Starting phenix.real_space_refine on Sat Aug 23 14:00:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nor_49608/08_2025/9nor_49608.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nor_49608/08_2025/9nor_49608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nor_49608/08_2025/9nor_49608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nor_49608/08_2025/9nor_49608.map" model { file = "/net/cci-nas-00/data/ceres_data/9nor_49608/08_2025/9nor_49608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nor_49608/08_2025/9nor_49608.cif" } resolution = 3.4 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= 0.006 sd= 0.021 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 97 5.16 5 C 8094 2.51 5 N 2093 2.21 5 O 2271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12555 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6059 Classifications: {'peptide': 780} Link IDs: {'PTRANS': 45, 'TRANS': 734} Chain breaks: 3 Chain: "A" Number of atoms: 6272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6272 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 40, 'TRANS': 744} Chain breaks: 2 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 3.24, per 1000 atoms: 0.26 Number of scatterers: 12555 At special positions: 0 Unit cell: (97.114, 90.53, 185.175, 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 97 16.00 O 2271 8.00 N 2093 7.00 C 8094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 517 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 415 " distance=2.04 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 518 " distance=2.02 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 538 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 554 " distance=2.04 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 722 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 513 " distance=2.03 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 366 " distance=2.03 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 517 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 551 " distance=2.04 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 720 " distance=2.03 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 527 " " NAG A 902 " - " ASN A 487 " " NAG A 903 " - " ASN A 84 " " NAG A 904 " - " ASN A 428 " " NAG A 905 " - " ASN A 312 " " NAG A 906 " - " ASN A 248 " " NAG A 907 " - " ASN A 292 " " NAG A 908 " - " ASN A 368 " " NAG B 901 " - " ASN B 475 " " NAG B 902 " - " ASN B 285 " " NAG B 903 " - " ASN B 264 " " NAG B 904 " - " ASN B 411 " " NAG B 905 " - " ASN B 85 " " NAG B 906 " - " ASN B 130 " " NAG B 907 " - " ASN B 380 " " NAG B 908 " - " ASN B 432 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 654.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 19 sheets defined 54.6% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 66 through 86 removed outlier: 3.635A pdb=" N LEU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 118 removed outlier: 4.196A pdb=" N LYS B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 130 through 134 removed outlier: 3.808A pdb=" N GLN B 133 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 161 removed outlier: 3.867A pdb=" N VAL B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.533A pdb=" N LEU B 174 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.919A pdb=" N GLN B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 234 Processing helix chain 'B' and resid 256 through 266 removed outlier: 3.667A pdb=" N SER B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 291 Processing helix chain 'B' and resid 300 through 305 removed outlier: 4.599A pdb=" N THR B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 333 through 347 Processing helix chain 'B' and resid 347 through 354 removed outlier: 3.642A pdb=" N CYS B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.730A pdb=" N ASP B 374 " --> pdb=" O PRO B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 385 removed outlier: 3.889A pdb=" N SER B 382 " --> pdb=" O GLN B 379 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ALA B 383 " --> pdb=" O ASN B 380 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 385 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 409 removed outlier: 3.851A pdb=" N SER B 392 " --> pdb=" O HIS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 425 Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.707A pdb=" N TYR B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 593 Processing helix chain 'B' and resid 596 through 602 Processing helix chain 'B' and resid 604 through 621 removed outlier: 3.544A pdb=" N CYS B 608 " --> pdb=" O GLY B 604 " (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 629 through 663 removed outlier: 5.270A pdb=" N GLN B 637 " --> pdb=" O CYS B 633 " (cutoff:3.500A) Proline residue: B 638 - end of helix Proline residue: B 643 - end of helix Processing helix chain 'B' and resid 665 through 677 removed outlier: 4.221A pdb=" N ARG B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY B 674 " --> pdb=" O ASP B 670 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS B 675 " --> pdb=" O ARG B 671 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG B 677 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 703 Processing helix chain 'B' and resid 728 through 749 removed outlier: 4.472A pdb=" N THR B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 785 Proline residue: B 780 - end of helix Processing helix chain 'B' and resid 786 through 788 No H-bonds generated for 'chain 'B' and