Starting phenix.real_space_refine on Sat Aug 23 14:02:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nos_49612/08_2025/9nos_49612.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nos_49612/08_2025/9nos_49612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nos_49612/08_2025/9nos_49612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nos_49612/08_2025/9nos_49612.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nos_49612/08_2025/9nos_49612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nos_49612/08_2025/9nos_49612.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.018 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 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12555 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6059 Classifications: {'peptide': 780} Link IDs: {'PTRANS': 45, 'TRANS': 734} Chain breaks: 3 Chain: "A" Number of atoms: 6272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6272 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 40, 'TRANS': 744} Chain breaks: 2 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 3.03, per 1000 atoms: 0.24 Number of scatterers: 12555 At special positions: 0 Unit cell: (95.468, 90.53, 184.352, 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=2.03 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=2.03 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=2.03 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: 0.85 Conformation dependent library (CDL) restraints added in 428.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 18 sheets defined 54.8% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 66 through 86 removed outlier: 3.613A pdb=" N LEU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 118 removed outlier: 4.164A 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: 3.951A pdb=" N GLN B 133 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 161 removed outlier: 3.924A pdb=" N VAL B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.515A pdb=" N LEU B 174 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.894A 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: 3.645A 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: 4.529A 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: 3.567A pdb=" N CYS B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.800A pdb=" N ASP B 374 " --> pdb=" O PRO B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 385 removed outlier: 3.956A pdb=" N SER B 382 " --> pdb=" O GLN B 379 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ALA B 383 " --> pdb=" O ASN B 380 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 385 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 409 removed outlier: 3.835A 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 Processing helix chain 'B' and resid 482 through 485 removed outlier: 3.585A pdb=" N ILE B 485 " --> pdb=" O ARG B 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 482 through 485' Processing helix chain 'B' and resid 566 through 593 Processing helix chain 'B' and resid 596 through 602 removed outlier: 3.543A pdb=" N GLN B 600 " --> pdb=" O SER B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 622 removed outlier: 3.839A pdb=" N LEU B 622 " --> pdb=" O CYS B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 664 removed outlier: 5.045A 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 removed outlier: 3.924A pdb=" N LEU B 664 " --> pdb=" O VAL B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 677 removed outlier: 4.285A pdb=" N ARG B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY B 674 " --> pdb=" O ASP B 670 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS B 675 " --> pdb=" O ARG B 671 " (cutoff:3.500A) removed outlier: 3.978A 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: 4.617A pdb=" N THR B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 4.731A 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: 4.712A pdb=" N LEU B 811 " --> pdb=" O ALA B 807 " (cutoff:3.500A) Proline residue: B 812 - end of helix removed outlier: 3.542A pdb=" N LEU B 816 " --> pdb=" O PRO B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 824 removed outlier: 3.825A pdb=" N LEU B 823 " --> pdb=" O GLN B 820 " (cutoff:3.500A) removed outlier: 3.894A 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: 4.349A 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: 3.703A pdb=" N LEU A 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP A 173 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 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 291 Processing helix chain 'A' and resid 307 through 313 removed outlier: 3.893A pdb=" N HIS A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 319 removed outlier: 4.623A pdb=" N ARG A 317 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS A 318 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 removed outlier: 3.593A pdb=" N GLY