -0.56 (0.30), residues: 302 loop : -0.67 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.021 0.001 TYR B 415 PHE 0.010 0.001 PHE A 113 TRP 0.010 0.001 TRP B 102 HIS 0.002 0.001 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 9515) covalent geometry : angle 0.49750 / 0.27 (12868) hydrogen bonds : bond 0.03115 / 2.00 ( 342) hydrogen bonds : angle 5.12129 / 3.65 ( 966) metal coordination : bond 0.00834 / 0.41 ( 4) metal coordination : angle 2.24317 / 1.53 ( 6) Misc. bond : bond 0.00064 / 0.03 ( 2) link_TRANS : bond 0.00087 / 0.05 ( 1) link_TRANS : angle 0.25760 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 75 time to evaluate : 0.297 Fit side-chains REVERT: A 181 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8369 (tt) REVERT: A 481 GLU cc_start: 0.1599 (OUTLIER) cc_final: 0.1101 (tm-30) REVERT: A 482 MET cc_start: 0.4129 (tpt) cc_final: 0.3711 (tpp) REVERT: A 566 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8860 (tt0) REVERT: B 396 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: B 644 GLN cc_start: 0.6515 (OUTLIER) cc_final: 0.6054 (mt0) REVERT: C 51 GLU cc_start: 0.8080 (mp0) cc_final: 0.7558 (mp0) outliers start: 38 outliers final: 29 residues processed: 106 average time/residue: 0.0946 time to fit residues: 14.5172 Evaluate side-chains 106 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 73 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 chunk 95 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.149623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.105846 restraints weight = 17008.450| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 4.07 r_work: 0.3411 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9522 Z= 0.112 Angle : 0.490 6.233 12876 Z= 0.259 Chirality : 0.042 0.170 1472 Planarity : 0.003 0.031 1645 Dihedral : 4.318 44.523 1258 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.32 % Allowed : 18.04 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.25), residues: 1159 helix: 1.42 (0.33), residues: 266 sheet: -0.52 (0.30), residues: 302 loop : -0.61 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.021 0.001 TYR B 415 PHE 0.010 0.001 PHE B 439 TRP 0.010 0.001 TRP B 102 HIS 0.003 0.000 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 9515) covalent geometry : angle 0.48755 / 0.26 (12868) hydrogen bonds : bond 0.02934 / 1.87 ( 342) hydrogen bonds : angle 4.98538 / 3.57 ( 966) metal coordination : bond 0.00550 / 0.27 ( 4) metal coordination : angle 2.22195 / 1.50 ( 6) Misc. bond : bond 0.00036 / 0.02 ( 2) link_TRANS : bond 0.00042 / 0.02 ( 1) link_TRANS : angle 0.21112 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 81 time to evaluate : 0.264 Fit side-chains REVERT: A 181 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8346 (tt) REVERT: A 481 GLU cc_start: 0.1788 (OUTLIER) cc_final: 0.1311 (tm-30) REVERT: A 566 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8887 (tt0) REVERT: B 110 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7352 (ptp) REVERT: B 396 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8289 (mp0) REVERT: B 644 GLN cc_start: 0.6504 (OUTLIER) cc_final: 0.6054 (mt0) REVERT: C 51 GLU cc_start: 0.8063 (mp0) cc_final: 0.7535 (mp0) outliers start: 35 outliers final: 27 residues processed: 106 average time/residue: 0.0906 time to fit residues: 14.2307 Evaluate side-chains 110 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 87 optimal weight: 0.0050 chunk 70 optimal weight: 0.5980 chunk 113 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 47 optimal weight: 0.0070 chunk 82 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.3812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.149500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.106561 restraints weight = 17034.744| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 3.92 r_work: 0.3439 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9522 Z= 0.102 Angle : 0.488 6.324 12876 Z= 0.259 Chirality : 0.041 0.155 1472 Planarity : 0.003 0.031 1645 Dihedral : 4.260 44.219 1258 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.94 % Allowed : 18.61 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1159 helix: 1.49 (0.33), residues: 263 sheet: -0.47 (0.30), residues: 307 loop : -0.51 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 655 TYR 0.020 0.001 TYR B 415 PHE 0.019 0.001 PHE A 113 TRP 0.010 0.001 TRP B 102 HIS 0.003 0.000 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 9515) covalent geometry : angle 0.48579 / 0.26 (12868) hydrogen