Starting phenix.real_space_refine on Mon Aug 25 11:59:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8x_36967/08_2025/8k8x_36967.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8x_36967/08_2025/8k8x_36967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k8x_36967/08_2025/8k8x_36967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8x_36967/08_2025/8k8x_36967.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k8x_36967/08_2025/8k8x_36967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8x_36967/08_2025/8k8x_36967.map" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.027 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 35 5.16 5 C 17625 2.51 5 N 5000 2.21 5 O 5220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27880 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "C" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "A" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "E" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Time building chain proxies: 6.59, per 1000 atoms: 0.24 Number of scatterers: 27880 At special positions: 0 Unit cell: (127.92, 157.44, 182.04, 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 35 16.00 O 5220 8.00 N 5000 7.00 C 17625 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: 2.22 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6600 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 57 sheets defined 54.3% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'D' and resid 4 through 9 removed outlier: 3.529A pdb=" N LEU D 8 " --> pdb=" O SER D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 58 through 68 Processing helix chain 'D' and resid 97 through 111 Processing helix chain 'D' and resid 111 through 120 Processing helix chain 'D' and resid 121 through 153 removed outlier: 3.559A pdb=" N ALA D 153 " --> pdb=" O GLU D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 221 removed outlier: 4.050A pdb=" N ASN D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG D 213 " --> pdb=" O TYR D 209 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 224 through 242 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 273 through 279 Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 322 through 333 Processing helix chain 'D' and resid 363 through 372 removed outlier: 3.887A pdb=" N GLY D 369 " --> pdb=" O GLU D 365 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 379 Processing helix chain 'D' and resid 393 through 407 Processing helix chain 'D' and resid 412 through 428 Processing helix chain 'D' and resid 436 through 452 Processing helix chain 'D' and resid 456 through 471 Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 543 through 557 Processing helix chain 'D' and resid 584 through 597 Processing helix chain 'D' and resid 621 through 636 Processing helix chain 'D' and resid 649 through 654 removed outlier: 3.664A pdb=" N ALA D 652 " --> pdb=" O ALA D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 666 Processing helix chain 'D' and resid 676 through 686 Processing helix chain 'D' and resid 694 through 713 removed outlier: 3.938A pdb=" N HIS D 713 " --> pdb=" O LEU D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 719 removed outlier: 3.652A pdb=" N GLU D 719 " --> pdb=" O GLU D 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 96 through 119 removed outlier: 4.392A pdb=" N HIS C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASN C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 153 removed outlier: 3.998A pdb=" N ALA C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 221 removed outlier: 4.144A pdb=" N ASN C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 224 through 242 removed outlier: 3.614A pdb=" N GLU C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 273 through 279 Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 300 through 305 removed outlier: 3.666A pdb=" N ARG C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'C' and resid 363 through 372 removed outlier: 4.037A pdb=" N GLY C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.691A pdb=" N SER C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 378 " --> pdb=" O PRO C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 407 Processing helix chain 'C' and resid 412 through 428 Processing helix chain 'C' and resid 436 through 451 Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.757A pdb=" N SER C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 543 through 557 Processing helix chain 'C' and resid 585 through 597 Processing helix chain 'C' and resid 621 through 636 removed outlier: 3.605A pdb=" N LYS C 625 " --> pdb=" O ALA C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 654 removed outlier: 3.895A pdb=" N ALA C 652 " --> pdb=" O ALA C 649 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 654 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 666 Processing helix chain 'C' and resid 676 through 686 Processing helix chain 'C' and resid 694 through 718 removed outlier: 3.646A pdb=" N GLU C 716 " --> pdb=" O GLY C 712 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG C 718 " --> pdb=" O ASP C 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 32 through 45 Processing helix chain 'B' and resid 58 through 70 removed outlier: 3.733A pdb=" N THR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 70 " --> pdb=" O TYR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 120 removed outlier: 4.381A pdb=" N HIS B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASN B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 152 Processing helix chain 'B' and resid 173 through 221 removed outlier: 4.321A pdb=" N ASN B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 224 through 242 Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 273 through 279 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 363 through 372 removed outlier: 3.852A pdb=" N GLU B 368 " --> pdb=" O PRO B 364 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 removed outlier: 3.890A pdb=" N SER B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 407 Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 436 through 452 Processing helix chain 'B' and resid 456 through 471 removed outlier: 3.811A pdb=" N SER B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 Processing helix chain 'B' and resid 532 through 534 No H-bonds generated