A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 373 removed outlier: 3.897A pdb=" N SER A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.863A 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 622 Proline residue: A 619 - end of helix removed outlier: 4.254A pdb=" N VAL A 622 " --> pdb=" O VAL A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 665 Proline residue: A 638 - end of helix removed outlier: 4.595A pdb=" N ALA A 658 " --> pdb=" O GLN A 654 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N PHE A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS A 660 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER A 663 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG A 664 " --> pdb=" O LYS A 660 " (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: 3.882A pdb=" N SER A 727 " --> pdb=" O ASN A 723 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 741 " --> pdb=" O LEU A 737 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 removed outlier: 3.625A pdb=" N PHE A 761 " --> pdb=" O ASN A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 818 removed outlier: 3.702A 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: 4.030A 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: 3.680A pdb=" N TYR B 97 " --> pdb=" O MET B 31 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TYR B 35 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ASP B 98 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU B 37 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE B 100 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY B 39 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA3, first strand: chain 'B' and resid 124 through 126 Processing sheet with id=AA4, first strand: chain 'B' and resid 141 through 143 removed outlier: 6.413A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLN B 164 " --> pdb=" O PHE B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.973A pdb=" N VAL B 209 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLU B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ALA B 211 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU B 242 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLY B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL B 270 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE B 324 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL B 321 " --> pdb=" O TRP B 459 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR B 454 " --> pdb=" O ARG B 473 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ARG B 473 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU B 456 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 462 " --> pdb=" O VAL B 465 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 434 through 437 Processing sheet with id=AA7, first strand: chain 'B' and resid 508 through 511 Processing sheet with id=AA8, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AA9, first strand: chain 'B' and resid 545 through 546 Processing sheet with id=AB1, first strand: chain 'B' and resid 706 through 708 Processing sheet with id=AB2, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.510A pdb=" N LEU A 29 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 96 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 39 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU A 34 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N ILE A 139 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY A 36 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AB4, first strand: chain 'A' and resid 161 through 163 removed outlier: 6.127A pdb=" N GLN A 161 " --> pdb=" O LEU A 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 233 through 240 removed outlier: 7.715A pdb=" N ILE A 206 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN A 237 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 208 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N THR A 239 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 210 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TRP A 205 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N VAL A 273 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 6.356A 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: 6.792A pdb=" N LEU A 209 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL A 272 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TRP A 298 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ILE A 325 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA A 300 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N ILE A 327 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N PHE A 322 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A 448 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N SER A 467 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 450 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 428 through 431 Processing sheet with id=AB7, first strand: chain 'A' and