Starting phenix.real_space_refine on Wed Jun 11 06:54:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nor_49608/06_2025/9nor_49608.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nor_49608/06_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_49608/06_2025/9nor_49608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nor_49608/06_2025/9nor_49608.map" model { file = "/net/cci-nas-00/data/ceres_data/9nor_49608/06_2025/9nor_49608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nor_49608/06_2025/9nor_49608.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.40, per 1000 atoms: 0.67 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: 2.97 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.40 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: 4.45 Time building geometry restraints manager: 3.58 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: 5.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 31.110 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.580 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.037 0.001 TRP B 775 HIS 0.007 0.001 HIS B 734 PHE 0.022 0.001 PHE A 552 TYR 0.012 0.001 TYR A 113 ARG 0.003 0.000 ARG A 821 Details of bonding type rmsd link_NAG-ASN : bond 0.00961 ( 16) link_NAG-ASN : angle 4.55373 ( 48) hydrogen bonds : bond 0.13695 ( 624) hydrogen bonds : angle 5.80523 ( 1782) SS BOND : bond 0.00383 ( 20) SS BOND : angle 1.14594 ( 40) covalent geometry : bond 0.00351 (12877) covalent geometry : angle 0.63859 (17546) *********************** 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 : 1.415 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: 0.2424 time to fit residues: 67.8360 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 : 1.313 ------------------------------------------------------------------------------- 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 131 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 A 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.124622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.103149 restraints weight = 23872.166| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.54 r_work: 0.3354 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.006 0.057 12913 Z= 0.243 Angle : 0.682 17.225 17634 Z= 0.325 Chirality : 0.047 0.405 2042 Planarity : 0.005 0.053 2203 Dihedral : 7.780 59.637 2065 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 7.63 % Allowed : 23.99 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.22), residues: 1551 helix: 1.35 (0.19), residues: 748 sheet: -1.55 (0.37), residues: 183 loop : -0.43 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 303 HIS 0.011 0.001 HIS B 734 PHE 0.028 0.002 PHE B 730 TYR 0.020 0.002 TYR A 389 ARG 0.004 0.000 ARG A 664 Details of bonding type rmsd link_NAG-ASN : bond 0.00979 ( 16) link_NAG-ASN : angle 4.64757 ( 48) hydrogen bonds : bond 0.04547 ( 624) hydrogen bonds : angle 4.85368 ( 1782) SS BOND : bond 0.00468 ( 20) SS BOND : angle 1.26678 ( 40) covalent geometry : bond 0.00594 (12877) covalent geometry : angle 0.63604 (17546) *********************** 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 261 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 157 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8935 (mm) REVERT: B 155 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8886 (mtmt) REVERT: B 260 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7421 (mm) REVERT: B 541 CYS cc_start: 0.3569 (OUTLIER) cc_final: 0.2386 (m) REVERT: B 709 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7643 (p) REVERT: B 717 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7309 (pt0) REVERT: A 253 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8081 (mm-30) REVERT: A 541 ASN cc_start: 0.6062 (OUTLIER) cc_final: 0.5734 (p0) REVERT: A 567 ILE cc_start: 0.6867 (OUTLIER) cc_final: 0.6588 (tt) REVERT: A 815 ILE cc_start: 0.7628 (mm) cc_final: 0.7298 (mt) outliers start: 104 outliers final: 65 residues processed: 241 average time/residue: 0.2266 time to fit residues: 83.1132 Evaluate side-chains 220 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 147 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 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 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 645 THR 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 769 LEU 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 B residue 802 VAL 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 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 541 ASN 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 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 748 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 796 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 449 ASN A 541 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.126103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.103205 restraints weight = 23929.888| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.83 r_work: 0.3355 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1013 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= 0.156 Angle : 0.624 17.347 17634 Z= 0.293 Chirality : 0.045 0.402 2042 Planarity : 0.004 0.054 2203 Dihedral : 7.315 58.446 2052 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.58 % Allowed : 26.