for 'chain 'B' and resid 532 through 534' Processing helix chain 'B' and resid 543 through 557 Processing helix chain 'B' and resid 584 through 597 Processing helix chain 'B' and resid 621 through 636 removed outlier: 3.665A pdb=" N LYS B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 654 removed outlier: 3.915A pdb=" N ALA B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 694 through 717 Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 58 through 69 Processing helix chain 'A' and resid 97 through 119 removed outlier: 4.084A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASN A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 152 removed outlier: 3.725A pdb=" N LEU A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 removed outlier: 4.160A pdb=" N ASN A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 224 through 242 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.165A pdb=" N GLY A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 393 through 407 Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 436 through 452 Processing helix chain 'A' and resid 456 through 471 removed outlier: 3.878A pdb=" N SER A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 543 through 557 removed outlier: 3.561A pdb=" N TYR A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 597 Processing helix chain 'A' and resid 621 through 636 removed outlier: 3.533A pdb=" N LYS A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 removed outlier: 4.073A pdb=" N ALA A 652 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 694 through 716 removed outlier: 3.860A pdb=" N GLU A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 58 through 69 removed outlier: 3.706A pdb=" N THR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 4.097A pdb=" N HIS E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASN E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 152 Processing helix chain 'E' and resid 173 through 221 removed outlier: 4.203A pdb=" N ASN E 212 " --> pdb=" O HIS E 208 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG E 213 " --> pdb=" O TYR E 209 " (cutoff:3.500A) Proline residue: E 216 - end of helix Processing helix chain 'E' and resid 224 through 242 Processing helix chain 'E' and resid 246 through 251 removed outlier: 4.096A pdb=" N ARG E 251 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 314 through 320 removed outlier: 3.627A pdb=" N GLU E 320 " --> pdb=" O SER E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 333 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 373 through 380 Processing helix chain 'E' and resid 393 through 407 Processing helix chain 'E' and resid 412 through 427 Processing helix chain 'E' and resid 436 through 452 Processing helix chain 'E' and resid 456 through 471 Processing helix chain 'E' and resid 471 through 485 removed outlier: 4.304A pdb=" N GLU E 475 " --> pdb=" O SER E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 557 removed outlier: 3.613A pdb=" N TYR E 557 " --> pdb=" O LEU E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 597 Processing helix chain 'E' and resid 621 through 636 Processing helix chain 'E' and resid 649 through 654 removed outlier: 4.067A pdb=" N ALA E 652 " --> pdb=" O ALA E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 666 removed outlier: 3.730A pdb=" N LEU E 661 " --> pdb=" O ARG E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 676 through 686 Processing helix chain 'E' and resid 694 through 718 removed outlier: 3.640A pdb=" N GLU E 716 " --> pdb=" O GLY E 712 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP E 717 " --> pdb=" O HIS E 713 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 3 removed outlier: 4.684A pdb=" N ILE D 671 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN D 642 " --> pdb=" O HIS D 670 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N TYR D 672 " --> pdb=" O GLN D 642 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL D 644 " --> pdb=" O TYR D 672 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL D 674 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU D 646 " --> pdb=" O VAL D 674 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA D 605 " --> pdb=" O ILE D 645 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 266 through 268 removed outlier: 6.547A pdb=" N VAL D 267 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ASP D 313 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU D 310 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL D 361 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU D 312 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N HIS D 48 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 382 " --> pdb=" O HIS D 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 77 through 82 Processing sheet with id=AA4, first strand: chain 'D' and resid 156 through 160 Processing sheet with id=AA5, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AA6, first strand: chain 'D' and resid 334 through 335 Processing sheet with id=AA7, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AA8, first strand: chain 'D' and resid 410 through 411 removed outlier: 7.282A pdb=" N GLN D 410 " --> pdb=" O LEU D 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AB1, first strand: chain 'D' and resid 498 through 504 Processing sheet with id=AB2, first strand: chain 'D' and resid 609 through 610 Processing sheet with id=AB3, first strand: chain 'C' and resid 266 through 268 removed outlier: 6.484A pdb=" N VAL C 267 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ASP C 313 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU C 310 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 361 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU C 312 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N HIS C 48 " --> pdb=" O PHE C 380 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 382 " --> pdb=" O HIS C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 77 through 82 removed outlier: 3.801A pdb=" N VAL C 88 " --> pdb=" O GLU C 348 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AB7, first strand: chain 'C' and resid 334 through 335 Processing sheet with id=AB8, first strand: chain 'C' and resid 389 through 391 Processing sheet with id=AB9, first strand: chain 'C' and resid 410 through 411 removed outlier: 7.484A pdb=" N