Starting phenix.real_space_refine on Thu Feb 5 00:03:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rpw_54173/02_2026/9rpw_54173.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rpw_54173/02_2026/9rpw_54173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rpw_54173/02_2026/9rpw_54173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rpw_54173/02_2026/9rpw_54173.map" model { file = "/net/cci-nas-00/data/ceres_data/9rpw_54173/02_2026/9rpw_54173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rpw_54173/02_2026/9rpw_54173.cif" } resolution = 3.2 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 8544 2.51 5 N 2357 2.21 5 O 2633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13588 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4594 Classifications: {'peptide': 560} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 539} Chain: "E" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1181 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "A" Number of atoms: 4694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4694 Classifications: {'peptide': 572} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 550} Chain breaks: 1 Chain: "B" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1181 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "C" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1938 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 13, 'TRANS': 240} Chain breaks: 2 Time building chain proxies: 2.60, per 1000 atoms: 0.19 Number of scatterers: 13588 At special positions: 0 Unit cell: (101.38, 114.7, 153.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2633 8.00 N 2357 7.00 C 8544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 438.9 milliseconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3158 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 25 sheets defined 10.9% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'D' and resid 295 through 302 Processing helix chain 'D' and resid 463 through 470 removed outlier: 4.014A pdb=" N SER D 468 " --> pdb=" O ASP D 464 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG D 469 " --> pdb=" O TRP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 500 removed outlier: 4.462A pdb=" N MET D 499 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 668 Processing helix chain 'D' and resid 671 through 675 removed outlier: 3.518A pdb=" N THR D 674 " --> pdb=" O TYR D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 774 removed outlier: 3.946A pdb=" N ARG D 774 " --> pdb=" O GLN D 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.507A pdb=" N ASN E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 137 removed outlier: 3.978A pdb=" N ALA E 133 " --> pdb=" O PRO E 130 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU E 134 " --> pdb=" O GLN E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 156 removed outlier: 3.721A pdb=" N VAL E 144 " --> pdb=" O GLN E 140 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS E 145 " --> pdb=" O ASP E 141 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASP E 149 " --> pdb=" O LYS E 145 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA E 151 " --> pdb=" O MET E 147 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA E 152 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU E 153 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 168 removed outlier: 3.749A pdb=" N ARG E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.658A pdb=" N ASP A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 removed outlier: 3.523A pdb=" N ARG A 469 " --> pdb=" O TRP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 660 through 668 Processing helix chain 'B' and resid 30 through 33 Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.785A pdb=" N ARG B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 157 removed outlier: 3.743A pdb=" N ASN B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 167 removed outlier: 3.577A pdb=" N ILE B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 270 through 273 removed outlier: 6.742A pdb=" N HIS D 745 " --> pdb=" O TRP D 739 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N TRP D 739 " --> pdb=" O HIS D 745 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL D 747 " --> pdb=" O ASN D 737 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS D 735 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY D 753 " --> pdb=" O GLY D 731 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 249 through 250 removed outlier: 3.921A pdb=" N ALA D 257 " --> pdb=" O TRP D 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 291 through 292 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 310 through 315 current: chain 'D' and resid 325 through 334 removed outlier: 3.724A pdb=" N THR D 332 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N THR D 356 " --> pdb=" O THR D 332 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 388 through 394 removed outlier: 3.601A pdb=" N GLN D 393 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ALA D 414 " --> pdb=" O GLN D 393 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN D 413 " --> pdb=" O HIS D 431 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS D 431 " --> pdb=" O GLN D 413 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 430 " --> pdb=" O HIS D 457 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 398 through 403 removed outlier: 3.724A pdb=" N ASP D 402 " --> pdb=" O PHE D 406 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE D 406 " --> pdb=" O ASP D 402 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 449 through 452 removed outlier: 3.804A pdb=" N GLY D 580 " --> pdb=" O ALA D 609 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 620 