Starting phenix.real_space_refine on Thu Feb 5 13:52:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9huj_52415/02_2026/9huj_52415_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9huj_52415/02_2026/9huj_52415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9huj_52415/02_2026/9huj_52415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9huj_52415/02_2026/9huj_52415.map" model { file = "/net/cci-nas-00/data/ceres_data/9huj_52415/02_2026/9huj_52415_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9huj_52415/02_2026/9huj_52415_neut.cif" } resolution = 3.57 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= 0.001 sd= 0.023 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 120 5.16 5 C 11128 2.51 5 N 2923 2.21 5 O 3239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17410 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4460 Classifications: {'peptide': 570} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 529} Chain breaks: 9 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4528 Classifications: {'peptide': 579} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 538} Chain breaks: 9 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4143 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 38, 'TRANS': 491} Chain breaks: 14 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 4272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4272 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 510} Chain breaks: 14 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.25, per 1000 atoms: 0.24 Number of scatterers: 17410 At special positions: 0 Unit cell: (125.149, 132.759, 164.046, 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 120 16.00 O 3239 8.00 N 2923 7.00 C 11128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 889.5 milliseconds 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4170 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 28 sheets defined 16.5% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 317 through 330 removed outlier: 3.559A pdb=" N LYS A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 444 through 454 removed outlier: 3.571A pdb=" N GLN A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 474 removed outlier: 3.735A pdb=" N GLU A 474 " --> pdb=" O HIS A 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 471 through 474' Processing helix chain 'A' and resid 494 through 506 removed outlier: 3.760A pdb=" N TYR A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 532 Processing helix chain 'A' and resid 534 through 558 removed outlier: 3.880A pdb=" N HIS A 538 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TRP A 548 " --> pdb=" O ARG A 544 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 611 through 621 removed outlier: 4.254A pdb=" N VAL A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N CYS A 617 " --> pdb=" O GLU A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 192 through 195 removed outlier: 3.713A pdb=" N THR B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 192 through 195' Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 317 through 329 Processing helix chain 'B' and resid 444 through 454 Processing helix chain 'B' and resid 495 through 507 Processing helix chain 'B' and resid 525 through 530 Processing helix chain 'B' and resid 532 through 557 removed outlier: 3.778A pdb=" N SER B 540 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 546 " --> pdb=" O VAL B 542 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 621 removed outlier: 4.148A pdb=" N VAL B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N CYS B 617 " --> pdb=" O GLU B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 624 No H-bonds generated for 'chain 'B' and resid 622 through 624' Processing helix chain 'B' and resid 657 through 661 Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.678A pdb=" N SER C 31 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 removed outlier: 3.789A pdb=" N ASP C 209 " --> pdb=" O ARG C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 326 removed outlier: 4.199A pdb=" N THR C 325 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU C 326 " --> pdb=" O SER C 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 321 through 326' Processing helix chain 'C' and resid 327 through 331 Processing helix chain 'C' and resid 445 through 453 removed outlier: 3.506A pdb=" N PHE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU C 451 " --> pdb=" O LEU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 497 removed outlier: 3.658A pdb=" N SER C 496 " --> pdb=" O SER C 493 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS C 497 " --> pdb=" O PRO C 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 493 through 497' Processing helix chain 'C' and resid 498 through 503 removed outlier: 4.112A pdb=" N GLU C 503 " --> pdb=" O LYS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 508 Processing helix chain 'C' and resid 525 through 531 removed outlier: 3.666A pdb=" N ILE C 529 " --> pdb=" O LYS C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 547 removed outlier: 3.631A pdb=" N ASN C 539 " --> pdb=" O LEU C 535 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE C 541 " --> pdb=" O GLU C 537 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL C 542 " --> pdb=" O HIS C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 558 Processing helix chain 'C' and resid 610 through 618 removed outlier: 3.589A pdb=" N GLU C 614 " --> pdb=" O CYS C 610 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS C 615 " --> pdb=" O CYS C 611 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL C 616 " --> pdb=" O LEU C 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 33 removed outlier: 3.869A pdb=" N ALA D 33 " --> pdb=" O CYS D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.949A pdb=" N GLN D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 174 through 179' Processing helix chain 'D' and resid 204 through 209 removed outlier: 4.194A pdb=" N ASP D 209 " --> pdb=" O ARG D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.715A pdb=" N ALA D 330 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 453 removed outlier: 3.521A pdb=" N GLN D 448 " --> pdb=" O HIS D 444 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU D 451 " --> pdb=" O