resid 786 through 788' Processing helix chain 'B' and resid 789 through 819 removed outlier: 4.828A pdb=" N LEU B 811 " --> pdb=" O ALA B 807 " (cutoff:3.500A) Proline residue: B 812 - end of helix removed outlier: 3.637A pdb=" N LEU B 816 " --> pdb=" O PRO B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 824 removed outlier: 3.994A pdb=" N LEU B 823 " --> pdb=" O GLN B 820 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN B 824 " --> pdb=" O PRO B 821 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 820 through 824' Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 65 through 85 removed outlier: 4.260A pdb=" N TYR A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.553A pdb=" N LEU A 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP A 173 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.510A pdb=" N HIS A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 228 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 250 through 267 Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 307 through 313 removed outlier: 3.775A pdb=" N HIS A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 319 removed outlier: 5.055A pdb=" N ARG A 317 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N HIS A 318 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 removed outlier: 3.672A pdb=" N GLY A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 373 removed outlier: 3.816A pdb=" N SER A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 384 through 404 Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 563 through 590 Processing helix chain 'A' and resid 593 through 599 Processing helix chain 'A' and resid 600 through 618 Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 626 through 665 Proline residue: A 638 - end of helix removed outlier: 4.502A pdb=" N ALA A 658 " --> pdb=" O GLN A 654 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS A 660 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER A 663 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 665 " --> pdb=" O MET A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 676 through 701 Processing helix chain 'A' and resid 723 through 749 removed outlier: 3.939A pdb=" N SER A 727 " --> pdb=" O ASN A 723 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 741 " --> pdb=" O LEU A 737 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 removed outlier: 3.550A pdb=" N PHE A 761 " --> pdb=" O ASN A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 818 removed outlier: 3.773A pdb=" N TYR A 807 " --> pdb=" O ILE A 803 " (cutoff:3.500A) Proline residue: A 810 - end of helix Processing helix chain 'A' and resid 823 through 828 removed outlier: 3.961A pdb=" N ASN A 828 " --> pdb=" O ALA A 825 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.749A pdb=" N TYR B 97 " --> pdb=" O MET B 31 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR B 35 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ASP B 98 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU B 37 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 40 through 41 Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA4, first strand: chain 'B' and resid 124 through 126 Processing sheet with id=AA5, first strand: chain 'B' and resid 141 through 143 removed outlier: 6.414A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLN B 164 " --> pdb=" O PHE B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 236 through 243 removed outlier: 8.053A pdb=" N VAL B 209 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLU B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ALA B 211 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU B 242 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL B 270 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP B 297 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N PHE B 324 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ALA B 299 " --> pdb=" O PHE B 324 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N GLN B 326 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL B 321 " --> pdb=" O TRP B 459 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR B 454 " --> pdb=" O ARG B 473 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG B 473 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU B 456 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 467 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 462 " --> pdb=" O VAL B 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 434 through 437 Processing sheet with id=AA8, first strand: chain 'B' and resid 508 through 512 removed outlier: 3.707A pdb=" N VAL B 508 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AB1, first strand: chain 'B' and resid 545 through 546 Processing sheet with id=AB2, first strand: chain 'B' and resid 706 through 708 Processing sheet with id=AB3, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.584A pdb=" N TYR A 96 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 39 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 34 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA A 137 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.625A pdb=" N GLU A 63 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 161 through 163 removed outlier: 6.097A pdb=" N GLN A 161 " --> pdb=" O LEU A 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 233 through 240 removed outlier: 7.752A pdb=" N ILE A 206 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN A 237 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 