through 623 current: chain 'D' and resid 637 through 647 removed outlier: 6.926A pdb=" N ARG D 650 " --> pdb=" O ARG D 646 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 651 " --> pdb=" O SER D 690 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN D 655 " --> pdb=" O GLY D 686 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AA8, first strand: chain 'E' and resid 35 through 40 removed outlier: 6.227A pdb=" N MET E 36 " --> pdb=" O LEU E 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 61 through 63 current: chain 'E' and resid 95 through 109 Processing sheet with id=AA9, first strand: chain 'A' and resid 198 through 207 removed outlier: 3.530A pdb=" N VAL A 205 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 232 " --> pdb=" O TYR A 244 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 269 " --> pdb=" O MET A 264 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 269 through 273 current: chain 'A' and resid 651 through 659 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 682 through 684 current: chain 'A' and resid 697 through 705 removed outlier: 6.761A pdb=" N SER A 698 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL A 719 " --> pdb=" O SER A 698 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A 700 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU A 717 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA A 702 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER A 715 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR A 704 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N ALA A 713 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 736 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 715 " --> pdb=" O ARG A 734 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL A 719 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL A 747 " --> pdb=" O ASN A 737 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 248 through 252 removed outlier: 3.886A pdb=" N ALA A 257 " --> pdb=" O TRP A 249 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N MET A 255 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 277 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 288 removed outlier: 3.568A pdb=" N GLU A 288 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 291 through 292 Processing sheet with id=AB4, first strand: chain 'A' and resid 327 through 331 removed outlier: 4.100A pdb=" N LYS A 358 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AB6, first strand: chain 'A' and resid 363 through 364 Processing sheet with id=AB7, first strand: chain 'A' and resid 393 through 403 removed outlier: 6.096A pdb=" N PHE A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 429 through 432 current: chain 'A' and resid 445 through 457 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 479 through 491 current: chain 'A' and resid 505 through 508 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 505 through 508 current: chain 'A' and resid 556 through 567 removed outlier: 7.472A pdb=" N ASN A 556 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 577 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 575 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY A 580 " --> pdb=" O TRP A 608 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TRP A 608 " --> pdb=" O GLY A 580 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE A 582 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.751A pdb=" N MET B 36 " --> pdb=" O GLU B 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 74 through 89 removed outlier: 7.263A pdb=" N SER B 74 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE B 110 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG B 76 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL B 108 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLY B 78 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA B 106 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL B 80 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 104 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE B 82 " --> pdb=" O MET B 102 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N MET B 102 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS B 84 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET B 100 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR B 86 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR B 98 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER B 88 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 40 through 41 removed outlier: 6.543A pdb=" N THR C 91 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL C 82 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG C 93 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 62 " --> pdb=" O PHE C 77 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 57 Processing sheet with id=AC3, first strand: chain 'C' and resid 163 through 165 removed outlier: 3.604A pdb=" N PHE C 206 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASN C 207 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N CYS C 144 " --> pdb=" O ASN C 207 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LYS C 233 " --> pdb=" O CYS C 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 155 through 157 Processing sheet with id=AC5, first strand: chain 'C' and resid 248 through 249 Processing sheet with id=AC6, first strand: chain 'C' and resid 253 through 255 Processing sheet with id=AC7, first strand: chain 'C' and resid 262 through 267 removed outlier: 5.624A pdb=" N ASN C 271 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASN C 295 " --> pdb=" O ASN C 271 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL C 273 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG C 291 " --> pdb=" O