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1551 helix: 1.48 (0.19), residues: 747 sheet: -1.51 (0.37), residues: 182 loop : -0.47 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 775 HIS 0.004 0.001 HIS B 405 PHE 0.019 0.001 PHE A 552 TYR 0.017 0.001 TYR A 389 ARG 0.003 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00974 ( 16) link_NAG-ASN : angle 4.59565 ( 48) hydrogen bonds : bond 0.04026 ( 624) hydrogen bonds : angle 4.59762 ( 1782) SS BOND : bond 0.00372 ( 20) SS BOND : angle 1.42546 ( 40) covalent geometry : bond 0.00370 (12877) covalent geometry : angle 0.57396 (17546) *********************** 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 232 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 156 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8880 (mm) REVERT: B 260 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7323 (mm) REVERT: B 469 HIS cc_start: 0.8354 (m-70) cc_final: 0.8091 (m90) REVERT: B 501 ARG cc_start: 0.8759 (mmm160) cc_final: 0.8515 (mmt180) REVERT: B 541 CYS cc_start: 0.3532 (OUTLIER) cc_final: 0.2353 (m) REVERT: B 690 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6591 (mt) REVERT: B 699 TYR cc_start: 0.6515 (OUTLIER) cc_final: 0.6289 (t80) REVERT: B 717 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7279 (pt0) REVERT: A 172 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7330 (mtt-85) REVERT: A 253 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8100 (mm-30) REVERT: A 567 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.6526 (tt) REVERT: A 679 TYR cc_start: 0.7133 (m-80) cc_final: 0.6526 (m-80) REVERT: A 815 ILE cc_start: 0.7599 (mm) cc_final: 0.7297 (mt) outliers start: 76 outliers final: 53 residues processed: 217 average time/residue: 0.3174 time to fit residues: 103.9840 Evaluate side-chains 209 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 148 time to evaluate : 1.586 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 613 VAL Chi-restraints excluded: chain A residue 620 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 774 VAL Chi-restraints excluded: chain A residue 797 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 79 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 135 optimal weight: 0.0970 chunk 115 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.125587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.103873 restraints weight = 23727.814| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.67 r_work: 0.3362 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12913 Z= 0.165 Angle : 0.620 17.129 17634 Z= 0.290 Chirality : 0.045 0.410 2042 Planarity : 0.004 0.054 2203 Dihedral : 7.261 59.970 2048 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 7.12 % Allowed : 25.46 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.22), residues: 1551 helix: 1.48 (0.19), residues: 749 sheet: -1.46 (0.37), residues: 183 loop : -0.46 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 775 HIS 0.005 0.001 HIS A 562 PHE 0.021 0.001 PHE A 552 TYR 0.018 0.001 TYR A 389 ARG 0.003 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00960 ( 16) link_NAG-ASN : angle 4.54602 ( 48) hydrogen bonds : bond 0.03904 ( 624) hydrogen bonds : angle 4.46166 ( 1782) SS BOND : bond 0.00336 ( 20) SS BOND : angle 1.24899 ( 40) covalent geometry : bond 0.00395 (12877) covalent geometry : angle 0.57109 (17546) *********************** 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 257 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 160 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8871 (mm) REVERT: B 155 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8855 (mtmt) REVERT: B 260 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7398 (mm) REVERT: B 501 ARG cc_start: 0.8735 (mmm160) cc_final: 0.8476 (mmt180) REVERT: B 502 GLN cc_start: 0.7898 (pp30) cc_final: 0.7514 (pp30) REVERT: B 541 CYS cc_start: 0.3410 (OUTLIER) cc_final: 0.2172 (m) REVERT: B 690 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6679 (mt) REVERT: B 717 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7207 (mt-10) REVERT: B 775 TRP cc_start: 0.6699 (m100) cc_final: 0.6155 (m100) REVERT: A 253 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8081 (mm-30) REVERT: A 567 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.6606 (tt) REVERT: A 621 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.6121 (t80) REVERT: A 679 TYR cc_start: 0.7137 (m-80) cc_final: 0.6472 (m-80) REVERT: A 815 ILE cc_start: 0.7632 (mm) cc_final: 0.7327 (mt) outliers start: 97 outliers final: 74 residues processed: 239 average time/residue: 0.2668 time to fit residues: 95.3922 Evaluate side-chains 232 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 150 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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 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 489 THR 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 541 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 647 CYS Chi-restraints excluded: chain B residue 658 ILE 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 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 776 VAL 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 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 647 CYS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 698 LEU 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 775 SER Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 797 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 65 optimal weight: 0.0570 chunk 80 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.126687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.103854 restraints weight = 23584.196| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.81 r_work: 0.3366 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12913 Z= 0.133 Angle : 0.601 16.859 17634 Z= 0.279 Chirality : 0.044 0.418 2042 Planarity : 0.004 0.053 2203 Dihedral : 7.041 59.327 2045 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.87 % Allowed : 26.