208 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR A 239 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 210 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N TRP A 205 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL A 273 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE A 207 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N PHE A 275 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 209 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 272 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TRP A 298 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE A 325 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA A 300 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ILE A 327 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N PHE A 322 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 448 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER A 467 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE A 450 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 428 through 430 Processing sheet with id=AB8, first strand: chain 'A' and resid 503 through 507 Processing sheet with id=AB9, first strand: chain 'A' and resid 524 through 527 removed outlier: 11.283A pdb=" N PHE A 525 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N TYR A 533 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN A 527 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 705 through 707 removed outlier: 3.571A pdb=" N SER A 719 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 717 " --> pdb=" O ARG A 707 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1782 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: 2.52 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3936 1.34 - 1.46: 3022 1.46 - 1.58: 5783 1.58 - 1.70: 0 1.70 - 1.83: 136 Bond restraints: 12877 Sorted by residual: bond pdb=" N ILE B 235 " pdb=" CA ILE B 235 " ideal model delta sigma weight residual 1.456 1.501 -0.046 1.30e-02 5.92e+03 1.23e+01 bond pdb=" N LEU B 642 " pdb=" CA LEU B 642 " ideal model delta sigma weight residual 1.462 1.495 -0.033 9.50e-03 1.11e+04 1.22e+01 bond pdb=" CA SER B 516 " pdb=" CB SER B 516 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.58e-02 4.01e+03 1.06e+01 bond pdb=" N ASP A 712 " pdb=" CA ASP A 712 " ideal model delta sigma weight residual 1.463 1.490 -0.028 8.80e-03 1.29e+04 9.91e+00 bond pdb=" N LEU B 89 " pdb=" CA LEU B 89 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.21e-02 6.83e+03 9.29e+00 ... (remaining 12872 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 17211 2.07 - 4.13: 286 4.13 - 6.20: 36 6.20 - 8.26: 11 8.26 - 10.33: 2 Bond angle restraints: 17546 Sorted by residual: angle pdb=" C CYS B 517 " pdb=" CA CYS B 517 " pdb=" CB CYS B 517 " ideal model delta sigma weight residual 110.86 103.65 7.21 1.65e+00 3.67e-01 1.91e+01 angle pdb=" CA LYS A 407 " pdb=" CB LYS A 407 " pdb=" CG LYS A 407 " ideal model delta sigma weight residual 114.10 122.07 -7.97 2.00e+00 2.50e-01 1.59e+01 angle pdb=" C LEU B 642 " pdb=" N PRO B 643 " pdb=" CA PRO B 643 " ideal model delta sigma weight residual 118.85 123.14 -4.29 1.09e+00 8.42e-01 1.55e+01 angle pdb=" CA ILE B 235 " pdb=" C ILE B 235 " pdb=" O ILE B 235 " ideal model delta sigma weight residual 121.58 117.98 3.60 1.00e+00 1.00e+00 1.30e+01 angle pdb=" C CYS B 518 " pdb=" CA CYS B 518 " pdb=" CB CYS B 518 " ideal model delta sigma weight residual 112.43 105.60 6.83 1.91e+00 2.74e-01 1.28e+01 ... (remaining 17541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 6662 17.79 - 35.58: 877 35.58 - 53.37: 270 53.37 - 71.15: 40 71.15 - 88.94: 21 Dihedral angle restraints: 7870 sinusoidal: 3298 harmonic: 4572 Sorted by residual: dihedral pdb=" CB CYS B 524 " pdb=" SG CYS B 524 " pdb=" SG CYS B 538 " pdb=" CB CYS B 538 " ideal model delta sinusoidal sigma weight residual -86.00 -174.94 88.94 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS A 233 " pdb=" SG CYS A 233 " pdb=" SG CYS A 513 " pdb=" CB CYS A 513 " ideal model delta sinusoidal sigma weight residual -86.00 -166.76 80.76 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 551 " pdb=" CB CYS A 551 " ideal model delta sinusoidal sigma weight residual 93.00 12.72 80.28 1 1.00e+01 1.00e-02 7.98e+01 ... (remaining 7867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1852 0.074 - 0.149: 172 0.149 - 0.223: 10 0.223 - 0.297: 4 0.297 - 0.372: 4 Chirality restraints: 2042 Sorted by residual: chirality pdb=" C1 NAG A 906 " pdb=" ND2 ASN A 248 " pdb=" C2 NAG A 906 " pdb=" O5 NAG A 906 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB THR A 754 " pdb=" CA THR A 754 " pdb=" OG1 THR A 754 " pdb=" CG2 THR A 754 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C1 NAG A 905 " pdb=" ND2 ASN A 312 " pdb=" C2 NAG A 905 " pdb=" O5 NAG A 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 2039 not shown) Planarity restraints: 2219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 234 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C GLY B 234 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY B 234 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE B 235 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 775 " 0.012 2.00e-02 2.50e+03 1.35e-02 4.59e+00 pdb=" CG TRP B 775 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 775 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 775 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 775 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 775 