MET C 275 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY C 277 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LYS C 289 " --> pdb=" O GLY C 277 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 897 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: 2.25 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4497 1.34 - 1.45: 2102 1.45 - 1.57: 7209 1.57 - 1.69: 1 1.69 - 1.81: 100 Bond restraints: 13909 Sorted by residual: bond pdb=" CB PRO D 392 " pdb=" CG PRO D 392 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" C LEU E 159 " pdb=" N PRO E 160 " ideal model delta sigma weight residual 1.334 1.358 -0.024 1.51e-02 4.39e+03 2.51e+00 bond pdb=" C PRO D 253 " pdb=" N ASN D 254 " ideal model delta sigma weight residual 1.332 1.312 0.021 1.40e-02 5.10e+03 2.22e+00 bond pdb=" C GLN A 677 " pdb=" N TYR A 678 " ideal model delta sigma weight residual 1.332 1.314 0.018 1.40e-02 5.10e+03 1.66e+00 bond pdb=" CA GLN A 393 " pdb=" C GLN A 393 " ideal model delta sigma weight residual 1.530 1.517 0.013 1.08e-02 8.57e+03 1.51e+00 ... (remaining 13904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 18733 2.52 - 5.04: 165 5.04 - 7.55: 3 7.55 - 10.07: 0 10.07 - 12.59: 1 Bond angle restraints: 18902 Sorted by residual: angle pdb=" N THR B 27 " pdb=" CA THR B 27 " pdb=" C THR B 27 " ideal model delta sigma weight residual 113.21 108.10 5.11 1.15e+00 7.56e-01 1.97e+01 angle pdb=" N GLY D 319 " pdb=" CA GLY D 319 " pdb=" C GLY D 319 " ideal model delta sigma weight residual 110.38 115.33 -4.95 1.48e+00 4.57e-01 1.12e+01 angle pdb=" N GLN D 393 " pdb=" CA GLN D 393 " pdb=" C GLN D 393 " ideal model delta sigma weight residual 111.71 107.47 4.24 1.34e+00 5.57e-01 1.00e+01 angle pdb=" C GLU D 391 " pdb=" N PRO D 392 " pdb=" CD PRO D 392 " ideal model delta sigma weight residual 125.00 112.41 12.59 4.10e+00 5.95e-02 9.43e+00 angle pdb=" C TYR D 678 " pdb=" N LYS D 679 " pdb=" CA LYS D 679 " ideal model delta sigma weight residual 122.58 116.26 6.32 2.07e+00 2.33e-01 9.33e+00 ... (remaining 18897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 7447 17.61 - 35.22: 593 35.22 - 52.83: 165 52.83 - 70.44: 37 70.44 - 88.05: 9 Dihedral angle restraints: 8251 sinusoidal: 3298 harmonic: 4953 Sorted by residual: dihedral pdb=" CA ILE B 156 " pdb=" C ILE B 156 " pdb=" N ARG B 157 " pdb=" CA ARG B 157 " ideal model delta harmonic sigma weight residual 180.00 150.17 29.83 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA GLU D 391 " pdb=" C GLU D 391 " pdb=" N PRO D 392 " pdb=" CA PRO D 392 " ideal model delta harmonic sigma weight residual -180.00 -153.36 -26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ALA D 252 " pdb=" C ALA D 252 " pdb=" N PRO D 253 " pdb=" CA PRO D 253 " ideal model delta harmonic sigma weight residual -180.00 -161.79 -18.21 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 8248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1423 0.045 - 0.091: 434 0.091 - 0.136: 139 0.136 - 0.182: 6 0.182 - 0.227: 1 Chirality restraints: 2003 Sorted by residual: chirality pdb=" CA PRO D 392 " pdb=" N PRO D 392 " pdb=" C PRO D 392 " pdb=" CB PRO D 392 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ILE A 525 " pdb=" N ILE A 525 " pdb=" C ILE A 525 " pdb=" CB ILE A 525 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA VAL D 361 " pdb=" N VAL D 361 " pdb=" C VAL D 361 " pdb=" CB VAL D 361 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 2000 not shown) Planarity restraints: 2490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 391 " 0.101 5.00e-02 4.00e+02 1.53e-01 3.72e+01 pdb=" N PRO D 392 " -0.264 5.00e-02 4.00e+02 pdb=" CA PRO D 392 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO D 392 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 116 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO B 117 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 117 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 117 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 42 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO E 43 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " -0.022 5.00e-02 4.00e+02 ... (remaining 2487 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 7534 3.00 - 3.48: 12568 3.48 - 3.95: 20610 3.95 - 4.43: 24482 4.43 - 4.90: 41818 Nonbonded interactions: 107012 Sorted by model distance: nonbonded pdb=" O GLU D 391 " pdb=" O PRO D 392 " model vdw 2.526 3.040 nonbonded pdb=" N THR A 385 " pdb=" OG1 THR A 385 " model vdw 2.533 2.496 nonbonded pdb=" C THR D 563 " pdb=" OG1 THR D 563 " model vdw 2.538 2.616 nonbonded pdb=" C THR A 374 " pdb=" OG1 THR A 374 " model vdw 2.541 2.616 nonbonded pdb=" N VAL A 361 " pdb=" O VAL A 361 " model vdw 2.549 2.496 ... (remaining 107007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 225 through 784) selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } 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: 18.210 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.830 Find NCS groups from input model: 0.110 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 0.086 13909 Z= 0.250 Angle : 0.640 12.591 18902 Z= 0.362 Chirality : 0.047 0.227 2003 Planarity : 0.006 0.153 2490 Dihedral : 14.411 88.048 5093 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.16 % Favored : 87.72 % Rotamer: Outliers : 5.85 % Allowed : 10.00 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -3.58 (0.19), residues: 1670 helix: -2.15 (0.37), residues: 143 sheet: -2.22 (0.18), residues: 798 loop : -2.41 (0.20), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 495 TYR 0.015 0.002 TYR D 398 PHE 0.014 0.002 PHE D 417 TRP 0.010 0.001 TRP E 21 HIS 0.006 0.001 HIS D 416 Details of bonding type rmsd covalent geometry : bond 0.00577 (13909) covalent