bonds : bond 0.02884 / 1.85 ( 342) hydrogen bonds : angle 4.90656 / 3.52 ( 966) metal coordination : bond 0.00422 / 0.21 ( 4) metal coordination : angle 2.08650 / 1.41 ( 6) Misc. bond : bond 0.00027 / 0.01 ( 2) link_TRANS : bond 0.00028 / 0.01 ( 1) link_TRANS : angle 0.17252 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.343 Fit side-chains REVERT: A 181 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8368 (tt) REVERT: A 481 GLU cc_start: 0.1826 (OUTLIER) cc_final: 0.1335 (tm-30) REVERT: A 482 MET cc_start: 0.3903 (tpt) cc_final: 0.3270 (tpt) REVERT: A 566 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.8880 (tt0) REVERT: B 110 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7396 (ptp) REVERT: B 396 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8380 (mp0) REVERT: B 644 GLN cc_start: 0.6644 (OUTLIER) cc_final: 0.6198 (mt0) REVERT: C 51 GLU cc_start: 0.8034 (mp0) cc_final: 0.7509 (mp0) outliers start: 31 outliers final: 20 residues processed: 103 average time/residue: 0.0940 time to fit residues: 13.8260 Evaluate side-chains 103 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.147889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.103655 restraints weight = 16961.799| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 4.07 r_work: 0.3383 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9522 Z= 0.188 Angle : 0.544 6.696 12876 Z= 0.286 Chirality : 0.043 0.170 1472 Planarity : 0.004 0.040 1645 Dihedral : 4.519 50.407 1258 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.66 % Allowed : 18.99 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.25), residues: 1159 helix: 1.33 (0.33), residues: 263 sheet: -0.62 (0.30), residues: 308 loop : -0.59 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.022 0.001 TYR B 415 PHE 0.018 0.001 PHE A 113 TRP 0.012 0.001 TRP B 102 HIS 0.003 0.001 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 ( 9515) covalent geometry : angle 0.54221 / 0.29 (12868) hydrogen bonds : bond 0.03244 / 2.07 ( 342) hydrogen bonds : angle 5.08844 / 3.63 ( 966) metal coordination : bond 0.01228 / 0.60 ( 4) metal coordination : angle 2.20271 / 1.51 ( 6) Misc. bond : bond 0.00077 / 0.04 ( 2) link_TRANS : bond 0.00130 / 0.07 ( 1) link_TRANS : angle 0.30193 / 0.17 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.308 Fit side-chains REVERT: A 181 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8379 (tt) REVERT: A 481 GLU cc_start: 0.1736 (OUTLIER) cc_final: 0.1202 (tm-30) REVERT: A 482 MET cc_start: 0.4012 (tpt) cc_final: 0.3378 (tpt) REVERT: A 566 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8904 (tt0) REVERT: B 396 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8169 (mm-30) REVERT: B 644 GLN cc_start: 0.6554 (OUTLIER) cc_final: 0.6109 (mt0) REVERT: C 51 GLU cc_start: 0.8063 (mp0) cc_final: 0.7534 (mp0) outliers start: 28 outliers final: 22 residues processed: 94 average time/residue: 0.0998 time to fit residues: 13.4337 Evaluate side-chains 101 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 47 optimal weight: 0.0270 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 92 optimal weight: 0.0370 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 90 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.150691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.107586 restraints weight = 16975.502| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.89 r_work: 0.3470 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9522 Z= 0.102 Angle : 0.502 6.278 12876 Z= 0.267 Chirality : 0.042 0.223 1472 Planarity : 0.003 0.032 1645 Dihedral : 4.355 49.918 1258 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.28 % Allowed : 19.37 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1159 helix: 1.34 (0.34), residues: 263 sheet: -0.52 (0.30), residues: 302 loop : -0.51 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 655 TYR 0.020 0.001 TYR B 415 PHE 0.016 0.001 PHE A 113 TRP 0.009 0.001 TRP B 195 HIS 0.003 0.001 HIS B 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 9515) covalent geometry : angle 0.49983 / 0.27 (12868) hydrogen bonds : bond 0.03005 / 1.93 ( 342) hydrogen bonds : angle 4.91973 / 3.52 ( 966) metal coordination : bond 0.00383 / 0.19 ( 4) metal coordination : angle 2.19291 / 1.50 ( 6) Misc. bond : bond 0.00027 / 0.01 ( 2) link_TRANS : bond 0.00019 / 0.01 ( 1) link_TRANS : angle 0.16592 / 0.09 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2733.60 seconds wall clock time: 47 minutes 36.86 seconds (2856.86 seconds total)