resid 503 through 507 Processing sheet with id=AB8, first strand: chain 'A' and resid 524 through 527 removed outlier: 5.681A pdb=" N ASN A 527 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLU A 534 " --> pdb=" O ASN A 527 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 555 through 557 removed outlier: 6.997A pdb=" N GLN A 555 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL A 718 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N VAL A 557 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 717 " --> pdb=" O ARG A 707 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1791 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.19 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: 3952 1.34 - 1.46: 3184 1.46 - 1.59: 5605 1.59 - 1.71: 0 1.71 - 1.83: 136 Bond restraints: 12877 Sorted by residual: bond pdb=" C LEU B 642 " pdb=" N PRO B 643 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.28e-02 6.10e+03 1.59e+00 bond pdb=" CG ASN A 248 " pdb=" ND2 ASN A 248 " ideal model delta sigma weight residual 1.328 1.354 -0.026 2.10e-02 2.27e+03 1.56e+00 bond pdb=" C5 NAG B 908 " pdb=" O5 NAG B 908 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.30e+00 bond pdb=" CB CYS B 517 " pdb=" SG CYS B 517 " ideal model delta sigma weight residual 1.808 1.772 0.036 3.30e-02 9.18e+02 1.16e+00 bond pdb=" C4 NAG B 908 " pdb=" C5 NAG B 908 " ideal model delta sigma weight residual 1.532 1.553 -0.021 2.00e-02 2.50e+03 1.09e+00 ... (remaining 12872 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 17248 1.87 - 3.73: 246 3.73 - 5.60: 38 5.60 - 7.47: 10 7.47 - 9.33: 4 Bond angle restraints: 17546 Sorted by residual: angle pdb=" C ASP A 406 " pdb=" N LYS A 407 " pdb=" CA LYS A 407 " ideal model delta sigma weight residual 121.54 128.15 -6.61 1.91e+00 2.74e-01 1.20e+01 angle pdb=" C2 NAG A 905 " pdb=" N2 NAG A 905 " pdb=" C7 NAG A 905 " ideal model delta sigma weight residual 124.56 133.89 -9.33 3.00e+00 1.11e-01 9.68e+00 angle pdb=" CA CYS B 410 " pdb=" CB CYS B 410 " pdb=" SG CYS B 410 " ideal model delta sigma weight residual 114.40 120.85 -6.45 2.30e+00 1.89e-01 7.87e+00 angle pdb=" CA GLU B 525 " pdb=" CB GLU B 525 " pdb=" CG GLU B 525 " ideal model delta sigma weight residual 114.10 119.69 -5.59 2.00e+00 2.50e-01 7.81e+00 angle pdb=" C VAL A 618 " pdb=" CA VAL A 618 " pdb=" CB VAL A 618 " ideal model delta sigma weight residual 113.70 111.16 2.54 9.50e-01 1.11e+00 7.18e+00 ... (remaining 17541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6662 17.94 - 35.87: 884 35.87 - 53.81: 257 53.81 - 71.74: 48 71.74 - 89.68: 19 Dihedral angle restraints: 7870 sinusoidal: 3298 harmonic: 4572 Sorted by residual: dihedral pdb=" CB CYS A 495 " pdb=" SG CYS A 495 " pdb=" SG CYS A 514 " pdb=" CB CYS A 514 " ideal model delta sinusoidal sigma weight residual -86.00 -175.23 89.23 1 1.00e+01 1.00e-02 9.47e+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 -165.46 79.46 1 1.00e+01 1.00e-02 7.84e+01 dihedral pdb=" CB CYS A 363 " pdb=" SG CYS A 363 " pdb=" SG CYS A 366 " pdb=" CB CYS A 366 " ideal model delta sinusoidal sigma weight residual -86.00 -159.54 73.54 1 1.00e+01 1.00e-02 6.88e+01 ... (remaining 7867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 2031 0.140 - 0.279: 7 0.279 - 0.419: 3 0.419 - 0.558: 0 0.558 - 0.698: 1 Chirality restraints: 2042 Sorted by residual: chirality pdb=" C1 NAG B 908 " pdb=" ND2 ASN B 432 " pdb=" C2 NAG B 908 " pdb=" O5 NAG B 908 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 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 -2.07 -0.33 2.00e-01 2.50e+01 2.78e+00 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 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 2039 not shown) Planarity restraints: 2219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 593 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A 594 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 594 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 594 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 627 " 0.026 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO B 628 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 628 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 628 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 809 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO A 810 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 810 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 810 " -0.021 5.00e-02 4.00e+02 ... (remaining 2216 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 6811 3.00 - 3.48: 12860 3.48 - 3.95: 20044 3.95 - 4.43: 22693 4.43 - 4.90: 36890 Nonbonded interactions: 99298 Sorted by model distance: nonbonded pdb=" O ASN A 487 " pdb=" OD1 ASN A 487 " model vdw 2.528 3.040 nonbonded pdb=" N ASP B 491 " pdb=" OD1 ASP B 491 " model vdw 2.564 3.120 nonbonded pdb=" N THR B 736 " pdb=" CG2 THR B 736 " model vdw 2.565 2.832 nonbonded pdb=" O ASP A 127 " pdb=" OD1 