geometry : angle 0.64002 (18902) hydrogen bonds : bond 0.25964 ( 335) hydrogen bonds : angle 10.42273 ( 897) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 142 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: D 264 MET cc_start: 0.8951 (mtm) cc_final: 0.8638 (mtm) REVERT: E 49 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6690 (ttm170) REVERT: E 116 TYR cc_start: 0.7690 (m-80) cc_final: 0.7385 (m-80) REVERT: A 249 TRP cc_start: 0.8141 (t60) cc_final: 0.7773 (t60) REVERT: A 321 MET cc_start: 0.7277 (tmm) cc_final: 0.6947 (tmm) REVERT: A 453 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8093 (t80) REVERT: B 115 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8842 (pp) REVERT: C 158 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8956 (mp) REVERT: C 291 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7801 (ttm-80) outliers start: 86 outliers final: 41 residues processed: 214 average time/residue: 0.1145 time to fit residues: 35.2283 Evaluate side-chains 158 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 611 ASP Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 291 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 ASN D 755 ASN C 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.091530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.072649 restraints weight = 31040.788| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.03 r_work: 0.3094 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 13909 Z= 0.136 Angle : 0.554 11.037 18902 Z= 0.298 Chirality : 0.045 0.245 2003 Planarity : 0.005 0.145 2490 Dihedral : 8.021 59.150 1992 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.59 % Favored : 93.29 % Rotamer: Outliers : 4.63 % Allowed : 13.06 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -3.05 (0.20), residues: 1670 helix: -0.62 (0.41), residues: 162 sheet: -2.01 (0.18), residues: 823 loop : -2.16 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 551 TYR 0.012 0.001 TYR D 363 PHE 0.013 0.001 PHE C 206 TRP 0.013 0.001 TRP B 21 HIS 0.003 0.001 HIS D 416 Details of bonding type rmsd covalent geometry : bond 0.00313 (13909) covalent geometry : angle 0.55417 (18902) hydrogen bonds : bond 0.03719 ( 335) hydrogen bonds : angle 6.65012 ( 897) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 123 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 391 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: D 651 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8766 (pp) REVERT: E 53 ASN cc_start: 0.8387 (m-40) cc_final: 0.8081 (t0) REVERT: E 116 TYR cc_start: 0.8219 (m-80) cc_final: 0.7337 (m-80) REVERT: A 249 TRP cc_start: 0.8019 (t60) cc_final: 0.7528 (t60) REVERT: A 321 MET cc_start: 0.6458 (tmm) cc_final: 0.6146 (tmm) REVERT: A 453 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8137 (t80) REVERT: A 470 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8453 (t0) REVERT: C 158 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8675 (mp) outliers start: 68 outliers final: 38 residues processed: 183 average time/residue: 0.0950 time to fit residues: 26.8034 Evaluate side-chains 157 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 263 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 153 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 48 optimal weight: 0.0070 chunk 57 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 345 ASN D 393 GLN D 460 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.091831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.073094 restraints weight = 31146.270| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.04 r_work: 0.3104 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 13909 Z= 0.122 Angle : 0.517 9.932 18902 Z= 0.277 Chirality : 0.045 0.252 2003 Planarity : 0.005 0.140 2490 Dihedral : 7.069 59.606 1958 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.60 % Favored : 92.34 % Rotamer: Outliers : 4.01 % Allowed : 14.15 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -2.78 (0.20), residues: 1670 helix: -0.26 (0.42), residues: 171 sheet: -1.85 (0.18), residues: 787 loop : -2.07 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 623 TYR 0.013 0.001 TYR D 537 PHE 0.011 0.001 PHE C 206 TRP 0.005 0.001 TRP B 21 HIS 0.003 0.001 HIS D 416 Details of bonding type rmsd covalent geometry : bond 0.00283 (13909) covalent geometry : angle 0.51664 (18902) hydrogen bonds : bond 0.03228 ( 335) hydrogen bonds : angle 5.95233 ( 897) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 123 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 249 TRP cc_start: 0.8323 (OUTLIER) cc_final: 0.6717 (t60) REVERT: D 289 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8291 (tt) REVERT: D 391 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: D 409 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7610 (ttp80) REVERT: D 565 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7479 (mtt-85) REVERT: D 651 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8814 (pp) REVERT: E 33 MET cc_start: 0.8471 (mtt) cc_final: 0.8259 (mtm) REVERT: E 53 ASN cc_start: 0.8321 (m-40) cc_final: 0.8051 (t0) REVERT: E 116 TYR cc_start: 0.8295 (m-80) cc_final: 0.7469 (m-80) REVERT: E 131 GLN cc_start: 0.8823 (tt0) cc_final: 0.8606 (tm-30) REVERT: E 146 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7940 (pt0) REVERT: A 321 MET cc_start: 0.6443 (tmm) cc_final: 0.6087 (tmm) REVERT: A 453 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8167 (t80) REVERT: A 611 ASP cc_start: 0.8241 (m-30) cc_final: 0.7939 (m-30) REVERT: C 158 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8634 (mp) outliers start: 59 outliers final: 35 residues processed: 177 average time/residue: 0.1044 time to fit residues: 28.0556 Evaluate