GLN C 410 " --> pdb=" O LEU C 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AC2, first strand: chain 'C' and resid 498 through 504 removed outlier: 6.796A pdb=" N ILE C 529 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N PHE C 571 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 583 through 584 removed outlier: 4.580A pdb=" N ALA C 583 " --> pdb=" O VAL C 610 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 604 through 606 removed outlier: 6.760A pdb=" N GLN C 642 " --> pdb=" O HIS C 670 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N TYR C 672 " --> pdb=" O GLN C 642 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL C 644 " --> pdb=" O TYR C 672 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL C 674 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU C 646 " --> pdb=" O VAL C 674 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 266 through 268 removed outlier: 6.682A pdb=" N VAL B 267 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ASP B 313 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU B 310 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 361 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU B 312 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR B 50 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 77 through 82 Processing sheet with id=AC7, first strand: chain 'B' and resid 156 through 160 Processing sheet with id=AC8, first strand: chain 'B' and resid 280 through 281 Processing sheet with id=AC9, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AD1, first strand: chain 'B' and resid 334 through 335 Processing sheet with id=AD2, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AD3, first strand: chain 'B' and resid 410 through 411 removed outlier: 7.394A pdb=" N GLN B 410 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AD5, first strand: chain 'B' and resid 498 through 504 removed outlier: 6.694A pdb=" N ILE B 529 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N PHE B 571 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 604 through 606 removed outlier: 5.827A pdb=" N VAL B 644 " --> pdb=" O TYR B 672 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B 674 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 646 " --> pdb=" O VAL B 674 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 609 through 610 removed outlier: 3.684A pdb=" N ALA B 609 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 2 through 3 removed outlier: 4.650A pdb=" N ILE A 671 " --> pdb=" O LEU A 3 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 266 through 269 removed outlier: 4.215A pdb=" N ASP A 313 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N HIS A 48 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ARG A 383 " --> pdb=" O HIS A 48 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR A 50 " --> pdb=" O ARG A 383 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLU A 385 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 52 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 76 through 82 Processing sheet with id=AE2, first strand: chain 'A' and resid 156 through 160 Processing sheet with id=AE3, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AE4, first strand: chain 'A' and resid 284 through 286 Processing sheet with id=AE5, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AE6, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AE7, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AE8, first strand: chain 'A' and resid 498 through 504 removed outlier: 3.756A pdb=" N SER A 501 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE A 529 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N PHE A 571 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 583 through 584 removed outlier: 4.116A pdb=" N ALA A 583 " --> pdb=" O VAL A 610 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 266 through 268 Processing sheet with id=AF2, first strand: chain 'E' and resid 77 through 82 Processing sheet with id=AF3, first strand: chain 'E' and resid 156 through 160 Processing sheet with id=AF4, first strand: chain 'E' and resid 280 through 281 Processing sheet with id=AF5, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AF6, first strand: chain 'E' and resid 334 through 335 Processing sheet with id=AF7, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AF8, first strand: chain 'E' and resid 410 through 411 removed outlier: 7.389A pdb=" N GLN E 410 " --> pdb=" O LEU E 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 494 through 495 Processing sheet with id=AG1, first strand: chain 'E' and resid 498 through 503 removed outlier: 7.283A pdb=" N ILE E 529 " --> pdb=" O LEU E 569 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 583 through 584 removed outlier: 4.275A pdb=" N ALA E 583 " --> pdb=" O VAL E 610 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 604 through 606 removed outlier: 6.312A pdb=" N ALA E 605 " --> pdb=" O ILE E 645 " (cutoff:3.500A) 1568 hydrogen bonds defined for protein. 4485 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: 6.58 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9698 1.34 - 1.46: 5227 1.46 - 1.57: 13450 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 28435 Sorted by residual: bond pdb=" CA ASN C 650 " pdb=" C ASN C 650 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.80e-02 3.09e+03 2.66e+00 bond pdb=" CB TYR E 575 " pdb=" CG TYR E 575 " ideal model delta sigma weight residual 1.512 1.547 -0.035 2.20e-02 2.07e+03 2.46e+00 bond pdb=" CB TYR A 575 " pdb=" CG TYR A 575 " ideal model delta sigma weight residual 1.512 1.545 -0.033 2.20e-02 2.07e+03 2.25e+00 bond pdb=" CB TYR B 575 " pdb=" CG TYR B 575 " ideal model delta sigma weight residual 1.512 1.544 -0.032 2.20e-02 2.07e+03 2.16e+00 bond pdb=" CB TYR C 575 " pdb=" CG TYR C 575 " ideal model delta sigma weight residual 1.512 1.544 -0.032 2.20e-02 2.07e+03 2.08e+00 ... (remaining 28430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 38083 2.22 - 4.44: 468 4.44 - 6.66: 47 6.66 - 8.88: 5 8.88 - 11.10: 2 Bond angle restraints: 38605 Sorted by residual: angle pdb=" C ASN E 574 " pdb=" N TYR E 575 " pdb=" CA TYR E 575 " ideal model delta sigma weight residual 121.54 130.72 -9.18 1.91e+00 2.74e-01 2.31e+01 angle pdb=" N PRO A 509 " pdb=" CD PRO A 509 " pdb=" CG PRO A 509 " ideal model delta sigma