ASP A 127 " model vdw 2.568 3.040 nonbonded pdb=" N GLU A 382 " pdb=" OE1 GLU A 382 " model vdw 2.571 3.120 ... (remaining 99293 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.220 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 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 : 0.003 0.036 12913 Z= 0.129 Angle : 0.664 21.130 17634 Z= 0.311 Chirality : 0.045 0.698 2042 Planarity : 0.004 0.043 2203 Dihedral : 17.374 89.677 4850 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.27 % Allowed : 29.20 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.22), residues: 1551 helix: 1.51 (0.19), residues: 750 sheet: -1.45 (0.42), residues: 163 loop : -0.53 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 498 TYR 0.017 0.001 TYR B 394 PHE 0.024 0.001 PHE A 659 TRP 0.013 0.001 TRP B 775 HIS 0.007 0.001 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00278 (12877) covalent geometry : angle 0.58487 (17546) SS BOND : bond 0.00259 ( 20) SS BOND : angle 1.24481 ( 40) hydrogen bonds : bond 0.14164 ( 628) hydrogen bonds : angle 5.68352 ( 1791) link_NAG-ASN : bond 0.01063 ( 16) link_NAG-ASN : angle 5.97385 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8416 (ptp-170) REVERT: B 214 SER cc_start: 0.8438 (p) cc_final: 0.8094 (p) REVERT: B 325 LEU cc_start: 0.8613 (tp) cc_final: 0.8285 (tp) REVERT: A 553 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7124 (tptp) REVERT: A 657 CYS cc_start: 0.6169 (t) cc_final: 0.5782 (t) REVERT: A 770 PHE cc_start: 0.7310 (t80) cc_final: 0.6974 (m-80) REVERT: A 776 LEU cc_start: 0.8065 (tp) cc_final: 0.7803 (tt) outliers start: 31 outliers final: 26 residues processed: 195 average time/residue: 0.0860 time to fit residues: 25.4553 Evaluate side-chains 191 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 712 HIS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 815 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0030 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 HIS A 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.118887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.099529 restraints weight = 24632.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.102170 restraints weight = 14940.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.103924 restraints weight = 10751.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.105103 restraints weight = 8600.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.105861 restraints weight = 7373.950| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.0553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12913 Z= 0.129 Angle : 0.620 18.256 17634 Z= 0.287 Chirality : 0.045 0.596 2042 Planarity : 0.004 0.044 2203 Dihedral : 8.081 57.320 2086 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.11 % Allowed : 27.44 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.22), residues: 1551 helix: 1.66 (0.19), residues: 744 sheet: -1.36 (0.38), residues: 187 loop : -0.42 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 498 TYR 0.017 0.001 TYR B 394 PHE 0.016 0.001 PHE A 591 TRP 0.008 0.001 TRP B 303 HIS 0.007 0.001 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00291 (12877) covalent geometry : angle 0.55500 (17546) SS BOND : bond 0.00311 ( 20) SS BOND : angle 1.10907 ( 40) hydrogen bonds : bond 0.04047 ( 628) hydrogen bonds : angle 4.54186 ( 1791) link_NAG-ASN : bond 0.01015 ( 16) link_NAG-ASN : angle 5.25491 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 170 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.5826 (ptm-80) REVERT: B 325 LEU cc_start: 0.8689 (tp) cc_final: 0.8411 (tp) REVERT: B 639 LEU cc_start: 0.7429 (mm) cc_final: 0.7024 (mp) REVERT: A 113 TYR cc_start: 0.8650 (t80) cc_final: 0.8394 (t80) REVERT: A 553 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6876 (tptp) REVERT: A 657 CYS cc_start: 0.6390 (t) cc_final: 0.5817 (t) REVERT: A 676 GLN cc_start: 0.4958 (mm-40) cc_final: 0.4711 (mm-40) REVERT: A 770 PHE cc_start: 0.7546 (t80) cc_final: 0.6978 (m-80) REVERT: A 776 LEU cc_start: 0.7882 (tp) cc_final: 0.7658 (tt) outliers start: 56 outliers final: 37 residues processed: 215 average time/residue: 0.0782 time to fit residues: 25.4165 Evaluate side-chains 198 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 216 ASP 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 430 MET Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 712 HIS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 812 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 88 optimal weight: 0.9980 chunk 54 optimal weight: 0.1980 chunk 126 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 HIS A 447 HIS ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.117663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.098646 restraints weight = 24850.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.101141 restraints weight = 15655.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.102789 restraints weight = 11476.