LEU D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 507 removed outlier: 3.599A pdb=" N PHE D 501 " --> pdb=" O CYS D 497 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN D 502 " --> pdb=" O TYR D 498 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU D 503 " --> pdb=" O LYS D 499 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN D 504 " --> pdb=" O LEU D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.852A pdb=" N PHE D 541 " --> pdb=" O GLU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 556 removed outlier: 4.508A pdb=" N GLU D 556 " --> pdb=" O LEU D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 617 removed outlier: 3.535A pdb=" N VAL D 616 " --> pdb=" O LEU D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 619 No H-bonds generated for 'chain 'D' and resid 618 through 619' Processing helix chain 'D' and resid 620 through 624 Processing helix chain 'D' and resid 657 through 661 removed outlier: 3.866A pdb=" N ASN D 660 " --> pdb=" O LYS D 657 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET D 661 " --> pdb=" O TRP D 658 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 657 through 661' Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 removed outlier: 6.455A pdb=" N ILE A 7 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR A 25 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL A 76 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20 removed outlier: 3.540A pdb=" N ALA A 17 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN A 90 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 20 removed outlier: 3.540A pdb=" N ALA A 17 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 187 " --> pdb=" O HIS A 245 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A 245 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL A 213 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.804A pdb=" N VAL A 283 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP A 273 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE A 285 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A 199 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 297 through 298 Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 334 removed outlier: 3.992A pdb=" N LYS A 333 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 307 " --> pdb=" O ARG A 650 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'A' and resid 416 through 418 Processing sheet with id=AA9, first strand: chain 'A' and resid 476 through 480 Processing sheet with id=AB1, first strand: chain 'A' and resid 571 through 573 Processing sheet with id=AB2, first strand: chain 'A' and resid 590 through 592 removed outlier: 6.432A pdb=" N LEU A 596 " --> pdb=" O THR A 628 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE A 630 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE A 598 " --> pdb=" O ILE A 630 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 15 through 20 removed outlier: 6.132A pdb=" N THR B 15 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR B 111 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA B 17 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL B 113 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N CYS B 19 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE B 115 " --> pdb=" O CYS B 19 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B 90 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 15 through 20 removed outlier: 6.132A pdb=" N THR B 15 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR B 111 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA B 17 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL B 113 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N CYS B 19 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE B 115 " --> pdb=" O CYS B 19 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS B 118 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 184 " --> pdb=" O CYS B 118 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 229 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLN B 215 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL B 227 " --> pdb=" O GLN B 215 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 48 through 50 Processing sheet with id=AB6, first strand: chain 'B' and resid 148 through 150 removed outlier: 6.170A pdb=" N VAL B 283 " --> pdb=" O ASP B 273 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP B 273 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE B 285 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU B 199 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 333 through 336 removed outlier: 4.072A pdb=" N LYS B 333 " --> pdb=" O GLN B 306 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG B 650 " --> pdb=" O GLN B 306 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL B 308 " --> pdb=" O ASN B 648 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN B 648 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 352 through 358 removed outlier: 3.674A pdb=" N GLU B 353 " --> pdb=" O PHE B 368 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE B 368 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 366 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL B 392 " --> pdb=" O PRO B 365 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL B 367 " --> pdb=" O VAL B 392 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 411 through 412 removed outlier: 6.591A pdb=" N ILE B 428 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU B 462 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE B 430 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 416 through 417 removed outlier: 3.521A pdb=" N VAL B 416 " --> pdb=" O TYR B 423 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 476 through 480 Processing sheet with id=AC3, first strand: chain 'B' and resid 590 through 592 Processing sheet with id=AC4, first strand: chain 'C' and resid 50 through 51 removed outlier: 4.046A pdb=" N ASP C 51 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR C 77 " --> pdb=" O ASP C 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'C' and resid 429 through 432 Processing sheet with id=AC7, first strand: chain 'D' and resid 305 through 310 Processing sheet with id=AC8, first strand: chain 'D' and resid 416 through 