side-chains 155 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 249 TRP Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 409 ARG Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 263 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.089506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.070693 restraints weight = 31625.609| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.00 r_work: 0.3058 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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 : 0.005 0.082 13909 Z= 0.228 Angle : 0.578 9.746 18902 Z= 0.313 Chirality : 0.047 0.262 2003 Planarity : 0.005 0.140 2490 Dihedral : 7.007 59.525 1950 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.34 % Favored : 90.60 % Rotamer: Outliers : 4.90 % Allowed : 15.03 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -2.85 (0.20), residues: 1670 helix: -0.05 (0.43), residues: 163 sheet: -1.95 (0.18), residues: 815 loop : -2.07 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 623 TYR 0.016 0.002 TYR D 398 PHE 0.015 0.002 PHE C 206 TRP 0.008 0.001 TRP B 21 HIS 0.005 0.001 HIS D 416 Details of bonding type rmsd covalent geometry : bond 0.00530 (13909) covalent geometry : angle 0.57794 (18902) hydrogen bonds : bond 0.03584 ( 335) hydrogen bonds : angle 6.09964 ( 897) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 111 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: D 249 TRP cc_start: 0.8422 (OUTLIER) cc_final: 0.6906 (t60) REVERT: D 289 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8377 (tt) REVERT: D 363 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.6320 (p90) REVERT: D 409 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7677 (ttp80) REVERT: D 482 MET cc_start: 0.8088 (pmm) cc_final: 0.7802 (pmm) REVERT: D 651 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8833 (pp) REVERT: D 716 MET cc_start: 0.9088 (ttp) cc_final: 0.8863 (ttt) REVERT: E 53 ASN cc_start: 0.8399 (m-40) cc_final: 0.8078 (t0) REVERT: E 116 TYR cc_start: 0.8399 (m-80) cc_final: 0.7853 (m-80) REVERT: E 131 GLN cc_start: 0.8834 (tt0) cc_final: 0.8616 (tm-30) REVERT: A 236 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8574 (p) REVERT: A 321 MET cc_start: 0.6592 (tmm) cc_final: 0.6174 (tmm) REVERT: A 453 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8070 (t80) REVERT: C 158 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8651 (mp) outliers start: 72 outliers final: 50 residues processed: 172 average time/residue: 0.0950 time to fit residues: 25.3136 Evaluate side-chains 165 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 107 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 249 TRP Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 363 TYR Chi-restraints excluded: chain D residue 409 ARG Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 424 MET Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 677 GLN Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 263 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 755 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.089501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.070602 restraints weight = 31735.503| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.06 r_work: 0.3058 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 13909 Z= 0.200 Angle : 0.564 9.408 18902 Z= 0.304 Chirality : 0.046 0.261 2003 Planarity : 0.005 0.138 2490 Dihedral : 6.832 57.925 1949 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.56 % Favored : 91.38 % Rotamer: Outliers : 4.97 % Allowed : 16.26 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -2.86 (0.20), residues: 1670 helix: -0.15 (0.42), residues: 168 sheet: -1.94 (0.18), residues: 819 loop : -2.08 (0.21), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 168 TYR 0.014 0.001 TYR D 398 PHE 0.014 0.001 PHE C 206 TRP 0.008 0.001 TRP B 21 HIS 0.004 0.001 HIS D 416 Details of bonding type rmsd covalent geometry : bond 0.00465 (13909) covalent geometry : angle 0.56401 (18902) hydrogen bonds : bond 0.03299 ( 335) hydrogen bonds : angle 5.91494 ( 897) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 109 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 249 TRP cc_start: 0.8386 (OUTLIER) cc_final: 0.6865 (t60) REVERT: D 289 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8345 (tt) REVERT: D 363 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.6315 (p90) REVERT: D 409 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7681 (ttp80) REVERT: D 651 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8825 (pp) REVERT: D 716 MET cc_start: 0.9087 (ttp) cc_final: 0.8844 (ttt) REVERT: D 755 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8315 (t0) REVERT: E 53 ASN cc_start: 0.8389 (m-40) cc_final: 0.8067 (t0) REVERT: E 116 TYR cc_start: 0.8382 (m-80) cc_final: 0.8031 (m-80) REVERT: E 131 GLN cc_start: 0.8807 (tt0) cc_final: 0.8546 (tm-30) REVERT: A 236 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8553 (p) REVERT: A 289 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8589 (tt) REVERT: A 321 MET cc_start: 0.6544 (tmm) cc_final: 0.6235 (tpp) REVERT: A 453 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8116 (t80) REVERT: A 611 ASP cc_start: 0.8242 (m-30) cc_final: 0.7960 (m-30) REVERT: C 158 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8625 (mp) outliers start: 73 outliers final: 54 residues processed: 172 average time/residue: 0.0910 time to fit residues: 24.2651 Evaluate side-chains 165 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 101 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 249 TRP Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 363 TYR Chi-restraints excluded: chain D residue 409 ARG Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 