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 775 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 775 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 775 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 775 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 809 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO A 810 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 810 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 810 " -0.027 5.00e-02 4.00e+02 ... (remaining 2216 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 3 2.49 - 3.10: 8943 3.10 - 3.70: 19138 3.70 - 4.30: 26874 4.30 - 4.90: 44839 Nonbonded interactions: 99797 Sorted by model distance: nonbonded pdb=" NH2 ARG B 54 " pdb=" O SER A 155 " model vdw 1.892 3.120 nonbonded pdb=" OE1 GLU B 82 " pdb=" OH TYR B 394 " model vdw 2.251 3.040 nonbonded pdb=" O LEU B 574 " pdb=" OG SER B 577 " model vdw 2.400 3.040 nonbonded pdb=" OE2 GLU A 80 " pdb=" OD1 ASN A 84 " model vdw 2.516 3.040 nonbonded pdb=" C THR B 736 " pdb=" OG1 THR B 736 " model vdw 2.561 2.616 ... (remaining 99792 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.480 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12913 Z= 0.202 Angle : 0.682 17.824 17634 Z= 0.355 Chirality : 0.046 0.372 2042 Planarity : 0.004 0.064 2203 Dihedral : 17.334 88.542 4850 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.91 % Allowed : 28.76 % Favored : 69.33 % 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 aren not related in a simple way. whole: 0.50 (0.22), residues: 1551 helix: 1.52 (0.19), residues: 742 sheet: -1.47 (0.38), residues: 189 loop : -0.45 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 821 TYR 0.012 0.001 TYR A 113 PHE 0.022 0.001 PHE A 552 TRP 0.037 0.001 TRP B 775 HIS 0.007 0.001 HIS B 734 Details of bonding type rmsd covalent geometry : bond 0.00351 (12877) covalent geometry : angle 0.63859 (17546) SS BOND : bond 0.00383 ( 20) SS BOND : angle 1.14594 ( 40) hydrogen bonds : bond 0.13695 ( 624) hydrogen bonds : angle 5.80523 ( 1782) link_NAG-ASN : bond 0.00961 ( 16) link_NAG-ASN : angle 4.55373 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 260 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7552 (mm) REVERT: B 514 PHE cc_start: 0.8687 (t80) cc_final: 0.8484 (t80) REVERT: B 598 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7129 (tt) REVERT: B 682 TRP cc_start: 0.7227 (m100) cc_final: 0.7023 (m100) REVERT: B 800 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8358 (mt) REVERT: A 133 SER cc_start: 0.8660 (t) cc_final: 0.8309 (m) REVERT: A 621 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.5873 (t80) REVERT: A 679 TYR cc_start: 0.7095 (m-80) cc_final: 0.6590 (m-80) REVERT: A 815 ILE cc_start: 0.7217 (mm) cc_final: 0.6864 (mt) outliers start: 26 outliers final: 18 residues processed: 188 average time/residue: 0.1109 time to fit residues: 31.1034 Evaluate side-chains 177 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 TRP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 774 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.126741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.104978 restraints weight = 23934.685| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.66 r_work: 0.3388 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12913 Z= 0.163 Angle : 0.624 17.321 17634 Z= 0.294 Chirality : 0.045 0.402 2042 Planarity : 0.004 0.050 2203 Dihedral : 7.585 58.836 2065 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.65 % Allowed : 25.90 % Favored : 68.45 % 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 aren not related in a simple way. whole: 0.64 (0.22), residues: 1551 helix: 1.57 (0.19), residues: 750 sheet: -1.46 (0.37), residues: 193 loop : -0.28 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 226 TYR 0.016 0.001 TYR A 389 PHE 0.027 0.001 PHE B 730 TRP 0.010 0.001 TRP B 303 HIS 0.008 0.001 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00386 (12877) covalent geometry : angle 0.57551 (17546) SS BOND : bond 0.00338 ( 20) SS BOND : angle 1.17073 ( 40) hydrogen bonds : bond 0.04019 ( 624) hydrogen bonds : angle 4.70885 ( 1782) link_NAG-ASN : bond 0.00988 ( 16) link_NAG-ASN : angle 4.56181 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 162 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8936 (mm) REVERT: B 155 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8514 (mtmt) REVERT: B 260 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7337 (mm) REVERT: B 409 GLN cc_start: 0.7847 (mt0) cc_final: 0.7391 (mm110) REVERT: B 541 CYS cc_start: 0.3332 (OUTLIER) cc_final: 0.2137 (m) REVERT: B 690 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6541 (mt) REVERT: B 709 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7513 (p) REVERT: B 717 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7112 (pt0) REVERT: A 253 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8103 (mm-30) REVERT: A 567 ILE cc_start: 0.6840 (tt) cc_final: 0.6558 (tt) REVERT: A 679 TYR cc_start: 0.7160 (m-80) cc_final: 0.6572 (m-80) outliers start: 77 outliers final: 48 residues processed: 222 average time/residue: 0.1052 time to fit residues: 35.1351 Evaluate side-chains 204 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 149 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 TRP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 748 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 88 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.126357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103749 