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.103884 restraints weight = 9317.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.104630 restraints weight = 8055.411| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12913 Z= 0.151 Angle : 0.609 17.982 17634 Z= 0.281 Chirality : 0.044 0.451 2042 Planarity : 0.004 0.045 2203 Dihedral : 7.367 58.118 2058 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.43 % Allowed : 26.49 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.22), residues: 1551 helix: 1.64 (0.19), residues: 746 sheet: -1.40 (0.37), residues: 198 loop : -0.41 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 498 TYR 0.019 0.001 TYR B 394 PHE 0.019 0.001 PHE B 730 TRP 0.008 0.001 TRP B 303 HIS 0.009 0.001 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00356 (12877) covalent geometry : angle 0.55057 (17546) SS BOND : bond 0.00361 ( 20) SS BOND : angle 1.10424 ( 40) hydrogen bonds : bond 0.03913 ( 628) hydrogen bonds : angle 4.29462 ( 1791) link_NAG-ASN : bond 0.01018 ( 16) link_NAG-ASN : angle 4.93645 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 163 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.5968 (ptm-80) REVERT: B 325 LEU cc_start: 0.8671 (tp) cc_final: 0.8406 (tp) REVERT: B 582 LEU cc_start: 0.5474 (OUTLIER) cc_final: 0.4976 (mp) REVERT: B 639 LEU cc_start: 0.7632 (mm) cc_final: 0.7237 (mp) REVERT: A 106 ASN cc_start: 0.7336 (t0) cc_final: 0.7098 (t0) REVERT: A 553 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6857 (tptp) REVERT: A 657 CYS cc_start: 0.6507 (t) cc_final: 0.5863 (t) REVERT: A 676 GLN cc_start: 0.4969 (mm-40) cc_final: 0.4741 (mm-40) REVERT: A 770 PHE cc_start: 0.7580 (t80) cc_final: 0.7024 (m-80) REVERT: A 776 LEU cc_start: 0.7879 (tp) cc_final: 0.7673 (tt) outliers start: 74 outliers final: 47 residues processed: 222 average time/residue: 0.0799 time to fit residues: 27.0604 Evaluate side-chains 205 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 712 HIS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain A residue 812 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 112 optimal weight: 0.5980 chunk 155 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 50 optimal weight: 0.0270 chunk 123 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 HIS A 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.118071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.098638 restraints weight = 24822.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.101325 restraints weight = 15100.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.103056 restraints weight = 10877.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.104253 restraints weight = 8730.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.104902 restraints weight = 7494.611| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12913 Z= 0.133 Angle : 0.615 18.087 17634 Z= 0.284 Chirality : 0.043 0.365 2042 Planarity : 0.004 0.044 2203 Dihedral : 7.899 76.955 2055 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.72 % Allowed : 26.49 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.22), residues: 1551 helix: 1.68 (0.19), residues: 746 sheet: -1.40 (0.37), residues: 200 loop : -0.36 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 498 TYR 0.018 0.001 TYR B 394 PHE 0.012 0.001 PHE B 730 TRP 0.015 0.001 TRP B 775 HIS 0.004 0.001 HIS B 734 Details of bonding type rmsd covalent geometry : bond 0.00308 (12877) covalent geometry : angle 0.55797 (17546) SS BOND : bond 0.00260 ( 20) SS BOND : angle 1.04452 ( 40) hydrogen bonds : bond 0.03684 ( 628) hydrogen bonds : angle 4.19539 ( 1791) link_NAG-ASN : bond 0.01066 ( 16) link_NAG-ASN : angle 4.93486 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 164 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.5962 (ptm-80) REVERT: B 325 LEU cc_start: 0.8662 (tp) cc_final: 0.8395 (tp) REVERT: B 535 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: B 582 LEU cc_start: 0.5432 (OUTLIER) cc_final: 0.4920 (mp) REVERT: B 639 LEU cc_start: 0.7637 (mm) cc_final: 0.7216 (mp) REVERT: A 106 ASN cc_start: 0.7299 (t0) cc_final: 0.7088 (t0) REVERT: A 113 TYR cc_start: 0.8720 (t80) cc_final: 0.8390 (t80) REVERT: A 553 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6886 (tptp) REVERT: A 613 VAL cc_start: 0.6787 (OUTLIER) cc_final: 0.6576 (p) REVERT: A 657 CYS cc_start: 0.6466 (t) cc_final: 0.5742 (t) REVERT: A 768 PHE cc_start: 0.7551 (t80) cc_final: 0.7212 (t80) REVERT: A 770 PHE cc_start: 0.7571 (t80) cc_final: 0.7012 (m-80) REVERT: A 776 LEU cc_start: 0.7883 (tp) cc_final: 0.7680 (tt) outliers start: 78 outliers final: 54 residues processed: 226 average time/residue: 0.0734 time to fit residues: 25.4785 Evaluate side-chains 215 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 156 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 712 HIS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 812 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 57 optimal weight: 0.0980 chunk 111 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 449 ASN B 721 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.117092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.097723 restraints weight = 25030.