418 removed outlier: 3.574A pdb=" N LYS D 421 " --> pdb=" O VAL D 418 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 429 through 432 Processing sheet with id=AD1, first strand: chain 'D' and resid 491 through 493 removed outlier: 6.522A pdb=" N LEU D 491 " --> pdb=" O ILE D 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 333 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.24: 2090 1.24 - 1.53: 14316 1.53 - 1.82: 1371 1.82 - 2.12: 0 2.12 - 2.41: 1 Bond restraints: 17778 Sorted by residual: bond pdb=" CB PRO A 601 " pdb=" CG PRO A 601 " ideal model delta sigma weight residual 1.492 2.412 -0.920 5.00e-02 4.00e+02 3.38e+02 bond pdb=" CG PRO A 601 " pdb=" CD PRO A 601 " ideal model delta sigma weight residual 1.503 0.943 0.560 3.40e-02 8.65e+02 2.71e+02 bond pdb=" N PRO A 601 " pdb=" CA PRO A 601 " ideal model delta sigma weight residual 1.469 1.355 0.114 1.28e-02 6.10e+03 7.91e+01 bond pdb=" N PRO A 601 " pdb=" CD PRO A 601 " ideal model delta sigma weight residual 1.473 1.554 -0.081 1.40e-02 5.10e+03 3.34e+01 bond pdb=" CA PRO A 601 " pdb=" CB PRO A 601 " ideal model delta sigma weight residual 1.533 1.494 0.039 1.42e-02 4.96e+03 7.67e+00 ... (remaining 17773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.22: 24098 21.22 - 42.43: 0 42.43 - 63.65: 0 63.65 - 84.87: 0 84.87 - 106.08: 1 Bond angle restraints: 24099 Sorted by residual: angle pdb=" CB PRO A 601 " pdb=" CG PRO A 601 " pdb=" CD PRO A 601 " ideal model delta sigma weight residual 106.10 0.02 106.08 3.20e+00 9.77e-02 1.10e+03 angle pdb=" N PRO A 601 " pdb=" CA PRO A 601 " pdb=" CB PRO A 601 " ideal model delta sigma weight residual 103.25 88.00 15.25 1.05e+00 9.07e-01 2.11e+02 angle pdb=" CA PRO A 601 " pdb=" N PRO A 601 " pdb=" CD PRO A 601 " ideal model delta sigma weight residual 112.00 92.49 19.51 1.40e+00 5.10e-01 1.94e+02 angle pdb=" CA PRO A 601 " pdb=" CB PRO A 601 " pdb=" CG PRO A 601 " ideal model delta sigma weight residual 104.50 90.58 13.92 1.90e+00 2.77e-01 5.37e+01 angle pdb=" N ASN D 409 " pdb=" CA ASN D 409 " pdb=" C ASN D 409 " ideal model delta sigma weight residual 110.61 116.72 -6.11 1.25e+00 6.40e-01 2.39e+01 ... (remaining 24094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9518 17.93 - 35.86: 949 35.86 - 53.79: 214 53.79 - 71.71: 39 71.71 - 89.64: 13 Dihedral angle restraints: 10733 sinusoidal: 4341 harmonic: 6392 Sorted by residual: dihedral pdb=" N PRO A 601 " pdb=" C PRO A 601 " pdb=" CA PRO A 601 " pdb=" CB PRO A 601 " ideal model delta harmonic sigma weight residual 115.10 97.88 17.22 0 2.50e+00 1.60e-01 4.74e+01 dihedral pdb=" CA SER D 406 " pdb=" C SER D 406 " pdb=" N PHE D 407 " pdb=" CA PHE D 407 " ideal model delta harmonic sigma weight residual 180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ASN C 660 " pdb=" C ASN C 660 " pdb=" N MET C 661 " pdb=" CA MET C 661 " ideal model delta harmonic sigma weight residual -180.00 -156.36 -23.64 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 10730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2147 0.050 - 0.099: 476 0.099 - 0.149: 121 0.149 - 0.199: 5 0.199 - 0.248: 3 Chirality restraints: 2752 Sorted by residual: chirality pdb=" CG LEU B 110 " pdb=" CB LEU B 110 " pdb=" CD1 LEU B 110 " pdb=" CD2 LEU B 110 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CG LEU A 150 " pdb=" CB LEU A 150 " pdb=" CD1 LEU A 150 " pdb=" CD2 LEU A 150 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CG LEU C 553 " pdb=" CB LEU C 553 " pdb=" CD1 LEU C 553 " pdb=" CD2 LEU C 553 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2749 not shown) Planarity restraints: 3077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 458 " -0.091 5.00e-02 4.00e+02 1.36e-01 2.97e+01 pdb=" N PRO A 459 " 0.236 5.00e-02 4.00e+02 pdb=" CA PRO A 459 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 459 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 600 " -0.099 5.00e-02 4.00e+02 1.36e-01 2.97e+01 pdb=" N PRO A 601 " 0.235 5.00e-02 4.00e+02 pdb=" CA PRO A 601 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 601 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 233 " 0.091 5.00e-02 4.00e+02 1.34e-01 2.86e+01 pdb=" N PRO A 234 " -0.231 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.068 5.00e-02 4.00e+02 ... (remaining 3074 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 154 2.61 - 3.18: 14211 3.18 - 3.76: 24327 3.76 - 4.33: 32628 4.33 - 4.90: 52544 Nonbonded interactions: 123864 Sorted by model distance: nonbonded pdb=" NH1 ARG A 555 " pdb=" OE1 GLN B 3 " model vdw 2.038 3.120 nonbonded pdb=" O ASN A 588 " pdb=" ND2 ASN A 588 " model vdw 2.099 3.120 nonbonded pdb=" NH1 ARG D 484 " pdb=" O PHE D 487 " model vdw 2.112 3.120 nonbonded pdb=" OG SER A 116 " pdb=" OG SER A 186 " model vdw 2.117 3.040 nonbonded pdb=" O LEU D 596 " pdb=" OG1 THR D 628 " model vdw 2.125 3.040 ... (remaining 123859 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 34 or resid 42 through 97 or resid 105 through 1 \ 28 or resid 136 through 155 or resid 173 through 191 or resid 198 through 216 or \ resid 229 through 234 or resid 248 through 273 or resid 279 through 311 or resi \ d 320 through 395 or resid 403 through 515 or resid 523 through 572 or resid 579 \ through 601 or resid 608 through 632 or resid 646 through 663)) selection = (chain 'B' and (resid 4 through 34 or resid 42 through 54 or resid 70 through 12 \ 8 or resid 136 through 155 or resid 157 or resid 174 through 191 or resid 198 th \ rough 216 or resid 229 through 234 or resid 248 through 273 or resid 279 through \ 311 or resid 320 through 337 or resid 350 through 370 or resid 388 through 515 \ or resid 523 through 572 or resid 579 through 601 or resid 608 through 663)) selection = (chain 'C' and (resid 4 through 34 or resid 42 through 54 or resid 70 through 97 \ or resid 105 through 155 or resid 157 through 311 or resid 320 through 337 or r \ esid 350 through 515 or resid 523 through 572 or resid 579 through 601 or resid \ 608 through 632 or resid 646 through 663)) selection = (chain 'D' and (resid 4 through 34 or resid 42 through 54 or resid 70 through 97 \ or resid 105 through 155 or resid 173 through 191 or resid 198 through 216 or r \ esid 229 through 234 or resid 248 through 273 or resid 279 through 311 or resid \ 320 through 337 or resid 350 through 515 or resid 523 through 