424 MET Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 677 GLN Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 755 ASN Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 263 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 113 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 755 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.088982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.069725 restraints weight = 32215.428| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.10 r_work: 0.2982 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13909 Z= 0.230 Angle : 0.585 9.307 18902 Z= 0.316 Chirality : 0.047 0.265 2003 Planarity : 0.005 0.137 2490 Dihedral : 6.814 56.966 1948 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.58 % Favored : 90.36 % Rotamer: Outliers : 5.51 % Allowed : 16.12 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -2.86 (0.20), residues: 1670 helix: 0.09 (0.43), residues: 162 sheet: -1.97 (0.18), residues: 830 loop : -2.09 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 623 TYR 0.016 0.002 TYR D 398 PHE 0.015 0.001 PHE C 206 TRP 0.017 0.001 TRP B 21 HIS 0.004 0.001 HIS D 416 Details of bonding type rmsd covalent geometry : bond 0.00534 (13909) covalent geometry : angle 0.58470 (18902) hydrogen bonds : bond 0.03430 ( 335) hydrogen bonds : angle 5.95512 ( 897) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 105 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 249 TRP cc_start: 0.8364 (OUTLIER) cc_final: 0.6827 (t60) REVERT: D 289 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8298 (tt) REVERT: D 363 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.6169 (p90) REVERT: D 409 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7709 (ttp80) REVERT: D 716 MET cc_start: 0.9118 (ttp) cc_final: 0.8905 (ttt) REVERT: D 755 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8222 (t0) REVERT: E 53 ASN cc_start: 0.8361 (m-40) cc_final: 0.8038 (t0) REVERT: E 116 TYR cc_start: 0.8435 (m-80) cc_final: 0.8173 (m-80) REVERT: E 131 GLN cc_start: 0.8834 (tt0) cc_final: 0.8555 (tm-30) REVERT: A 236 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8536 (p) REVERT: A 289 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8571 (tt) REVERT: A 321 MET cc_start: 0.6505 (tmm) cc_final: 0.6183 (tpp) REVERT: A 453 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.8057 (t80) REVERT: A 720 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: B 75 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8336 (tt) REVERT: B 79 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8289 (pttp) REVERT: C 158 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8621 (mp) outliers start: 81 outliers final: 59 residues processed: 174 average time/residue: 0.0949 time to fit residues: 25.4674 Evaluate side-chains 172 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 101 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 249 TRP Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 363 TYR Chi-restraints excluded: chain D residue 409 ARG Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 424 MET Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 755 ASN Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 720 GLN Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 263 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 62 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 79 optimal weight: 0.0040 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 470 ASN ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.090855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.071649 restraints weight = 31822.658| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.09 r_work: 0.3015 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 13909 Z= 0.136 Angle : 0.532 8.810 18902 Z= 0.284 Chirality : 0.046 0.259 2003 Planarity : 0.004 0.134 2490 Dihedral : 6.446 56.755 1946 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.89 % Favored : 93.05 % Rotamer: Outliers : 4.63 % Allowed : 17.96 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -2.70 (0.20), residues: 1670 helix: 0.12 (0.43), residues: 169 sheet: -1.82 (0.18), residues: 804 loop : -2.06 (0.21), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 429 TYR 0.014 0.001 TYR D 537 PHE 0.011 0.001 PHE C 206 TRP 0.010 0.001 TRP B 21 HIS 0.005 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00318 (13909) covalent geometry : angle 0.53162 (18902) hydrogen bonds : bond 0.02918 ( 335) hydrogen bonds : angle 5.60375 ( 897) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 114 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 249 TRP cc_start: 0.8299 (OUTLIER) cc_final: 0.6783 (t60) REVERT: D 289 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8225 (tt) REVERT: D 363 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.6049 (p90) REVERT: D 397 ASN cc_start: 0.7821 (t0) cc_final: 0.7399 (t0) REVERT: D 409 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7612 (ttp80) REVERT: D 565 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7611 (mtt-85) REVERT: E 53 ASN cc_start: 0.8350 (m-40) cc_final: 0.8028 (t0) REVERT: E 116 TYR cc_start: 0.8364 (m-80) cc_final: 0.8058 (m-80) REVERT: A 236 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8485 (p) REVERT: A 289 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8592 (tt) REVERT: A 321 MET cc_start: 0.6444 (tmm) cc_final: 0.6152 (tpp) REVERT: A 453 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8144 (t80) REVERT: A 499 MET cc_start: 0.7947 (pmm) cc_final: 0.7745 (pmm) REVERT: A 611 ASP cc_start: 0.8252 (m-30) cc_final: 0.7950 (m-30) REVERT: A 720 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: A 724 CYS cc_start: 0.8562 (p) cc_final: 0.8188 (t) REVERT: B 75 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8248 (tt) REVERT: B 79 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8270 (pttp) REVERT: C 142 MET cc_start: 0.8503 (mtp) cc_final: 0.8187 (mtt) outliers start: 68 outliers final: 47 residues processed: 168 average time/residue: 0.0885 time to fit residues: 22.9673 Evaluate side-chains 165 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 107 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 249 TRP Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 363 TYR Chi-restraints excluded: chain D residue 409 ARG Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 424 MET Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 720 GLN Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 263 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 99 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 684 GLN D 755 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.070304 restraints weight = 31949.161| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.08 r_work: 0.2993 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13909 Z= 0.208 Angle : 0.574 8.699 18902 Z= 0.308 Chirality : 0.046 0.266 2003 Planarity : 0.005 0.134 2490 Dihedral : 6.368 56.250 1942 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.10 % Favored : 90.84 % Rotamer: Outliers : 4.83 % Allowed : 18.10 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -2.72 (0.20), residues: 1670 helix: 0.26 (0.43), residues: 163 sheet: -1.88 (0.18), residues: 829 loop : -2.01 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 124 TYR 0.014 0.001 TYR E 148 PHE 0.014 0.001 PHE C 206 TRP 0.011 0.001 TRP B 21 HIS 0.004 0.001 HIS D 416 Details of bonding type rmsd covalent geometry : bond 0.00483 (13909) covalent geometry : angle 0.57359 (18902) hydrogen bonds : bond 0.03269 ( 335) hydrogen bonds : angle 5.72320 ( 897) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 107 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 249 TRP cc_start: 0.8335 (OUTLIER) cc_final: 0.6788 (t60) REVERT: D 289 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8293 (tt) REVERT: D 363 TYR cc_start: 0.6860 (OUTLIER) cc_final: 0.6059 (p90) REVERT: D 409 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7541 (ttp80) REVERT: D 716 MET cc_start: 0.9121 (ttp) cc_final: 0.8902 (ttt) REVERT: E 53 ASN cc_start: 0.8361 (m-40) cc_final: 0.8033 (t0) REVERT: E 116 TYR cc_start: 0.8444 (m-80) cc_final: 0.8176 (m-80) REVERT: A 236 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8557 (p) REVERT: A 289 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8604 (tt) REVERT: A 321 MET cc_start: 0.6448 (tmm) cc_final: 0.6150 (tpp) REVERT: A 453 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.8076 (t80) REVERT: A 499 MET cc_start: 0.7927 (pmm) cc_final: 0.7718 (pmm) REVERT: A 720 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: B 75 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8252 (tt) REVERT: B 79 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8294 (pttp) outliers start: 71 outliers final: 55 residues processed: 168 average time/residue: 0.0917 time to fit residues: 23.7279 Evaluate side-chains 170 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 105 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 249 TRP Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 363 TYR Chi-restraints excluded: chain D residue 409 ARG Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 424 MET Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 755 ASN Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 720 GLN Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 263 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 142 optimal weight: 0.4980 chunk 123 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 0.0970 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.091111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071939 restraints weight = 31804.957| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.07 r_work: 0.3027 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 13909 Z= 0.131 Angle : 0.529 8.114 18902 Z= 0.283 Chirality : 0.045 0.260 2003 Planarity : 0.004 0.131 2490 Dihedral : 6.136 56.270 1942 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.11 % Favored : 93.83 % Rotamer: Outliers : 4.83 % Allowed : 18.23 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -2.59 (0.20), residues: 1670 helix: 0.26 (0.43), residues: 169 sheet: -1.76 (0.18), residues: 810 loop : -1.99 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 124 TYR 0.014 0.001 TYR D 537 PHE 0.012 0.001 PHE C 206 TRP 0.010 0.001 TRP A 249 HIS 0.003 0.001 HIS D 416 Details of bonding type rmsd covalent geometry : bond 0.00306 (13909) covalent geometry : angle 0.52882 (18902) hydrogen bonds : bond 0.02818 ( 335) hydrogen bonds : angle 5.44813 ( 897) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 115 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 249 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.6765 (t60) REVERT: D 289 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8206 (tt) REVERT: D 363 TYR cc_start: 0.6870 (OUTLIER) cc_final: 0.6016 (p90) REVERT: D 397 ASN cc_start: 0.7804 (t0) cc_final: 0.7401 (t0) REVERT: D 409 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7497 (ttp80) REVERT: D 499 MET cc_start: 0.7531 (pmm) cc_final: 0.6909 (pmm) REVERT: D 565 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7645 (mtt-85) REVERT: E 53 ASN cc_start: 0.8340 (m-40) cc_final: 0.8042 (t0) REVERT: E 116 TYR cc_start: 0.8371 (m-80) cc_final: 0.8059 (m-80) REVERT: A 236 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8485 (p) REVERT: A 321 MET cc_start: 0.6414 (tmm) cc_final: 0.6123 (tpp) REVERT: A 453 