restraints weight = 23956.221| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.83 r_work: 0.3362 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12913 Z= 0.162 Angle : 0.617 17.365 17634 Z= 0.289 Chirality : 0.045 0.407 2042 Planarity : 0.004 0.052 2203 Dihedral : 7.169 57.960 2049 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 6.24 % Allowed : 25.75 % Favored : 68.01 % 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 aren not related in a simple way. whole: 0.59 (0.22), residues: 1551 helix: 1.56 (0.19), residues: 750 sheet: -1.45 (0.37), residues: 183 loop : -0.40 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 498 TYR 0.018 0.001 TYR A 389 PHE 0.015 0.001 PHE B 65 TRP 0.022 0.001 TRP B 775 HIS 0.006 0.001 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00387 (12877) covalent geometry : angle 0.56772 (17546) SS BOND : bond 0.00351 ( 20) SS BOND : angle 1.21840 ( 40) hydrogen bonds : bond 0.03957 ( 624) hydrogen bonds : angle 4.51545 ( 1782) link_NAG-ASN : bond 0.00983 ( 16) link_NAG-ASN : angle 4.55692 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 158 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.8890 (mm) REVERT: B 260 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7314 (mm) REVERT: B 469 HIS cc_start: 0.8346 (m-70) cc_final: 0.8079 (m90) REVERT: B 541 CYS cc_start: 0.3177 (OUTLIER) cc_final: 0.1834 (m) REVERT: B 690 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6558 (mt) REVERT: B 709 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7513 (p) REVERT: B 717 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7233 (pt0) REVERT: A 172 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7351 (mtt-85) REVERT: A 253 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8104 (mm-30) REVERT: A 567 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6628 (tt) outliers start: 85 outliers final: 61 residues processed: 228 average time/residue: 0.1100 time to fit residues: 37.6162 Evaluate side-chains 221 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 152 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 TRP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 796 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 112 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 136 optimal weight: 0.0670 chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 449 ASN B 734 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.126813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.104004 restraints weight = 23912.567| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.83 r_work: 0.3371 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12913 Z= 0.137 Angle : 0.600 17.116 17634 Z= 0.279 Chirality : 0.044 0.414 2042 Planarity : 0.004 0.051 2203 Dihedral : 7.101 57.858 2049 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 6.09 % Allowed : 26.19 % Favored : 67.72 % 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 aren not related in a simple way. whole: 0.64 (0.22), residues: 1551 helix: 1.62 (0.19), residues: 750 sheet: -1.38 (0.37), residues: 180 loop : -0.40 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 530 TYR 0.016 0.001 TYR A 389 PHE 0.019 0.001 PHE A 552 TRP 0.025 0.001 TRP B 775 HIS 0.004 0.001 HIS B 469 Details of bonding type rmsd covalent geometry : bond 0.00319 (12877) covalent geometry : angle 0.55006 (17546) SS BOND : bond 0.00297 ( 20) SS BOND : angle 1.33158 ( 40) hydrogen bonds : bond 0.03707 ( 624) hydrogen bonds : angle 4.39925 ( 1782) link_NAG-ASN : bond 0.00973 ( 16) link_NAG-ASN : angle 4.51600 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 164 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8887 (mm) REVERT: B 260 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7318 (mm) REVERT: B 501 ARG cc_start: 0.8741 (mmm160) cc_final: 0.8498 (mmt180) REVERT: B 502 GLN cc_start: 0.7907 (pp30) cc_final: 0.7508 (pp30) REVERT: B 541 CYS cc_start: 0.3206 (OUTLIER) cc_final: 0.1920 (m) REVERT: B 690 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6551 (mt) REVERT: B 709 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7477 (p) REVERT: B 717 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7168 (mt-10) REVERT: A 253 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8125 (mm-30) REVERT: A 567 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6621 (tt) REVERT: A 621 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.6140 (t80) outliers start: 83 outliers final: 62 residues processed: 231 average time/residue: 0.1107 time to fit residues: 37.8999 Evaluate side-chains 225 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 155 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 TRP Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 796 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 44 optimal weight: 0.0270 chunk 57 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 449 ASN ** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.127231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.104269 restraints weight = 24049.996| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.88 r_work: 0.3376 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12913 Z= 0.125 Angle : 0.592 16.942 17634 Z= 0.274 Chirality : 0.044 0.418 2042 Planarity : 0.004 0.051 2203 Dihedral : 7.052 59.512 2047 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 6.24 % Allowed : 25.68 % Favored : 68.09 % 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 