632 or resid 646 t \ hrough 663)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.760 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 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 : 0.009 0.920 17778 Z= 0.265 Angle : 1.023 106.084 24099 Z= 0.481 Chirality : 0.045 0.248 2752 Planarity : 0.008 0.136 3077 Dihedral : 15.288 89.643 6563 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.30 % Allowed : 16.97 % Favored : 82.72 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.17), residues: 2125 helix: -1.35 (0.32), residues: 247 sheet: -1.01 (0.25), residues: 420 loop : -1.69 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 651 TYR 0.012 0.001 TYR D 423 PHE 0.037 0.002 PHE D 487 TRP 0.076 0.002 TRP B 139 HIS 0.005 0.001 HIS B 509 Details of bonding type rmsd covalent geometry : bond 0.00888 (17778) covalent geometry : angle 1.02300 (24099) hydrogen bonds : bond 0.21239 ( 328) hydrogen bonds : angle 7.92040 ( 888) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 253 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7649 (mt-10) REVERT: A 629 PHE cc_start: 0.7665 (m-10) cc_final: 0.7406 (m-10) REVERT: B 183 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7122 (mtp) REVERT: B 441 ARG cc_start: 0.7850 (mtm180) cc_final: 0.7557 (ptp-170) REVERT: B 601 PRO cc_start: 0.7781 (Cg_endo) cc_final: 0.7423 (Cg_exo) REVERT: C 467 LEU cc_start: 0.3979 (mt) cc_final: 0.2708 (mt) outliers start: 6 outliers final: 3 residues processed: 254 average time/residue: 0.1382 time to fit residues: 52.7906 Evaluate side-chains 253 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 249 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain C residue 583 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 0.4980 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.4980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 9.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.255803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.211263 restraints weight = 31395.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.215954 restraints weight = 16737.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.218997 restraints weight = 10371.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.221206 restraints weight = 7157.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.222685 restraints weight = 5295.993| |-----------------------------------------------------------------------------| r_work (final): 0.4470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5692 moved from start: 0.0658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17778 Z= 0.119 Angle : 0.603 13.758 24099 Z= 0.304 Chirality : 0.044 0.159 2752 Planarity : 0.006 0.089 3077 Dihedral : 4.952 45.435 2322 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.44 % Allowed : 15.80 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.17), residues: 2125 helix: -1.07 (0.31), residues: 266 sheet: -0.74 (0.25), residues: 435 loop : -1.70 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 651 TYR 0.007 0.001 TYR C 309 PHE 0.022 0.001 PHE A 576 TRP 0.030 0.001 TRP B 139 HIS 0.004 0.001 HIS B 509 Details of bonding type rmsd covalent geometry : bond 0.00277 (17778) covalent geometry : angle 0.60328 (24099) hydrogen bonds : bond 0.04433 ( 328) hydrogen bonds : angle 6.03067 ( 888) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 257 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7497 (mt-10) REVERT: A 629 PHE cc_start: 0.7278 (m-10) cc_final: 0.7058 (m-10) REVERT: B 8 ARG cc_start: 0.6954 (mtt-85) cc_final: 0.6652 (mtt-85) REVERT: B 556 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6760 (mm-30) REVERT: B 601 PRO cc_start: 0.7491 (Cg_endo) cc_final: 0.7135 (Cg_exo) REVERT: B 614 GLU cc_start: 0.6615 (tp30) cc_final: 0.6377 (tp30) REVERT: C 467 LEU cc_start: 0.3737 (mt) cc_final: 0.2438 (mt) REVERT: D 352 MET cc_start: 0.1622 (OUTLIER) cc_final: 0.1164 (tpt) outliers start: 48 outliers final: 25 residues processed: 282 average time/residue: 0.1270 time to fit residues: 54.4968 Evaluate side-chains 273 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 HIS Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 582 PHE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 428 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 146 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 134 optimal weight: 40.0000 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.253818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.208115 restraints weight = 31401.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.212863 restraints weight = 17117.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.216031 restraints weight = 10709.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.218148 restraints weight = 7431.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.219737 restraints weight = 5583.697| |-----------------------------------------------------------------------------| r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5787 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17778 Z= 0.167 Angle : 0.611 9.229 24099 Z= 0.310 Chirality : 0.045 0.173 2752 Planarity : 0.006 0.079 3077 Dihedral : 4.798 29.862 2313 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.61 % Allowed : 15.65 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.17), residues: 2125 helix: -1.07 (0.30), residues: 274 sheet: -0.73 (0.25), residues: 421 loop : -1.68 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 484 TYR 0.013 0.001 TYR B 250 PHE 0.028 0.002 PHE A 583 TRP 0.030 0.002 TRP B 139 HIS 0.007 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00395 (17778) covalent geometry : angle 0.61073 (24099) hydrogen bonds : bond 0.04463 ( 328) hydrogen bonds : angle 5.65688 ( 888) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 252 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 587 VAL cc_start: 0.7147 (OUTLIER) cc_final: 0.6911 (t) REVERT: A 621 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7604 (mt-10) REVERT: B 465 ASP cc_start: 0.7857 (t0) cc_final: 0.7609 (t0) REVERT: B 556 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6758 (mm-30) REVERT: B 601 PRO cc_start: 0.7608 (Cg_endo) cc_final: 0.7174 (Cg_exo) REVERT: C 489 LEU cc_start: 0.3611 (OUTLIER) cc_final: 0.1536 (mp) REVERT: D 137 ARG cc_start: 0.1457 (OUTLIER) cc_final: 0.0277 (tpt170) REVERT: D 352 MET cc_start: 0.1729 (OUTLIER) cc_final: 0.1186 (tpt) outliers start: 71 outliers final: 44 residues processed: 299 average time/residue: 0.1272 time to fit residues: 58.1321 Evaluate side-chains 292 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 244 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 471 HIS Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 582 PHE Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 479 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 81 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 115 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 80 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 160 optimal weight: 0.2980 chunk 138 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.253916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.208896 restraints weight = 31445.