weight residual 103.20 96.86 6.34 1.50e+00 4.44e-01 1.79e+01 angle pdb=" N TYR E 575 " pdb=" CA TYR E 575 " pdb=" CB TYR E 575 " ideal model delta sigma weight residual 110.49 117.31 -6.82 1.69e+00 3.50e-01 1.63e+01 angle pdb=" CA PRO A 509 " pdb=" N PRO A 509 " pdb=" CD PRO A 509 " ideal model delta sigma weight residual 112.00 106.44 5.56 1.40e+00 5.10e-01 1.58e+01 angle pdb=" C TYR E 510 " pdb=" N TRP E 511 " pdb=" CA TRP E 511 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.58e+01 ... (remaining 38600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 15763 17.96 - 35.91: 1042 35.91 - 53.87: 186 53.87 - 71.83: 156 71.83 - 89.78: 123 Dihedral angle restraints: 17270 sinusoidal: 6995 harmonic: 10275 Sorted by residual: dihedral pdb=" CA ASN B 574 " pdb=" C ASN B 574 " pdb=" N TYR B 575 " pdb=" CA TYR B 575 " ideal model delta harmonic sigma weight residual -180.00 -138.28 -41.72 0 5.00e+00 4.00e-02 6.96e+01 dihedral pdb=" CA ASN E 574 " pdb=" C ASN E 574 " pdb=" N TYR E 575 " pdb=" CA TYR E 575 " ideal model delta harmonic sigma weight residual -180.00 -138.50 -41.50 0 5.00e+00 4.00e-02 6.89e+01 dihedral pdb=" CA ASN C 574 " pdb=" C ASN C 574 " pdb=" N TYR C 575 " pdb=" CA TYR C 575 " ideal model delta harmonic sigma weight residual -180.00 -139.52 -40.48 0 5.00e+00 4.00e-02 6.55e+01 ... (remaining 17267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2836 0.032 - 0.063: 1047 0.063 - 0.095: 280 0.095 - 0.126: 134 0.126 - 0.158: 8 Chirality restraints: 4305 Sorted by residual: chirality pdb=" CA ARG D 708 " pdb=" N ARG D 708 " pdb=" C ARG D 708 " pdb=" CB ARG D 708 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CA VAL E 289 " pdb=" N VAL E 289 " pdb=" C VAL E 289 " pdb=" CB VAL E 289 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CB ILE A 558 " pdb=" CA ILE A 558 " pdb=" CG1 ILE A 558 " pdb=" CG2 ILE A 558 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 4302 not shown) Planarity restraints: 5155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 574 " 0.021 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C ASN D 574 " -0.076 2.00e-02 2.50e+03 pdb=" O ASN D 574 " 0.029 2.00e-02 2.50e+03 pdb=" N TYR D 575 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 574 " 0.021 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C ASN B 574 " -0.076 2.00e-02 2.50e+03 pdb=" O ASN B 574 " 0.029 2.00e-02 2.50e+03 pdb=" N TYR B 575 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 574 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C ASN A 574 " -0.070 2.00e-02 2.50e+03 pdb=" O ASN A 574 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR A 575 " 0.024 2.00e-02 2.50e+03 ... (remaining 5152 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 294 2.65 - 3.21: 26365 3.21 - 3.77: 45653 3.77 - 4.34: 61225 4.34 - 4.90: 100664 Nonbonded interactions: 234201 Sorted by model distance: nonbonded pdb=" OG SER A 593 " pdb=" O LEU A 598 " model vdw 2.085 3.040 nonbonded pdb=" NH2 ARG E 708 " pdb=" OE2 GLU E 711 " model vdw 2.169 3.120 nonbonded pdb=" OG SER B 593 " pdb=" O LEU B 598 " model vdw 2.186 3.040 nonbonded pdb=" O THR B 456 " pdb=" OG SER B 459 " model vdw 2.195 3.040 nonbonded pdb=" O PHE A 221 " pdb=" NH2 ARG A 225 " model vdw 2.196 3.120 ... (remaining 234196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.580 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.250 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 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 : 0.004 0.045 28435 Z= 0.201 Angle : 0.628 11.103 38605 Z= 0.361 Chirality : 0.038 0.158 4305 Planarity : 0.005 0.056 5155 Dihedral : 16.366 89.782 10670 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.32 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: 0.94 (0.14), residues: 3585 helix: 1.70 (0.12), residues: 1826 sheet: -0.54 (0.23), residues: 453 loop : -0.42 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 708 TYR 0.021 0.002 TYR C 420 PHE 0.017 0.002 PHE C 629 TRP 0.055 0.002 TRP A 205 HIS 0.005 0.001 HIS C 527 Details of bonding type rmsd covalent geometry : bond 0.00409 (28435) covalent geometry : angle 0.62753 (38605) hydrogen bonds : bond 0.14111 ( 1568) hydrogen bonds : angle 5.73617 ( 4485) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 542 PHE cc_start: 0.6744 (m-10) cc_final: 0.6412 (m-10) REVERT: D 582 SER cc_start: 0.8709 (t) cc_final: 0.8370 (m) REVERT: C 56 SER cc_start: 0.8863 (m) cc_final: 0.8601 (p) REVERT: C 195 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8285 (mt-10) REVERT: C 243 GLU cc_start: 0.6835 (pt0) cc_final: 0.6608 (pt0) REVERT: C 327 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8104 (ttpp) REVERT: C 498 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7035 (mt-10) REVERT: C 557 TYR cc_start: 0.6474 (m-80) cc_final: 0.6184 (m-80) REVERT: C 581 ASP cc_start: 0.7496 (p0) cc_final: 0.7193 (p0) REVERT: B 91 LEU cc_start: 0.8241 (tp) cc_final: 0.7962 (tt) REVERT: B 251 ARG cc_start: 0.8141 (mtt180) cc_final: 0.7800 (ttm110) REVERT: B 527 HIS cc_start: 0.6381 (t-90) cc_final: 0.5874 (p90) REVERT: B 641 THR cc_start: 0.8574 (p) cc_final: 0.8330 (t) REVERT: B 679 GLN cc_start: 0.7215 (mt0) cc_final: 0.6947 (mm-40) REVERT: A 312 LEU cc_start: 0.6523 (mt) cc_final: 0.6155 (mp) REVERT: A 356 MET cc_start: 0.7304 (ppp) cc_final: 0.7047 (ppp) REVERT: A 403 TRP cc_start: 0.8121 (t60) cc_final: 0.7916 (t60) REVERT: A 544 LYS cc_start: 0.7325 (tppt) cc_final: 0.6812 (tptp) REVERT: A 688 ARG cc_start: 0.7170 (mtp180) cc_final: 0.6592 (mmm-85) REVERT: A 698 LYS cc_start: 0.7698 (mttm) cc_final: 0.7430 (mmmt) REVERT: A 704 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7244 (pp20) REVERT: A 709 LEU cc_start: 0.7623 (mt) cc_final: 0.7384 (mt) REVERT: E 293 ASN cc_start: 0.7867 (p0) cc_final: 0.7459 (p0) REVERT: E 600 LEU cc_start: 0.6900 (mt) cc_final: 0.6658 (mt) REVERT: E 688 ARG cc_start: 0.5430 (mtp180) cc_final: 0.5165 (mpt180) outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.2171 time to fit residues: 133.2291 Evaluate side-chains 185 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 357 GLN C 303 HIS A 60 HIS A 160 ASN A 208 HIS E 130 GLN E 396 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.175614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.140372 restraints weight = 55295.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.138065 restraints weight = 52600.