aren not related in a simple way. whole: 0.73 (0.22), residues: 1551 helix: 1.68 (0.19), residues: 751 sheet: -1.31 (0.38), residues: 180 loop : -0.36 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.018 0.001 TYR A 783 PHE 0.019 0.001 PHE A 552 TRP 0.017 0.001 TRP B 775 HIS 0.005 0.001 HIS B 734 Details of bonding type rmsd covalent geometry : bond 0.00290 (12877) covalent geometry : angle 0.54237 (17546) SS BOND : bond 0.00286 ( 20) SS BOND : angle 1.17794 ( 40) hydrogen bonds : bond 0.03594 ( 624) hydrogen bonds : angle 4.32044 ( 1782) link_NAG-ASN : bond 0.00973 ( 16) link_NAG-ASN : angle 4.45527 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 161 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8854 (mm) REVERT: B 260 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7310 (mm) REVERT: B 501 ARG cc_start: 0.8764 (mmm160) cc_final: 0.8522 (mmt180) REVERT: B 598 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7364 (tt) REVERT: B 685 VAL cc_start: 0.6125 (t) cc_final: 0.5877 (p) REVERT: B 690 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6547 (mt) REVERT: B 709 THR cc_start: 0.7754 (OUTLIER) cc_final: 0.7422 (p) REVERT: B 717 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: B 775 TRP cc_start: 0.6582 (m100) cc_final: 0.6036 (m100) REVERT: A 253 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8118 (mm-30) REVERT: A 567 ILE cc_start: 0.6869 (OUTLIER) cc_final: 0.6590 (tt) REVERT: A 621 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.6191 (t80) outliers start: 85 outliers final: 62 residues processed: 228 average time/residue: 0.1094 time to fit residues: 36.9148 Evaluate side-chains 229 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 159 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 TRP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 796 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.125885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103245 restraints weight = 23902.267| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.79 r_work: 0.3356 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12913 Z= 0.161 Angle : 0.615 16.593 17634 Z= 0.287 Chirality : 0.045 0.422 2042 Planarity : 0.004 0.051 2203 Dihedral : 6.987 59.749 2045 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 6.46 % Allowed : 25.61 % Favored : 67.94 % 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 aren not related in a simple way. whole: 0.60 (0.22), residues: 1551 helix: 1.56 (0.19), residues: 754 sheet: -1.28 (0.37), residues: 183 loop : -0.44 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 558 TYR 0.018 0.002 TYR A 389 PHE 0.021 0.001 PHE A 552 TRP 0.015 0.001 TRP B 775 HIS 0.004 0.001 HIS A 562 Details of bonding type rmsd covalent geometry : bond 0.00387 (12877) covalent geometry : angle 0.56864 (17546) SS BOND : bond 0.00291 ( 20) SS BOND : angle 1.14781 ( 40) hydrogen bonds : bond 0.03808 ( 624) hydrogen bonds : angle 4.31984 ( 1782) link_NAG-ASN : bond 0.00943 ( 16) link_NAG-ASN : angle 4.42595 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 164 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8867 (mm) REVERT: B 260 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7380 (mm) REVERT: B 501 ARG cc_start: 0.8744 (mmm160) cc_final: 0.8474 (mmt180) REVERT: B 598 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7434 (tt) REVERT: B 690 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6669 (mt) REVERT: B 709 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7489 (p) REVERT: B 717 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7240 (mt-10) REVERT: B 775 TRP cc_start: 0.6737 (m100) cc_final: 0.6180 (m100) REVERT: A 253 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8122 (mm-30) REVERT: A 567 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6669 (tt) REVERT: A 621 TYR cc_start: 0.7703 (OUTLIER) cc_final: 0.6187 (t80) REVERT: A 656 VAL cc_start: 0.7903 (t) cc_final: 0.7528 (p) outliers start: 88 outliers final: 71 residues processed: 237 average time/residue: 0.1082 time to fit residues: 38.2541 Evaluate side-chains 237 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 158 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 TRP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 796 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 155 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 7 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 449 ASN B 469 HIS ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.124768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.102086 restraints weight = 23878.830| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.84 r_work: 0.3336 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12913 Z= 0.201 Angle : 0.649 16.246 17634 Z= 0.304 Chirality : 0.046 0.420 2042 Planarity : 0.004 0.053 2203 Dihedral : 7.077 59.948 2045 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 6.53 % Allowed : 25.75 % Favored : 67.72 % 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 aren not related in a simple way. whole: 0.45 (0.22), residues: 1551 helix: 1.43 (0.19), residues: 752 sheet: -1.26 (0.38), residues: 183 loop : -0.54 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 76 TYR 0.018 0.002 TYR A 389 PHE 0.015 0.001 PHE A 552 TRP 0.020 0.001 TRP B 775 HIS 0.005 0.001 HIS A 562 Details of bonding type rmsd covalent geometry : bond 0.00491 (12877) covalent geometry : angle 0.60563 (17546) SS BOND : bond 0.00352 ( 20) SS BOND : angle 1.20144 ( 40) hydrogen