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.213567 restraints weight = 17155.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.216683 restraints weight = 10827.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.218587 restraints weight = 7541.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.220198 restraints weight = 5742.971| |-----------------------------------------------------------------------------| r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5768 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17778 Z= 0.134 Angle : 0.581 10.116 24099 Z= 0.291 Chirality : 0.044 0.157 2752 Planarity : 0.006 0.069 3077 Dihedral : 4.664 26.689 2313 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.61 % Allowed : 17.33 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.17), residues: 2125 helix: -0.96 (0.30), residues: 280 sheet: -0.65 (0.25), residues: 436 loop : -1.62 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 484 TYR 0.018 0.001 TYR D 250 PHE 0.021 0.001 PHE C 478 TRP 0.026 0.002 TRP B 139 HIS 0.005 0.001 HIS B 509 Details of bonding type rmsd covalent geometry : bond 0.00319 (17778) covalent geometry : angle 0.58077 (24099) hydrogen bonds : bond 0.03789 ( 328) hydrogen bonds : angle 5.37843 ( 888) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 248 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.7667 (mm) cc_final: 0.7324 (mm) REVERT: A 322 SER cc_start: 0.7841 (OUTLIER) cc_final: 0.7373 (t) REVERT: A 501 PHE cc_start: 0.6789 (m-80) cc_final: 0.6553 (m-80) REVERT: A 621 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7465 (mt-10) REVERT: B 29 ILE cc_start: 0.7470 (mm) cc_final: 0.7124 (tp) REVERT: B 441 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7250 (mtt180) REVERT: B 465 ASP cc_start: 0.7872 (t0) cc_final: 0.7460 (t0) REVERT: B 503 GLU cc_start: 0.7140 (tp30) cc_final: 0.6895 (tp30) REVERT: B 556 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6741 (mm-30) REVERT: B 601 PRO cc_start: 0.7560 (Cg_endo) cc_final: 0.7190 (Cg_exo) REVERT: C 251 VAL cc_start: 0.4768 (t) cc_final: 0.4339 (p) REVERT: C 489 LEU cc_start: 0.3736 (OUTLIER) cc_final: 0.1645 (mp) REVERT: C 536 ARG cc_start: 0.4603 (OUTLIER) cc_final: 0.4169 (tpt170) REVERT: D 137 ARG cc_start: 0.1433 (OUTLIER) cc_final: 0.0248 (tpt170) REVERT: D 410 LEU cc_start: 0.4698 (pp) cc_final: 0.4185 (mp) outliers start: 71 outliers final: 51 residues processed: 289 average time/residue: 0.1269 time to fit residues: 55.5615 Evaluate side-chains 305 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 249 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 471 HIS Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 536 ARG Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 582 PHE Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 479 VAL Chi-restraints excluded: chain D residue 488 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 78 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 217 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN ** D 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.253075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.207462 restraints weight = 30930.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.212311 restraints weight = 16731.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.215411 restraints weight = 10452.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.217617 restraints weight = 7284.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.219117 restraints weight = 5443.946| |-----------------------------------------------------------------------------| r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5813 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17778 Z= 0.167 Angle : 0.606 9.231 24099 Z= 0.304 Chirality : 0.045 0.173 2752 Planarity : 0.006 0.070 3077 Dihedral : 4.701 25.212 2313 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.37 % Allowed : 17.48 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.17), residues: 2125 helix: -0.92 (0.31), residues: 274 sheet: -0.59 (0.26), residues: 425 loop : -1.60 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 484 TYR 0.017 0.001 TYR D 250 PHE 0.026 0.002 PHE C 478 TRP 0.027 0.002 TRP B 139 HIS 0.006 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00399 (17778) covalent geometry : angle 0.60644 (24099) hydrogen bonds : bond 0.04087 ( 328) hydrogen bonds : angle 5.30862 ( 888) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 257 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.7727 (mm) cc_final: 0.7379 (mm) REVERT: A 621 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7489 (mt-10) REVERT: A 632 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7865 (t0) REVERT: B 29 ILE cc_start: 0.7458 (mm) cc_final: 0.7147 (tp) REVERT: B 441 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7308 (mtt180) REVERT: B 461 LYS cc_start: 0.7665 (ttpt) cc_final: 0.7444 (mtpt) REVERT: B 465 ASP cc_start: 0.7902 (t0) cc_final: 0.7422 (t0) REVERT: B 503 GLU cc_start: 0.7130 (tp30) cc_final: 0.6886 (tp30) REVERT: B 556 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6725 (mm-30) REVERT: B 601 PRO cc_start: 0.7600 (Cg_endo) cc_final: 0.7175 (Cg_exo) REVERT: C 251 VAL cc_start: 0.4732 (OUTLIER) cc_final: 0.4305 (p) REVERT: C 536 ARG cc_start: 0.4636 (OUTLIER) cc_final: 0.4172 (tpt170) REVERT: D 137 ARG cc_start: 