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.140129 restraints weight = 48522.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.139828 restraints weight = 34784.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.140529 restraints weight = 30158.325| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28435 Z= 0.137 Angle : 0.575 8.449 38605 Z= 0.293 Chirality : 0.039 0.181 4305 Planarity : 0.005 0.050 5155 Dihedral : 4.229 42.072 4000 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.37 % Favored : 97.52 % Rotamer: Outliers : 0.74 % Allowed : 6.23 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: 0.95 (0.14), residues: 3585 helix: 1.61 (0.12), residues: 1846 sheet: -0.45 (0.24), residues: 430 loop : -0.32 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 657 TYR 0.034 0.002 TYR C 5 PHE 0.019 0.002 PHE B 221 TRP 0.025 0.002 TRP A 205 HIS 0.009 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00300 (28435) covalent geometry : angle 0.57458 (38605) hydrogen bonds : bond 0.04162 ( 1568) hydrogen bonds : angle 4.66131 ( 4485) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 557 TYR cc_start: 0.6472 (m-80) cc_final: 0.6230 (m-80) REVERT: C 581 ASP cc_start: 0.7445 (p0) cc_final: 0.7095 (p0) REVERT: B 1 MET cc_start: 0.7042 (ppp) cc_final: 0.6392 (ptt) REVERT: B 91 LEU cc_start: 0.8464 (tp) cc_final: 0.8258 (tt) REVERT: B 108 LEU cc_start: 0.7835 (mt) cc_final: 0.7564 (mt) REVERT: A 464 ILE cc_start: 0.8534 (mt) cc_final: 0.8221 (mt) REVERT: A 544 LYS cc_start: 0.7720 (tppt) cc_final: 0.7182 (tptp) REVERT: A 688 ARG cc_start: 0.7053 (mtp180) cc_final: 0.6830 (mmm-85) REVERT: E 603 ASP cc_start: 0.6587 (m-30) cc_final: 0.6362 (t0) outliers start: 21 outliers final: 12 residues processed: 265 average time/residue: 0.1844 time to fit residues: 74.8892 Evaluate side-chains 170 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 546 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 187 optimal weight: 0.3980 chunk 78 optimal weight: 6.9990 chunk 328 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 304 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 329 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 341 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 HIS B 573 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.169529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.125635 restraints weight = 55471.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.124183 restraints weight = 38491.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.124608 restraints weight = 30479.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.125338 restraints weight = 29365.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.125311 restraints weight = 26332.923| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28435 Z= 0.212 Angle : 0.615 14.278 38605 Z= 0.307 Chirality : 0.040 0.169 4305 Planarity : 0.005 0.060 5155 Dihedral : 4.233 40.462 4000 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.40 % Favored : 97.49 % Rotamer: Outliers : 1.37 % Allowed : 9.05 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: 0.79 (0.14), residues: 3585 helix: 1.44 (0.12), residues: 1854 sheet: -0.62 (0.23), residues: 451 loop : -0.28 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 665 TYR 0.030 0.002 TYR B 575 PHE 0.029 0.002 PHE E 571 TRP 0.022 0.002 TRP C 290 HIS 0.005 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00490 (28435) covalent geometry : angle 0.61450 (38605) hydrogen bonds : bond 0.04157 ( 1568) hydrogen bonds : angle 4.60373 ( 4485) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 LEU cc_start: 0.8300 (tp) cc_final: 0.7837 (mt) REVERT: C 327 LYS cc_start: 0.8504 (ttpt) cc_final: 0.8219 (ttpp) REVERT: C 581 ASP cc_start: 0.7299 (p0) cc_final: 0.6987 (p0) REVERT: B 91 LEU cc_start: 0.8557 (tp) cc_final: 0.8226 (tt) REVERT: B 108 LEU cc_start: 0.8028 (mt) cc_final: 0.7802 (mt) REVERT: A 193 GLU cc_start: 0.7288 (tp30) cc_final: 0.6123 (mm-30) REVERT: A 312 LEU cc_start: 0.7731 (mt) cc_final: 0.7526 (mp) REVERT: A 544 LYS cc_start: 0.7738 (tppt) cc_final: 0.7139 (tptp) REVERT: A 657 ARG cc_start: 0.7314 (mmp80) cc_final: 0.7111 (mmp80) REVERT: A 688 ARG cc_start: 0.7213 (mtp180) cc_final: 0.6849 (mmm-85) REVERT: E 603 ASP cc_start: 0.7234 (m-30) cc_final: 0.6805 (t0) outliers start: 39 outliers final: 22 residues processed: 197 average time/residue: 0.1746 time to fit residues: 53.1335 Evaluate side-chains 160 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 582 SER Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 546 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 299 optimal weight: 20.0000 chunk 175 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 293 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 285 optimal weight: 0.0050 chunk 275 optimal weight: 2.9990 chunk 351 optimal weight: 20.0000 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 HIS D 573 GLN C 696 GLN B 573 GLN A 208 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.169966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.135016 restraints weight = 54696.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.131934 restraints weight = 56240.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.133687 restraints weight = 49356.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.134058 restraints weight = 33291.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.134274 restraints weight = 30876.830| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28435 Z= 0.161 Angle : 0.556 12.288 38605 Z= 0.278 Chirality : 0.038 0.165 4305 Planarity : 0.004 0.060 5155 Dihedral : 4.127 39.845 4000 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.18 % Favored : 97.71 % Rotamer: Outliers : 1.58 % Allowed : 10.25 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 0.87 (0.14), residues: 3585 helix: 1.52 (0.12), residues: 1850 sheet: -0.50 (0.23), residues: 440 loop : -0.31 (0.18), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 232 TYR 0.029 0.002 TYR B 575 PHE 0.019 0.002 PHE A 218 TRP 0.025 0.002 TRP E 205 HIS 0.011 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00366 (28435) covalent geometry : angle 0.55592 (38605) hydrogen bonds : bond 0.03856 ( 1568) hydrogen bonds : angle 4.42810 ( 4485) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 LEU cc_start: 