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1551 helix: 1.61 (0.19), residues: 749 sheet: -1.41 (0.37), residues: 183 loop : -0.41 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 775 HIS 0.004 0.001 HIS B 405 PHE 0.017 0.001 PHE B 65 TYR 0.020 0.001 TYR A 783 ARG 0.003 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00962 ( 16) link_NAG-ASN : angle 4.43592 ( 48) hydrogen bonds : bond 0.03685 ( 624) hydrogen bonds : angle 4.31802 ( 1782) SS BOND : bond 0.00305 ( 20) SS BOND : angle 1.15804 ( 40) covalent geometry : bond 0.00309 (12877) covalent geometry : angle 0.55379 (17546) *********************** 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 238 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 158 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8929 (mm) REVERT: B 260 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7296 (mm) REVERT: B 501 ARG cc_start: 0.8757 (mmm160) cc_final: 0.8401 (mmt180) REVERT: B 541 CYS cc_start: 0.3268 (OUTLIER) cc_final: 0.2041 (m) REVERT: B 598 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7374 (tt) REVERT: B 690 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6605 (mt) REVERT: B 717 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7211 (pt0) REVERT: A 567 ILE cc_start: 0.6860 (tt) cc_final: 0.6567 (tt) REVERT: A 621 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.6171 (t80) REVERT: A 815 ILE cc_start: 0.7588 (mm) cc_final: 0.7289 (mt) outliers start: 80 outliers final: 64 residues processed: 224 average time/residue: 0.2332 time to fit residues: 77.4574 Evaluate side-chains 221 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 150 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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 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 541 CYS 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 621 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 658 ILE 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 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 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 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 471 LEU 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 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 627 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 117 optimal weight: 0.0570 chunk 104 optimal weight: 3.9990 chunk 148 optimal weight: 0.0170 chunk 55 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.126927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.104164 restraints weight = 23946.908| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.84 r_work: 0.3368 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12913 Z= 0.124 Angle : 0.586 16.405 17634 Z= 0.273 Chirality : 0.044 0.420 2042 Planarity : 0.004 0.052 2203 Dihedral : 6.888 59.558 2045 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 6.02 % Allowed : 26.41 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.22), residues: 1551 helix: 1.67 (0.19), residues: 752 sheet: -1.31 (0.38), residues: 180 loop : -0.40 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 775 HIS 0.004 0.001 HIS B 405 PHE 0.013 0.001 PHE A 552 TYR 0.016 0.001 TYR A 96 ARG 0.004 0.000 ARG A 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00947 ( 16) link_NAG-ASN : angle 4.32720 ( 48) hydrogen bonds : bond 0.03581 ( 624) hydrogen bonds : angle 4.23524 ( 1782) SS BOND : bond 0.00298 ( 20) SS BOND : angle 1.09470 ( 40) covalent geometry : bond 0.00288 (12877) covalent geometry : angle 0.54004 (17546) *********************** 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 251 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 169 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8854 (mm) REVERT: B 260 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7366 (mm) REVERT: B 501 ARG cc_start: 0.8754 (mmm160) cc_final: 0.8403 (mmt180) REVERT: B 502 GLN cc_start: 0.7822 (pp30) cc_final: 0.7514 (pp30) REVERT: B 598 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7460 (tt) REVERT: B 685 VAL cc_start: 0.6154 (t) cc_final: 0.5902 (p) REVERT: B 690 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6653 (mt) REVERT: B 717 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7210 (pt0) REVERT: A 253 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8128 (mm-30) REVERT: A 567 ILE cc_start: 0.6881 (OUTLIER) cc_final: 0.6570 (tt) outliers start: 82 outliers final: 71 residues processed: 234 average time/residue: 0.2317 time to fit residues: 80.6201 Evaluate side-chains 235 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 158 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 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 658 ILE Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 693 VAL 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 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 183 THR Chi-restraints excluded: chain A residue 231 ASP 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 471 LEU 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 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 748 MET Chi-restraints excluded: chain A residue 797 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 257 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.126243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.103504 restraints weight = 23784.440| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.82 r_work: 0.3359 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 : 0.004 0.109 12913 Z= 0.164 Angle : 0.615 16.137 17634 Z= 0.289 Chirality : 0.045 0.424 2042 Planarity : 0.004 0.052 2203 Dihedral : 6.950 58.774 2045 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 6.53 % Allowed : 25.97 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.22), residues: 1551 helix: 1.54 (0.19), residues: 753 sheet: -1.30 (0.37), residues: 183 loop : -0.45 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 775 HIS 0.004 0.001 HIS B 405 PHE 0.014 0.001 PHE A 770 TYR 0.017 0.001 TYR A 389 ARG 0.002 0.000 ARG A 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00927 ( 16) link_NAG-ASN : angle 4.28877 ( 