0.1555 (OUTLIER) cc_final: 0.0468 (tpt90) outliers start: 86 outliers final: 64 residues processed: 314 average time/residue: 0.1167 time to fit residues: 56.4216 Evaluate side-chains 314 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 245 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 471 HIS Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 522 LYS Chi-restraints excluded: chain C residue 536 ARG Chi-restraints excluded: chain C residue 582 PHE Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 479 VAL Chi-restraints excluded: chain D residue 484 ARG Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 628 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 30 optimal weight: 0.5980 chunk 158 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 168 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 49 optimal weight: 0.0670 chunk 157 optimal weight: 0.9980 chunk 55 optimal weight: 0.1980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.253435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.208488 restraints weight = 31052.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.213336 restraints weight = 16783.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.216328 restraints weight = 10477.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.218705 restraints weight = 7293.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.220050 restraints weight = 5444.466| |-----------------------------------------------------------------------------| r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17778 Z= 0.121 Angle : 0.573 10.065 24099 Z= 0.287 Chirality : 0.044 0.162 2752 Planarity : 0.005 0.064 3077 Dihedral : 4.549 24.028 2313 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.81 % Allowed : 18.60 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.17), residues: 2125 helix: -0.81 (0.31), residues: 275 sheet: -0.49 (0.26), residues: 423 loop : -1.58 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 484 TYR 0.017 0.001 TYR D 250 PHE 0.017 0.001 PHE C 249 TRP 0.025 0.001 TRP B 139 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00287 (17778) covalent geometry : angle 0.57259 (24099) hydrogen bonds : bond 0.03512 ( 328) hydrogen bonds : angle 5.12774 ( 888) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 252 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.7696 (mm) cc_final: 0.7347 (mm) REVERT: A 322 SER cc_start: 0.7774 (OUTLIER) cc_final: 0.7401 (t) REVERT: A 501 PHE cc_start: 0.6781 (m-80) cc_final: 0.6498 (m-80) REVERT: A 621 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7395 (mt-10) REVERT: A 632 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7838 (t70) REVERT: B 29 ILE cc_start: 0.7415 (mm) cc_final: 0.7057 (tp) REVERT: B 441 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7289 (mtt180) REVERT: B 461 LYS cc_start: 0.7678 (ttpt) cc_final: 0.7459 (mtpt) REVERT: B 465 ASP cc_start: 0.7887 (t0) cc_final: 0.7435 (t0) REVERT: B 556 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6700 (mm-30) REVERT: B 601 PRO cc_start: 0.7593 (Cg_endo) cc_final: 0.7172 (Cg_exo) REVERT: C 536 ARG cc_start: 0.4661 (OUTLIER) cc_final: 0.4197 (tpt170) REVERT: D 137 ARG cc_start: 0.1411 (OUTLIER) cc_final: 0.0580 (tpt90) REVERT: D 410 LEU cc_start: 0.4656 (pp) cc_final: 0.4208 (mp) outliers start: 75 outliers final: 51 residues processed: 301 average time/residue: 0.1186 time to fit residues: 54.7262 Evaluate side-chains 307 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 250 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 471 HIS Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 536 ARG Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 582 PHE Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 484 ARG Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 596 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 9.9990 chunk 89 optimal weight: 0.0770 chunk 177 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 217 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 86 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS C 595 HIS ** D 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.253510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.208252 restraints weight = 31338.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.214664 restraints weight = 17186.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.216382 restraints weight = 9506.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.217050 restraints weight = 7965.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.217912 restraints weight = 6886.290| |-----------------------------------------------------------------------------| r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17778 Z= 0.112 Angle : 0.566 11.083 24099 Z= 0.282 Chirality : 0.044 0.143 2752 Planarity : 0.005 0.066 3077 Dihedral : 4.392 23.092 2313 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.96 % Allowed : 18.55 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.18), residues: 2125 helix: -0.59 (0.32), residues: 275 sheet: -0.45 (0.25), residues: 429 loop : -1.54 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 484 TYR 0.015 0.001 TYR D 250 PHE 0.038 0.001 PHE C 249 TRP 0.023 0.001 TRP B 139 HIS 0.004 0.001 HIS B 509 Details of bonding type rmsd covalent geometry : bond 0.00267 (17778) covalent geometry : angle 0.56560 (24099) hydrogen bonds : bond 0.03283 ( 328) hydrogen bonds : angle 4.97763 ( 888) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 244 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ASP cc_start: 0.7543 (t70) cc_final: 0.7308 (t0) REVERT: A 322 SER cc_start: 0.7619 (OUTLIER) cc_final: 0.7257 (t) REVERT: A 430 PHE cc_start: 0.7448 (p90) cc_final: 0.7236 (p90) REVERT: A 461 LYS cc_start: 0.7490 (ttpp) cc_final: 0.7232 (mtpp) REVERT: A 501 PHE cc_start: 0.6774 (m-80) cc_final: 0.6533 (m-80) REVERT: A 621 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: A 632 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7363 (t0) REVERT: B 441 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7285 (mtt180) REVERT: B 461 LYS cc_start: 0.7663 (ttpt) cc_final: 0.7444 (mtpt) REVERT: B 465 ASP cc_start: 0.7938 (t0) cc_final: 0.7435 (t0) REVERT: B 555 ARG cc_start: 0.7270 (ttm-80) cc_final: 0.6886 (ttm-80) REVERT: B 556 