0.8264 (tp) cc_final: 0.7972 (mt) REVERT: D 488 ARG cc_start: 0.6481 (mtm-85) cc_final: 0.6128 (mtm-85) REVERT: C 498 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6478 (mt-10) REVERT: C 581 ASP cc_start: 0.7557 (p0) cc_final: 0.7229 (p0) REVERT: B 91 LEU cc_start: 0.8482 (tp) cc_final: 0.8186 (tt) REVERT: B 108 LEU cc_start: 0.7878 (mt) cc_final: 0.7652 (mt) REVERT: A 312 LEU cc_start: 0.7978 (mt) cc_final: 0.7755 (mp) REVERT: A 532 ASP cc_start: 0.6123 (t0) cc_final: 0.5904 (t0) REVERT: A 544 LYS cc_start: 0.7571 (tppt) cc_final: 0.7030 (tptp) REVERT: A 688 ARG cc_start: 0.7059 (mtp180) cc_final: 0.6839 (mmm-85) REVERT: E 527 HIS cc_start: 0.6400 (t70) cc_final: 0.5506 (m-70) outliers start: 45 outliers final: 22 residues processed: 190 average time/residue: 0.1680 time to fit residues: 52.0123 Evaluate side-chains 153 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 546 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 295 optimal weight: 9.9990 chunk 272 optimal weight: 0.8980 chunk 211 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 281 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 310 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 HIS C 602 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.161490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.117139 restraints weight = 54414.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.117048 restraints weight = 38091.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.116812 restraints weight = 27323.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.117207 restraints weight = 27195.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.117368 restraints weight = 25193.877| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 28435 Z= 0.202 Angle : 0.588 12.855 38605 Z= 0.292 Chirality : 0.040 0.186 4305 Planarity : 0.004 0.048 5155 Dihedral : 4.150 40.057 4000 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Rotamer: Outliers : 1.90 % Allowed : 11.02 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.85 (0.14), residues: 3585 helix: 1.49 (0.12), residues: 1850 sheet: -0.66 (0.23), residues: 460 loop : -0.21 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 556 TYR 0.028 0.002 TYR D 575 PHE 0.020 0.002 PHE D 472 TRP 0.040 0.002 TRP E 205 HIS 0.020 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00466 (28435) covalent geometry : angle 0.58808 (38605) hydrogen bonds : bond 0.03898 ( 1568) hydrogen bonds : angle 4.45634 ( 4485) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 144 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 488 ARG cc_start: 0.6518 (mtm-85) cc_final: 0.6053 (mtm-85) REVERT: D 542 PHE cc_start: 0.7148 (m-10) cc_final: 0.6887 (m-10) REVERT: C 498 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6540 (mt-10) REVERT: C 556 ARG cc_start: 0.6232 (mmm-85) cc_final: 0.6007 (mmm-85) REVERT: C 581 ASP cc_start: 0.7423 (p0) cc_final: 0.7120 (p0) REVERT: B 91 LEU cc_start: 0.8585 (tp) cc_final: 0.8210 (tt) REVERT: B 327 LYS cc_start: 0.7534 (pttt) cc_final: 0.7083 (pttm) REVERT: A 193 GLU cc_start: 0.7308 (tp30) cc_final: 0.6155 (mm-30) REVERT: A 312 LEU cc_start: 0.7615 (mt) cc_final: 0.7350 (mp) REVERT: A 532 ASP cc_start: 0.6079 (t0) cc_final: 0.5829 (t0) REVERT: A 544 LYS cc_start: 0.7625 (tppt) cc_final: 0.6987 (tptp) REVERT: A 554 ARG cc_start: 0.6553 (mtm-85) cc_final: 0.6153 (ttp80) REVERT: A 688 ARG cc_start: 0.7308 (mtp180) cc_final: 0.7017 (mmm-85) REVERT: E 520 ARG cc_start: 0.4957 (mmm160) cc_final: 0.4593 (tpt90) REVERT: E 603 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6614 (t70) outliers start: 54 outliers final: 33 residues processed: 187 average time/residue: 0.1703 time to fit residues: 50.3367 Evaluate side-chains 169 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 526 ASP Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 603 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 265 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 245 optimal weight: 20.0000 chunk 302 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 chunk 229 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 612 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.159007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.112219 restraints weight = 54650.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.110948 restraints weight = 41532.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.111891 restraints weight = 31913.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.112368 restraints weight = 27867.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.112770 restraints weight = 26304.972| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 28435 Z= 0.309 Angle : 0.703 12.623 38605 Z= 0.351 Chirality : 0.043 0.192 4305 Planarity : 0.005 0.053 5155 Dihedral : 4.510 39.717 4000 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.29 % Favored : 96.57 % Rotamer: Outliers : 2.29 % Allowed : 11.80 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.44 (0.14), residues: 3585 helix: 1.20 (0.12), residues: 1850 sheet: -0.77 (0.24), residues: 426 loop : -0.53 (0.18), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 516 TYR 0.029 0.003 TYR C 420 PHE 0.027 0.003 PHE D 571 TRP 0.025 0.002 TRP E 205 HIS 0.008 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00721 (28435) covalent geometry : angle 0.70287 (38605) hydrogen bonds : bond 0.04312 ( 1568) hydrogen bonds : angle 4.77959 ( 4485) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 146 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.7249 (tmm) cc_final: 0.6966 (pmm) REVERT: D 135 PHE cc_start: 0.7770 (m-10) cc_final: 0.6688 (m-10) REVERT: D 488 ARG cc_start: 0.6515 (mtm-85) cc_final: 0.6266 (mtm-85) REVERT: D 542 PHE cc_start: 0.7234 (m-10) cc_final: 0.6976 (m-10) REVERT: C 581 ASP cc_start: 0.7565 (p0) cc_final: 0.7217 (p0) REVERT: B 108 LEU cc_start: 0.8124 (mt) cc_final: 0.7921 (tp) REVERT: B 327 LYS cc_start: 0.7631 (pttt) cc_final: 0.7168 (pttm) REVERT: B 405 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8610 (mm) REVERT: A 193 GLU cc_start: 0.7422 (tp30) cc_final: 0.6188 (mm-30) REVERT: A 312 LEU cc_start: 0.7542 (mt) cc_final: 0.7280 (mp) REVERT: A 544 LYS cc_start: 0.7667 (tppt) cc_final: 0.7060 (tptp) REVERT: A 554 ARG cc_start: 0.6585 (mtm-85) cc_final: 0.6170 (ttp80) REVERT: A 688 ARG cc_start: 0.7269 (mtp180) cc_final: 0.7023 (mmm-85) REVERT: E 520 ARG cc_start: 0.4963 (mmm160) cc_final: 0.4565 (tpt90) REVERT: E 542 PHE cc_start: 0.6169 (OUTLIER) cc_final: 0.5085 (p90) REVERT: E 603 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6662 (t70) outliers start: 65 outliers final: 46 residues processed: 203 average time/residue: 0.1662 time to fit residues: 53.0921 Evaluate side-chains 180 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 526 ASP Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 688 ARG Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 542 PHE Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 603 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 214 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 257 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 272 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 334 optimal weight: 10.0000 chunk 313 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 527 HIS B 527 HIS A 208 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.161903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.126630 restraints weight = 54122.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.123541 restraints weight = 51241.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.125113 restraints weight = 46357.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.125944 restraints weight = 30761.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.126541 restraints weight = 27926.331| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28435 Z= 0.127 Angle : 0.546 14.344 38605 Z= 0.270 Chirality : 0.038 0.157 4305 Planarity : 0.004 0.050 5155 Dihedral : 4.142 38.873 4000 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.12 % Favored : 97.77 % Rotamer: Outliers : 1.55 % Allowed : 12.99 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.73 (0.14), residues: 3585 helix: 1.45 (0.12), residues: 1878 sheet: -0.63 (0.24), residues: 430 loop : -0.47 (0.18), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 139 TYR 0.027 0.002 TYR D 575 PHE 0.015 0.001 PHE D 571 TRP 0.044 0.002 TRP E 205 HIS 0.012 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00279 (28435) covalent geometry : angle 0.54561 (38605) hydrogen bonds : bond 0.03707 ( 1568) hydrogen bonds : angle 4.35777 ( 4485) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: D 1 MET cc_start: 0.7088 (tmm) cc_final: 0.6725 (pmm) REVERT: C 581 ASP cc_start: 0.7430 (p0) cc_final: 0.7068 (p0) REVERT: B 327 LYS cc_start: 0.7336 (pttt) cc_final: 0.6965 (pttp) REVERT: B 405 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8566 (mm) REVERT: A 193 GLU cc_start: 0.7068 (tp30) cc_final: 0.6156 (mm-30) REVERT: E 520 ARG cc_start: 0.4965 (mmm160) cc_final: 0.4655 (tpt90) REVERT: E 542 PHE cc_start: 0.5872 (OUTLIER) cc_final: 0.4542 (m-10) REVERT: E 603 ASP cc_start: 0.6825 (OUTLIER) cc_final: 0.6543 (t70) outliers start: 44 outliers final: 28 residues processed: 186 average time/residue: 0.1668 time to fit residues: 50.1167 Evaluate side-chains 162 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 542 PHE Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 603 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 227 optimal weight: 30.0000 chunk 85 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 351 optimal weight: 30.0000 chunk 262 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 335 optimal weight: 7.9990 chunk 298 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 413 GLN E 668 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.158789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.110643 restraints weight = 55240.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.110937 restraints weight = 36343.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.110863 restraints weight = 26652.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.111617 restraints weight = 28042.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.111732 restraints weight = 24416.632| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 28435 Z= 0.323 Angle : 0.713 14.334 38605 Z= 0.358 Chirality : 0.044 0.220 4305 Planarity : 0.006 0.049 5155 Dihedral : 4.509 38.575 4000 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.54 % Favored : 96.35 % Rotamer: Outliers : 1.94 % Allowed : 13.20 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.38 (0.14), residues: 3585 helix: 1.18 (0.12), residues: 1844 sheet: -0.90 (0.24), residues: 426 loop : -0.57 (0.18), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 139 TYR 0.029 0.003 TYR C 420 PHE 0.026 0.002 PHE D 472 TRP 0.048 0.003 TRP E 205 HIS 0.028 0.002 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00757 (28435) covalent geometry : angle 0.71324 (38605) hydrogen bonds : bond 0.04310 ( 1568) hydrogen bonds : angle 4.77229 ( 4485) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 129 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.7303 (tmm) cc_final: 0.6878 (pmm) REVERT: D 488 ARG cc_start: 0.6554 (mtm-85) cc_final: 0.6213 (mtm-85) REVERT: B 108 LEU cc_start: 0.8105 (mt) cc_final: 0.7899 (tp) REVERT: B 405 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8618 (mm) REVERT: A 193 GLU cc_start: 0.7442 (tp30) cc_final: 0.7218 (tm-30) REVERT: A 544 LYS cc_start: 0.7633 (tppt) cc_final: 0.6927 (tptp) REVERT: E 520 ARG cc_start: 0.4743 (mmm160) cc_final: 0.4310 (tpt90) REVERT: E 542 PHE cc_start: 0.6144 (OUTLIER) cc_final: 0.4364 (m-10) REVERT: E 603 ASP cc_start: 0.7203 (OUTLIER) cc_final: 0.6663 (t70) outliers start: 55 outliers final: 40 residues processed: 177 average time/residue: 0.1592 time to fit residues: 46.8133 Evaluate side-chains 162 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 542 PHE Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 671 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 117 optimal weight: 0.9990 chunk 351 optimal weight: 30.0000 chunk 209 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 287 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 330 optimal weight: 20.0000 chunk 216 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.162169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.117179 restraints weight = 54408.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.117774 restraints weight = 39292.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.117880 restraints weight = 26413.