bonds : bond 0.04052 ( 624) hydrogen bonds : angle 4.39953 ( 1782) link_NAG-ASN : bond 0.00928 ( 16) link_NAG-ASN : angle 4.41380 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 161 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8957 (mm) REVERT: B 155 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8846 (mtmt) REVERT: B 260 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7347 (mm) REVERT: B 501 ARG cc_start: 0.8756 (mmm160) cc_final: 0.8473 (mmt180) REVERT: B 598 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7458 (tt) REVERT: B 690 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6618 (mt) REVERT: B 709 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7593 (p) REVERT: B 717 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7286 (pt0) REVERT: B 734 HIS cc_start: 0.6768 (m170) cc_final: 0.6506 (m170) REVERT: A 253 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8128 (mm-30) REVERT: A 567 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6466 (tt) REVERT: A 656 VAL cc_start: 0.7929 (t) cc_final: 0.7571 (p) outliers start: 89 outliers final: 75 residues processed: 234 average time/residue: 0.1125 time to fit residues: 39.1381 Evaluate side-chains 236 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 153 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 TRP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 796 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 45 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 136 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 449 ASN ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.126368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.103744 restraints weight = 23631.861| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.77 r_work: 0.3363 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 12913 Z= 0.143 Angle : 0.621 15.881 17634 Z= 0.290 Chirality : 0.044 0.424 2042 Planarity : 0.004 0.053 2203 Dihedral : 6.943 58.272 2045 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.72 % Allowed : 26.49 % Favored : 67.79 % 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 aren not related in a simple way. whole: 0.58 (0.22), residues: 1551 helix: 1.53 (0.19), residues: 752 sheet: -1.16 (0.39), residues: 173 loop : -0.50 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 76 TYR 0.017 0.001 TYR A 389 PHE 0.019 0.001 PHE A 552 TRP 0.016 0.001 TRP B 775 HIS 0.004 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00338 (12877) covalent geometry : angle 0.57500 (17546) SS BOND : bond 0.00336 ( 20) SS BOND : angle 1.61324 ( 40) hydrogen bonds : bond 0.03767 ( 624) hydrogen bonds : angle 4.31882 ( 1782) link_NAG-ASN : bond 0.00933 ( 16) link_NAG-ASN : angle 4.31131 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 159 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8860 (mm) REVERT: B 260 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7351 (mm) REVERT: B 458 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8614 (tp) REVERT: B 501 ARG cc_start: 0.8775 (mmm160) cc_final: 0.8495 (mmt180) REVERT: B 502 GLN cc_start: 0.7808 (pp30) cc_final: 0.7494 (pp30) REVERT: B 690 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6597 (mt) REVERT: B 709 THR cc_start: 0.7841 (OUTLIER) cc_final: 0.7516 (p) REVERT: B 717 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: B 734 HIS cc_start: 0.6692 (m170) cc_final: 0.6145 (m170) REVERT: A 567 ILE cc_start: 0.6766 (OUTLIER) cc_final: 0.6466 (tt) REVERT: A 621 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.6407 (t80) REVERT: A 656 VAL cc_start: 0.7896 (t) cc_final: 0.7541 (p) outliers start: 78 outliers final: 67 residues processed: 224 average time/residue: 0.1052 time to fit residues: 35.3839 Evaluate side-chains 227 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 152 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 TRP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 796 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 119 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 73 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.126545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.104585 restraints weight = 23910.640| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.75 r_work: 0.3379 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12913 Z= 0.135 Angle : 0.608 15.487 17634 Z= 0.283 Chirality : 0.044 0.424 2042 Planarity : 0.004 0.053 2203 Dihedral : 6.826 57.419 2045 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.65 % Allowed : 26.49 % Favored : 67.87 % 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 aren not related in a simple way. whole: 0.66 (0.22), residues: 1551 helix: 1.61 (0.19), residues: 753 sheet: -1.15 (0.39), residues: 173 loop : -0.48 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 76 TYR 0.016 0.001 TYR A 389 PHE 0.018 0.001 PHE A 552 TRP 0.028 0.001 TRP B 775 HIS 0.004 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00321 (12877) covalent geometry : angle 0.56387 (17546) SS BOND : bond 0.00365 ( 20) SS BOND : angle 1.43405 ( 40) hydrogen bonds : bond 0.03631 ( 624) hydrogen bonds : angle 4.24295 ( 1782) link_NAG-ASN : bond 0.00914 ( 16) link_NAG-ASN : angle 4.20752 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 161 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8836 (mm) REVERT: B 260 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7323 (mm) REVERT: B 501 ARG cc_start: 0.8786 (mmm160) cc_final: 0.8503 (mmt180) REVERT: B 502 GLN cc_start: 0.7830 (pp30) cc_final: 0.7525 (pp30) REVERT: B 598 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7464 (tt) REVERT: B 690 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6614 (mt) REVERT: B 709 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7482 (p) REVERT: B 717 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7182 (pt0) REVERT: B 775 TRP cc_start: 0.6825 (m100) cc_final: 0.6338 (m100) REVERT: A 567 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.6390 (tt) REVERT: A 621 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.6324 (t80) REVERT: A 656 VAL cc_start: 0.7891 (t) cc_final: 0.7541 (p) outliers start: 77 outliers final: 68 residues processed: 224 average time/residue: 0.1095 time to fit residues: 36.4578 Evaluate side-chains 232 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 156 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 TRP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 796 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 56 optimal weight: 0.6980 chunk 6 optimal weight: 0.0870 chunk 118 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 44 optimal weight: 0.1980 chunk 73 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 HIS ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 GLN ** A 189 HIS ** 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 = 0.3884 r_free = 0.3884 target = 0.128416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.105954 restraints weight = 23788.300| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.77 r_work: 0.3383 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 12913 Z= 0.110 Angle : 0.590 14.884 17634 Z= 0.274 Chirality : 0.043 0.419 2042 Planarity : 0.004 0.053 2203 Dihedral : 6.634 56.344 2043 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.99 % Allowed : 27.37 % Favored : 67.64 % 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 aren not related in a simple way. whole: 0.81 (0.22), residues: 1551 helix: 1.74 (0.19), residues: 752 sheet: -1.21 (0.39), residues: 172 loop : -0.35 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.017 0.001 TYR A 96 PHE 0.021 0.001 PHE A 552 TRP 0.017 0.001 TRP B 775 HIS 0.004 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00244 (12877) covalent geometry : angle 0.54816 (17546) SS BOND : bond 0.00329 ( 20) SS BOND : angle 1.25782 ( 40) hydrogen bonds : bond 0.03412 ( 624) hydrogen bonds : angle 4.16282 ( 1782) link_NAG-ASN : bond 0.00931 ( 16) link_NAG-ASN : angle 4.07551 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 172 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8824 (mm) REVERT: B 260 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7331 (mm) REVERT: B 501 ARG cc_start: 0.8788 (mmm160) cc_final: 0.8515 (mmt180) REVERT: B 502 GLN cc_start: 0.7826 (pp30) cc_final: 0.7518 (pp30) REVERT: B 598 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7325 (tt) REVERT: B 619 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7725 (mp) REVERT: B 690 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6586 (mt) REVERT: B 709 THR cc_start: 0.7746 (OUTLIER) cc_final: 0.7408 (p) REVERT: B 717 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7153 (pt0) REVERT: B 775 TRP cc_start: 0.6756 (m100) cc_final: 0.6187 (m100) REVERT: B 820 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7606 (pt0) REVERT: A 113 TYR cc_start: 0.8507 (t80) cc_final: 0.8112 (t80) REVERT: A 567 ILE cc_start: 0.6802 (OUTLIER) cc_final: 0.6473 (tt) REVERT: A 616 MET cc_start: 0.7551 (tpt) cc_final: 0.7169 (ttt) REVERT: A 621 TYR cc_start: 0.7561 (OUTLIER) cc_final: 0.6433 (t80) outliers start: 68 outliers final: 52 residues processed: 227 average time/residue: 0.1138 time to fit residues: 38.0178 Evaluate side-chains 222 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 160 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 820 GLN Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 TRP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 774 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 48 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 118 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 257 GLN B 469 HIS B 721 HIS ** B 734 HIS ** 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 = 0.3865 r_free = 0.3865 target = 0.127263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.105265 restraints weight = 23857.286| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.69 r_work: 0.3390 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12913 Z= 0.140 Angle : 0.624 14.516 17634 Z= 0.289 Chirality : 0.044 0.416 2042 Planarity : 0.004 0.052 2203 Dihedral : 6.672 56.591 2042 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.62 % Allowed : 27.59 % Favored : 67.79 % 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 aren not related in a simple way. whole: 0.72 (0.22), residues: 1551 helix: 1.67 (0.19), residues: 755 sheet: -1.20 (0.39), residues: 172 loop : -0.42 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.027 0.001 TYR A 113 PHE 0.023 0.001 PHE B 703 TRP 0.018 0.001 TRP B 775 HIS 0.004 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00335 (12877) covalent geometry : angle 0.58555 (17546) SS BOND : bond 0.00330 ( 20) SS BOND : angle 1.26230 ( 40) hydrogen bonds : bond 0.03563 ( 624) hydrogen bonds : angle 4.20281 ( 1782) link_NAG-ASN : bond 0.00897 ( 16) link_NAG-ASN : angle 4.05349 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3071.04 seconds wall clock time: 53 minutes 37.75 seconds (3217.75 seconds total)