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8151 (t80) REVERT: A 499 MET cc_start: 0.7914 (pmm) cc_final: 0.7706 (pmm) REVERT: A 611 ASP cc_start: 0.8257 (m-30) cc_final: 0.7949 (m-30) REVERT: A 720 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: A 724 CYS cc_start: 0.8566 (p) cc_final: 0.8200 (t) REVERT: B 75 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8233 (tt) REVERT: B 79 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8265 (pttp) REVERT: C 158 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8610 (mp) outliers start: 71 outliers final: 54 residues processed: 173 average time/residue: 0.0902 time to fit residues: 24.2069 Evaluate side-chains 176 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 111 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 249 TRP Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 363 TYR Chi-restraints excluded: chain D residue 409 ARG Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 424 MET Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 534 GLN Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 752 ILE Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 720 GLN Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 263 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 101 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 166 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 128 optimal weight: 0.0980 chunk 20 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.091332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.072187 restraints weight = 31726.787| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.06 r_work: 0.3031 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 13909 Z= 0.130 Angle : 0.541 9.143 18902 Z= 0.286 Chirality : 0.045 0.262 2003 Planarity : 0.004 0.129 2490 Dihedral : 6.040 56.104 1942 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.01 % Favored : 92.93 % Rotamer: Outliers : 4.69 % Allowed : 18.44 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -2.45 (0.20), residues: 1670 helix: 0.53 (0.43), residues: 163 sheet: -1.66 (0.18), residues: 821 loop : -1.93 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 429 TYR 0.013 0.001 TYR E 148 PHE 0.010 0.001 PHE C 206 TRP 0.007 0.001 TRP B 21 HIS 0.003 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00306 (13909) covalent geometry : angle 0.54095 (18902) hydrogen bonds : bond 0.02769 ( 335) hydrogen bonds : angle 5.36626 ( 897) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 116 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 249 TRP cc_start: 0.8336 (OUTLIER) cc_final: 0.6699 (t60) REVERT: D 289 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8182 (tt) REVERT: D 363 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.5959 (p90) REVERT: D 397 ASN cc_start: 0.7769 (t0) cc_final: 0.7371 (t0) REVERT: D 409 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7395 (ttp80) REVERT: D 565 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7633 (mtt-85) REVERT: E 53 ASN cc_start: 0.8337 (m-40) cc_final: 0.8040 (t0) REVERT: E 116 TYR cc_start: 0.8376 (m-80) cc_final: 0.8072 (m-80) REVERT: A 236 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8468 (p) REVERT: A 321 MET cc_start: 0.6382 (tmm) cc_final: 0.5995 (tmm) REVERT: A 453 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.8155 (t80) REVERT: A 499 MET cc_start: 0.7955 (pmm) cc_final: 0.7733 (pmm) REVERT: A 611 ASP cc_start: 0.8244 (m-30) cc_final: 0.7941 (m-30) REVERT: A 724 CYS cc_start: 0.8562 (p) cc_final: 0.8218 (t) REVERT: B 75 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8254 (tt) REVERT: B 79 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8296 (pttp) REVERT: C 158 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8613 (mp) outliers start: 69 outliers final: 54 residues processed: 171 average time/residue: 0.0907 time to fit residues: 24.0067 Evaluate side-chains 177 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 113 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 249 TRP Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 363 TYR Chi-restraints excluded: chain D residue 409 ARG Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 424 MET Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 534 GLN Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 752 ILE Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 263 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 77 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 98 optimal weight: 0.1980 chunk 129 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 755 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.091297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.072121 restraints weight = 31953.011| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.07 r_work: 0.3029 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 13909 Z= 0.139 Angle : 0.541 8.973 18902 Z= 0.287 Chirality : 0.046 0.261 2003 Planarity : 0.004 0.127 2490 Dihedral : 6.018 55.551 1942 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.65 % Favored : 93.29 % Rotamer: Outliers : 4.76 % Allowed : 18.44 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -2.42 (0.20), residues: 1670 helix: 0.58 (0.43), residues: 163 sheet: -1.64 (0.18), residues: 821 loop : -1.92 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 124 TYR 0.013 0.001 TYR E 148 PHE 0.011 0.001 PHE C 206 TRP 0.008 0.001 TRP B 21 HIS 0.003 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00326 (13909) covalent geometry : angle 0.54147 (18902) hydrogen bonds : bond 0.02790 ( 335) hydrogen bonds : angle 5.33424 ( 897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2849.10 seconds wall clock time: 49 minutes 52.14 seconds (2992.14 seconds total)