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.118014 restraints weight = 26514.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.118331 restraints weight = 25252.294| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28435 Z= 0.119 Angle : 0.552 15.627 38605 Z= 0.273 Chirality : 0.038 0.157 4305 Planarity : 0.004 0.050 5155 Dihedral : 4.142 37.835 4000 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.98 % Favored : 97.91 % Rotamer: Outliers : 1.16 % Allowed : 14.01 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.70 (0.14), residues: 3585 helix: 1.45 (0.12), residues: 1872 sheet: -0.74 (0.24), residues: 432 loop : -0.47 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 516 TYR 0.026 0.002 TYR D 575 PHE 0.021 0.001 PHE D 135 TRP 0.036 0.002 TRP E 205 HIS 0.004 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00262 (28435) covalent geometry : angle 0.55159 (38605) hydrogen bonds : bond 0.03653 ( 1568) hydrogen bonds : angle 4.31937 ( 4485) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.7199 (tmm) cc_final: 0.6738 (pmm) REVERT: D 196 VAL cc_start: 0.9165 (m) cc_final: 0.8937 (p) REVERT: D 291 SER cc_start: 0.7850 (p) cc_final: 0.7305 (m) REVERT: D 623 ASN cc_start: 0.7422 (p0) cc_final: 0.7171 (p0) REVERT: B 405 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8553 (mm) REVERT: A 193 GLU cc_start: 0.7382 (tp30) cc_final: 0.6170 (mm-30) REVERT: E 520 ARG cc_start: 0.4762 (mmm160) cc_final: 0.4344 (tpt90) REVERT: E 542 PHE cc_start: 0.6047 (OUTLIER) cc_final: 0.5042 (p90) REVERT: E 603 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6636 (t70) outliers start: 33 outliers final: 23 residues processed: 167 average time/residue: 0.1639 time to fit residues: 44.7341 Evaluate side-chains 158 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 542 PHE Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 603 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 79 optimal weight: 0.0040 chunk 73 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 231 optimal weight: 30.0000 chunk 84 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 157 optimal weight: 30.0000 chunk 118 optimal weight: 0.0970 chunk 350 optimal weight: 7.9990 chunk 325 optimal weight: 6.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.160838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.123409 restraints weight = 53445.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.121144 restraints weight = 48142.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.122801 restraints weight = 36461.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.123108 restraints weight = 27539.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.123238 restraints weight = 25363.658| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28435 Z= 0.103 Angle : 0.525 15.830 38605 Z= 0.258 Chirality : 0.037 0.161 4305 Planarity : 0.004 0.074 5155 Dihedral : 3.906 36.708 4000 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.01 % Favored : 97.88 % Rotamer: Outliers : 0.95 % Allowed : 14.23 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.98 (0.14), residues: 3585 helix: 1.66 (0.12), residues: 1876 sheet: -0.70 (0.24), residues: 460 loop : -0.26 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 280 TYR 0.030 0.002 TYR A 227 PHE 0.018 0.001 PHE B 278 TRP 0.029 0.002 TRP E 205 HIS 0.014 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00223 (28435) covalent geometry : angle 0.52530 (38605) hydrogen bonds : bond 0.03408 ( 1568) hydrogen bonds : angle 4.11421 ( 4485) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.7107 (tmm) cc_final: 0.6767 (pmm) REVERT: D 196 VAL cc_start: 0.9100 (m) cc_final: 0.8862 (p) REVERT: D 291 SER cc_start: 0.7709 (p) cc_final: 0.7185 (m) REVERT: D 623 ASN cc_start: 0.7378 (p0) cc_final: 0.7082 (p0) REVERT: D 641 THR cc_start: 0.7966 (p) cc_final: 0.7552 (t) REVERT: B 557 TYR cc_start: 0.8018 (m-80) cc_final: 0.7567 (m-80) REVERT: A 193 GLU cc_start: 0.7073 (tp30) cc_final: 0.6088 (mm-30) REVERT: A 271 TYR cc_start: 0.5314 (m-80) cc_final: 0.4824 (m-80) REVERT: A 464 ILE cc_start: 0.8568 (mt) cc_final: 0.8181 (mt) REVERT: E 520 ARG cc_start: 0.4913 (mmm160) cc_final: 0.4255 (mmt-90) REVERT: E 542 PHE cc_start: 0.5899 (OUTLIER) cc_final: 0.4929 (p90) REVERT: E 603 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6550 (t70) outliers start: 27 outliers final: 21 residues processed: 181 average time/residue: 0.1558 time to fit residues: 46.9811 Evaluate side-chains 162 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 542 PHE Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 603 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 112 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 352 optimal weight: 0.7980 chunk 202 optimal weight: 6.9990 chunk 231 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 chunk 227 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 623 ASN A 208 HIS A 253 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.163507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.128744 restraints weight = 54133.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.125383 restraints weight = 52681.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.126976 restraints weight = 48050.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.128091 restraints weight = 30280.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.128288 restraints weight = 27492.347| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28435 Z= 0.112 Angle : 0.539 15.414 38605 Z= 0.261 Chirality : 0.038 0.202 4305 Planarity : 0.004 0.055 5155 Dihedral : 3.863 36.456 4000 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.65 % Favored : 98.24 % Rotamer: Outliers : 0.92 % Allowed : 14.65 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 1.03 (0.14), residues: 3585 helix: 1.68 (0.12), residues: 1876 sheet: -0.71 (0.24), residues: 462 loop : -0.18 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 280 TYR 0.023 0.002 TYR D 575 PHE 0.024 0.001 PHE C 214 TRP 0.038 0.002 TRP E 205 HIS 0.018 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00250 (28435) covalent geometry : angle 0.53933 (38605) hydrogen bonds : bond 0.03403 ( 1568) hydrogen bonds : angle 4.11742 ( 4485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3829.26 seconds wall clock time: 66 minutes 59.37 seconds (4019.37 seconds total)