48) hydrogen bonds : bond 0.03779 ( 624) hydrogen bonds : angle 4.27349 ( 1782) SS BOND : bond 0.00396 ( 20) SS BOND : angle 1.55369 ( 40) covalent geometry : bond 0.00399 (12877) covalent geometry : angle 0.56895 (17546) *********************** 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 249 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 160 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8945 (mm) REVERT: B 260 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7305 (mm) REVERT: B 501 ARG cc_start: 0.8761 (mmm160) cc_final: 0.8389 (mmt180) REVERT: B 598 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7489 (tt) REVERT: B 690 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6634 (mt) REVERT: B 717 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7239 (pt0) REVERT: A 253 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8123 (mm-30) REVERT: A 567 ILE cc_start: 0.6677 (OUTLIER) cc_final: 0.6361 (tt) REVERT: A 621 TYR cc_start: 0.7592 (OUTLIER) cc_final: 0.6361 (t80) outliers start: 89 outliers final: 76 residues processed: 233 average time/residue: 0.2273 time to fit residues: 78.6327 Evaluate side-chains 240 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 157 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 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 689 MET Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 693 VAL 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 751 VAL 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 471 LEU 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 738 LEU Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 797 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 27 optimal weight: 0.2980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3819 r_free = 0.3819 target = 0.124234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102548 restraints weight = 23951.836| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.58 r_work: 0.3343 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12913 Z= 0.223 Angle : 0.661 15.736 17634 Z= 0.313 Chirality : 0.047 0.419 2042 Planarity : 0.004 0.054 2203 Dihedral : 7.127 58.733 2045 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 6.53 % Allowed : 26.12 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1551 helix: 1.35 (0.19), residues: 752 sheet: -1.27 (0.38), residues: 178 loop : -0.59 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 775 HIS 0.006 0.001 HIS A 562 PHE 0.015 0.002 PHE B 435 TYR 0.019 0.002 TYR A 389 ARG 0.003 0.000 ARG A 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00892 ( 16) link_NAG-ASN : angle 4.31384 ( 48) hydrogen bonds : bond 0.04208 ( 624) hydrogen bonds : angle 4.42737 ( 1782) SS BOND : bond 0.00401 ( 20) SS BOND : angle 1.42455 ( 40) covalent geometry : bond 0.00547 (12877) covalent geometry : angle 0.61975 (17546) *********************** 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 251 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 162 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8978 (mm) REVERT: B 260 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7342 (mm) REVERT: B 458 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8587 (tp) REVERT: B 501 ARG cc_start: 0.8767 (mmm160) cc_final: 0.8381 (mmt180) REVERT: B 598 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7542 (tt) REVERT: B 690 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6588 (mt) REVERT: B 717 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: A 214 THR cc_start: 0.8179 (t) cc_final: 0.7705 (m) REVERT: A 253 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8102 (mm-30) REVERT: A 567 ILE cc_start: 0.6710 (OUTLIER) cc_final: 0.6411 (tt) REVERT: A 656 VAL cc_start: 0.7974 (t) cc_final: 0.7618 (p) outliers start: 89 outliers final: 73 residues processed: 237 average time/residue: 0.2251 time to fit residues: 79.4252 Evaluate side-chains 235 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 155 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 67 SER 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 647 CYS Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 693 VAL 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 751 VAL 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 306 ILE 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 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 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 738 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 797 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.126423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103827 restraints weight = 23697.605| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.82 r_work: 0.3361 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1660 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= 0.135 Angle : 0.606 15.223 17634 Z= 0.285 Chirality : 0.044 0.416 2042 Planarity : 0.004 0.053 2203 Dihedral : 6.878 57.095 2045 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.43 % Allowed : 27.22 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1551 helix: 1.56 (0.19), residues: 748 sheet: -1.19 (0.39), residues: 173 loop : -0.46 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 303 HIS 0.004 0.001 HIS B 405 PHE 0.018 0.001 PHE A 770 TYR 0.017 0.001 TYR A 96 ARG 0.004 0.000 ARG A 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00912 ( 16) link_NAG-ASN : angle 4.17248 ( 48) hydrogen bonds : bond 0.03724 ( 624) hydrogen bonds : angle 4.29901 ( 1782) SS BOND : bond 0.00350 ( 20) SS BOND : angle 1.21133 ( 40) covalent geometry : bond 0.00316 (12877) covalent geometry : angle 0.56418 (17546) *********************** 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 235 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 161 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8935 (mm) REVERT: B 260 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7297 (mm) REVERT: B 449 ASN cc_start: 0.7807 (m-40) cc_final: 0.7363 (m-40) REVERT: B 501 ARG cc_start: 0.8808 (mmm160) cc_final: 0.8431 (mmt180) REVERT: B 502 GLN cc_start: 0.7798 (pp30) cc_final: 0.7492 (pp30) REVERT: B 598 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7446 (tt) REVERT: B 690 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6569 (mt) REVERT: B 699 TYR cc_start: 0.6584 (t80) cc_final: 0.6185 (t80) REVERT: B 717 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7042 (mt-10) REVERT: A 567 ILE cc_start: 0.6689 (tt) cc_final: 0.6353 (tt) REVERT: A 621 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.6345 (t80) outliers start: 74 outliers final: 66 residues processed: 222 average time/residue: 0.2386 time to fit residues: 78.1190 Evaluate side-chains 229 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 157 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 647 CYS Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 693 VAL 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 751 VAL 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 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 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 31 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 2 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.0270 chunk 24 optimal weight: 0.5980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 257 GLN ** 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 = 0.3868 r_free = 0.3868 target = 0.127455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.105706 restraints weight = 23606.550| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.77 r_work: 0.3392 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12913 Z= 0.117 Angle : 0.586 14.778 17634 Z= 0.274 Chirality : 0.044 0.419 2042 Planarity : 0.004 0.053 2203 Dihedral : 6.695 56.666 2043 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.21 % Allowed : 27.29 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1551 helix: 1.70 (0.19), residues: 752 sheet: -1.18 (0.39), residues: 169 loop : -0.38 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 424 HIS 0.004 0.001 HIS B 405 PHE 0.020 0.001 PHE A 770 TYR 0.018 0.001 TYR A 96 ARG 0.004 0.000 ARG A 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00898 ( 16) link_NAG-ASN : angle 4.01586 ( 48) hydrogen bonds : bond 0.03509 ( 624) hydrogen bonds : angle 4.18975 ( 1782) SS BOND : bond 0.00310 ( 20) SS BOND : angle 1.07207 ( 40) covalent geometry : bond 0.00268 (12877) covalent geometry : angle 0.54578 (17546) ********************** 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: 71 poor density : 169 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8840 (mm) REVERT: B 260 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7315 (mm) REVERT: B 449 ASN cc_start: 0.7800 (m-40) cc_final: 0.7490 (t0) REVERT: B 501 ARG cc_start: 0.8792 (mmm160) cc_final: 0.8425 (mmt180) REVERT: B 502 GLN cc_start: 0.7806 (pp30) cc_final: 0.7516 (pp30) REVERT: B 598 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7348 (tt) REVERT: B 619 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7736 (mp) REVERT: B 685 VAL cc_start: 0.6119 (t) cc_final: 0.5879 (p) REVERT: B 690 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6613 (mt) REVERT: B 699 TYR cc_start: 0.6605 (t80) cc_final: 0.6228 (t80) REVERT: B 717 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7159 (pt0) REVERT: A 113 TYR cc_start: 0.8385 (t80) cc_final: 0.8169 (t80) REVERT: A 253 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8086 (mm-30) REVERT: A 616 MET cc_start: 0.7526 (tpt) cc_final: 0.7174 (ttt) outliers start: 71 outliers final: 56 residues processed: 226 average time/residue: 0.2397 time to fit residues: 80.5116 Evaluate side-chains 225 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 163 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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 341 HIS Chi-restraints excluded: chain B residue 381 VAL 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 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 658 ILE Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 693 VAL 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 793 VAL 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 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 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 76 optimal weight: 0.2980 chunk 100 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 148 optimal weight: 0.0040 chunk 103 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.127708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.105831 restraints weight = 23746.196| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.81 r_work: 0.3392 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12913 Z= 0.118 Angle : 0.591 14.348 17634 Z= 0.277 Chirality : 0.044 0.415 2042 Planarity : 0.004 0.053 2203 Dihedral : 6.592 56.787 2040 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.77 % Allowed : 27.73 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1551 helix: 1.73 (0.19), residues: 752 sheet: -1.15 (0.40), residues: 169 loop : -0.40 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 424 HIS 0.004 0.001 HIS B 405 PHE 0.019 0.001 PHE B 703 TYR 0.022 0.001 TYR A 669 ARG 0.005 0.000 ARG A 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00893 ( 16) link_NAG-ASN : angle 3.94089 ( 48) hydrogen bonds : bond 0.03471 ( 624) hydrogen bonds : angle 4.15150 ( 1782) SS BOND : bond 0.00302 ( 20) SS BOND : angle 1.05885 ( 40) covalent geometry : bond 0.00274 (12877) covalent geometry : angle 0.55310 (17546) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6149.52 seconds wall clock time: 108 minutes 9.60 seconds (6489.60 seconds total)