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6659 (mm-30) REVERT: B 601 PRO cc_start: 0.7595 (Cg_endo) cc_final: 0.7200 (Cg_exo) REVERT: C 251 VAL cc_start: 0.4465 (OUTLIER) cc_final: 0.4123 (p) REVERT: C 536 ARG cc_start: 0.4761 (OUTLIER) cc_final: 0.4271 (tpt170) REVERT: D 137 ARG cc_start: 0.1374 (OUTLIER) cc_final: 0.0495 (tpt90) outliers start: 78 outliers final: 60 residues processed: 294 average time/residue: 0.1185 time to fit residues: 53.3577 Evaluate side-chains 306 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 239 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 471 HIS Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 536 ARG Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 582 PHE Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 479 VAL Chi-restraints excluded: chain D residue 484 ARG Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 596 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 25 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 220 optimal weight: 7.9990 chunk 182 optimal weight: 0.0050 chunk 1 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 187 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 202 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN B 246 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.253262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.208522 restraints weight = 31272.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.213309 restraints weight = 16824.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.216368 restraints weight = 10500.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.218642 restraints weight = 7280.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.220013 restraints weight = 5429.840| |-----------------------------------------------------------------------------| r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5764 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17778 Z= 0.119 Angle : 0.569 11.954 24099 Z= 0.283 Chirality : 0.044 0.144 2752 Planarity : 0.005 0.068 3077 Dihedral : 4.388 22.438 2313 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.37 % Allowed : 18.60 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.18), residues: 2125 helix: -0.55 (0.32), residues: 275 sheet: -0.40 (0.25), residues: 428 loop : -1.53 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 484 TYR 0.017 0.001 TYR D 250 PHE 0.018 0.001 PHE C 249 TRP 0.023 0.001 TRP B 139 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00284 (17778) covalent geometry : angle 0.56914 (24099) hydrogen bonds : bond 0.03369 ( 328) hydrogen bonds : angle 4.94880 ( 888) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 248 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 SER cc_start: 0.7680 (OUTLIER) cc_final: 0.7313 (t) REVERT: A 353 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6910 (mm-30) REVERT: A 461 LYS cc_start: 0.7489 (ttpp) cc_final: 0.7243 (mtpp) REVERT: A 501 PHE cc_start: 0.6860 (m-80) cc_final: 0.6606 (m-80) REVERT: A 621 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: A 632 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7496 (t70) REVERT: B 48 VAL cc_start: 0.8398 (m) cc_final: 0.8155 (p) REVERT: B 441 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7312 (mtt180) REVERT: B 443 MET cc_start: 0.7737 (tpp) cc_final: 0.7508 (ttt) REVERT: B 465 ASP cc_start: 0.7922 (t0) cc_final: 0.7480 (t0) REVERT: B 556 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6659 (mm-30) REVERT: B 601 PRO cc_start: 0.7587 (Cg_endo) cc_final: 0.7192 (Cg_exo) REVERT: C 251 VAL cc_start: 0.4625 (OUTLIER) cc_final: 0.4314 (p) REVERT: C 536 ARG cc_start: 0.4788 (OUTLIER) cc_final: 0.4275 (tpt170) REVERT: D 137 ARG cc_start: 0.1128 (OUTLIER) cc_final: 0.0665 (tpt90) REVERT: D 410 LEU cc_start: 0.4728 (pp) cc_final: 0.4183 (mp) outliers start: 86 outliers final: 65 residues processed: 305 average time/residue: 0.1199 time to fit residues: 55.8598 Evaluate side-chains 319 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 246 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 607 ASN Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 471 HIS Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 536 ARG Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 582 PHE Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 479 VAL Chi-restraints excluded: chain D residue 484 ARG Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 596 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 26 optimal weight: 0.0050 chunk 206 optimal weight: 0.7980 chunk 202 optimal weight: 0.1980 chunk 194 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 165 optimal weight: 0.0980 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 216 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 HIS B 245 HIS B 246 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.250853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.209095 restraints weight = 31838.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.212722 restraints weight = 18903.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.215298 restraints weight = 11346.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.215337 restraints weight = 9853.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.215963 restraints weight = 8917.507| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17778 Z= 0.104 Angle : 0.565 12.176 24099 Z= 0.280 Chirality : 0.043 0.143 2752 Planarity : 0.005 0.070 3077 Dihedral : 4.329 25.587 2313 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.96 % Allowed : 18.90 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.18), residues: 2125 helix: -0.39 (0.32), residues: 269 sheet: -0.34 (0.25), residues: 428 loop : -1.48 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 651 TYR 0.020 0.001 TYR D 250 PHE 0.020 0.001 PHE D 475 TRP 0.022 0.001 TRP B 139 HIS 0.003 0.000 HIS D 361 Details of bonding type rmsd covalent geometry : bond 0.00248 (17778) covalent geometry : angle 0.56503 (24099) hydrogen bonds : bond 0.03152 ( 328) hydrogen bonds : angle 4.87157 ( 888) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 247 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 SER cc_start: 0.7633 (OUTLIER) cc_final: 0.7270 (t) REVERT: A 461 LYS cc_start: 0.7368 (ttpp) cc_final: 0.7145 (mtpp) REVERT: A 501 PHE cc_start: 0.6899 (m-80) cc_final: 0.6686 (m-80) REVERT: A 621 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: B 441 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7277 (mtt180) REVERT: B 443 MET cc_start: 0.7713 (tpp) cc_final: 0.7497 (ttt) REVERT: B 461 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7477 (mtpt) REVERT: B 465 ASP cc_start: 0.7862 (t0) cc_final: 0.7414 (t0) REVERT: B 556 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6653 (mm-30) REVERT: B 601 PRO cc_start: 0.7569 (Cg_endo) cc_final: 0.7194 (Cg_exo) REVERT: C 251 VAL cc_start: 0.4504 (OUTLIER) cc_final: 0.4177 (p) REVERT: C 536 ARG cc_start: 0.4824 (OUTLIER) cc_final: 0.4311 (tpt170) REVERT: D 137 ARG cc_start: 0.1135 (OUTLIER) cc_final: 0.0637 (tpt90) REVERT: D 410 LEU cc_start: 0.4629 (pp) cc_final: 0.4107 (mp) outliers start: 78 outliers final: 64 residues processed: 295 average time/residue: 0.1231 time to fit residues: 55.2736 Evaluate side-chains 313 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 243 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 471 HIS Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 536 ARG Chi-restraints excluded: chain C residue 582 PHE Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 479 VAL Chi-restraints excluded: chain D residue 484 ARG Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 589 MET Chi-restraints excluded: chain D residue 596 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 139 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 41 optimal weight: 0.2980 chunk 86 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN B 246 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.252215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.207564 restraints weight = 31000.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.212796 restraints weight = 17448.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.217054 restraints weight = 10191.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.217357 restraints weight = 7545.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.217563 restraints weight = 5992.699| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17778 Z= 0.127 Angle : 0.581 13.245 24099 Z= 0.289 Chirality : 0.044 0.149 2752 Planarity : 0.005 0.071 3077 Dihedral : 4.349 20.682 2313 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.76 % Allowed : 19.05 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.18), residues: 2125 helix: -0.44 (0.32), residues: 270 sheet: -0.35 (0.26), residues: 425 loop : -1.49 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 651 TYR 0.021 0.001 TYR D 250 PHE 0.034 0.001 PHE B 249 TRP 0.022 0.001 TRP B 139 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00306 (17778) covalent geometry : angle 0.58058 (24099) hydrogen bonds : bond 0.03475 ( 328) hydrogen bonds : angle 4.88247 ( 888) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 251 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 SER cc_start: 0.7623 (OUTLIER) cc_final: 0.7290 (t) REVERT: A 461 LYS cc_start: 0.7495 (ttpp) cc_final: 0.7210 (mtpp) REVERT: A 501 PHE cc_start: 0.6847 (m-80) cc_final: 0.6588 (m-80) REVERT: A 621 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: B 441 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7319 (mtt180) REVERT: B 443 MET cc_start: 0.7766 (tpp) cc_final: 0.7486 (ttt) REVERT: B 461 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7454 (mtpt) REVERT: B 465 ASP cc_start: 0.7968 (t0) cc_final: 0.7551 (t0) REVERT: B 474 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6780 (mt-10) REVERT: B 556 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6657 (mm-30) REVERT: B 601 PRO cc_start: 0.7579 (Cg_endo) cc_final: 0.7182 (Cg_exo) REVERT: C 251 VAL cc_start: 0.4498 (OUTLIER) cc_final: 0.4189 (p) REVERT: C 536 ARG cc_start: 0.5018 (OUTLIER) cc_final: 0.4485 (tpt170) REVERT: C 557 LEU cc_start: 0.7772 (tp) cc_final: 0.7446 (tp) REVERT: D 137 ARG cc_start: 0.1251 (OUTLIER) cc_final: 0.0691 (tpt90) outliers start: 74 outliers final: 64 residues processed: 299 average time/residue: 0.1168 time to fit residues: 53.1762 Evaluate side-chains 317 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 247 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 536 ARG Chi-restraints excluded: chain C residue 582 PHE Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 479 VAL Chi-restraints excluded: chain D residue 484 ARG Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 589 MET Chi-restraints excluded: chain D residue 596 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 172 optimal weight: 10.0000 chunk 171 optimal weight: 0.0870 chunk 78 optimal weight: 0.4980 chunk 80 optimal weight: 0.6980 chunk 185 optimal weight: 2.9990 chunk 177 optimal weight: 0.0070 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN B 246 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.253119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.208206 restraints weight = 31406.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.214386 restraints weight = 17399.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.216091 restraints weight = 9622.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.217854 restraints weight = 7856.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.218210 restraints weight = 6701.453| |-----------------------------------------------------------------------------| r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17778 Z= 0.107 Angle : 0.564 12.134 24099 Z= 0.279 Chirality : 0.043 0.161 2752 Planarity : 0.005 0.069 3077 Dihedral : 4.243 20.592 2313 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.51 % Allowed : 19.56 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.18), residues: 2125 helix: -0.33 (0.32), residues: 270 sheet: -0.26 (0.25), residues: 437 loop : -1.44 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 651 TYR 0.022 0.001 TYR D 250 PHE 0.028 0.001 PHE B 249 TRP 0.021 0.001 TRP B 139 HIS 0.003 0.000 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00259 (17778) covalent geometry : angle 0.56382 (24099) hydrogen bonds : bond 0.03137 ( 328) hydrogen bonds : angle 4.81116 ( 888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3206.15 seconds wall clock time: 55 minutes 55.57 seconds (3355.57 seconds total)