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.100411 restraints weight = 15228.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.102217 restraints weight = 10946.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.103398 restraints weight = 8739.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.104052 restraints weight = 7480.862| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12913 Z= 0.144 Angle : 0.615 17.988 17634 Z= 0.281 Chirality : 0.043 0.370 2042 Planarity : 0.004 0.044 2203 Dihedral : 7.171 59.877 2055 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.94 % Allowed : 26.12 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.22), residues: 1551 helix: 1.61 (0.19), residues: 752 sheet: -1.46 (0.37), residues: 200 loop : -0.38 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 498 TYR 0.018 0.001 TYR B 394 PHE 0.013 0.001 PHE B 730 TRP 0.021 0.001 TRP B 775 HIS 0.004 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00342 (12877) covalent geometry : angle 0.55669 (17546) SS BOND : bond 0.00285 ( 20) SS BOND : angle 1.07316 ( 40) hydrogen bonds : bond 0.03733 ( 628) hydrogen bonds : angle 4.14035 ( 1791) link_NAG-ASN : bond 0.00984 ( 16) link_NAG-ASN : angle 4.98524 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 159 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.5976 (ptm-80) REVERT: B 325 LEU cc_start: 0.8588 (tp) cc_final: 0.8333 (tp) REVERT: B 535 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: B 558 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7078 (ptm-80) REVERT: B 582 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.4967 (mp) REVERT: B 639 LEU cc_start: 0.7667 (mm) cc_final: 0.7234 (mp) REVERT: A 106 ASN cc_start: 0.7259 (t0) cc_final: 0.7041 (t0) REVERT: A 552 PHE cc_start: 0.8172 (p90) cc_final: 0.7747 (p90) REVERT: A 553 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6743 (tptp) REVERT: A 613 VAL cc_start: 0.6740 (OUTLIER) cc_final: 0.6528 (p) REVERT: A 657 CYS cc_start: 0.6548 (t) cc_final: 0.5765 (t) REVERT: A 770 PHE cc_start: 0.7584 (t80) cc_final: 0.7012 (m-80) outliers start: 81 outliers final: 56 residues processed: 226 average time/residue: 0.0710 time to fit residues: 24.8479 Evaluate side-chains 215 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 153 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 712 HIS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 613 VAL 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 633 ARG Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 812 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 12 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.0270 chunk 57 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.117584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.097852 restraints weight = 24821.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.100693 restraints weight = 14630.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.102575 restraints weight = 10352.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.103754 restraints weight = 8213.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.104589 restraints weight = 7035.474| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12913 Z= 0.132 Angle : 0.599 17.855 17634 Z= 0.274 Chirality : 0.043 0.379 2042 Planarity : 0.004 0.045 2203 Dihedral : 7.144 59.299 2053 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.72 % Allowed : 26.41 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.22), residues: 1551 helix: 1.67 (0.19), residues: 752 sheet: -1.40 (0.37), residues: 194 loop : -0.35 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.017 0.001 TYR B 394 PHE 0.015 0.001 PHE A 659 TRP 0.013 0.001 TRP B 775 HIS 0.003 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00310 (12877) covalent geometry : angle 0.54596 (17546) SS BOND : bond 0.00261 ( 20) SS BOND : angle 1.05393 ( 40) hydrogen bonds : bond 0.03631 ( 628) hydrogen bonds : angle 4.08891 ( 1791) link_NAG-ASN : bond 0.00986 ( 16) link_NAG-ASN : angle 4.70391 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 157 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.5980 (ptm-80) REVERT: B 325 LEU cc_start: 0.8588 (tp) cc_final: 0.8360 (tp) REVERT: B 535 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: B 582 LEU cc_start: 0.5439 (OUTLIER) cc_final: 0.4926 (mp) REVERT: B 639 LEU cc_start: 0.7702 (mm) cc_final: 0.7271 (mp) REVERT: A 106 ASN cc_start: 0.7261 (t0) cc_final: 0.7050 (t0) REVERT: A 383 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7279 (mtt90) REVERT: A 471 LEU cc_start: 0.8614 (mt) cc_final: 0.8291 (mp) REVERT: A 552 PHE cc_start: 0.8190 (p90) cc_final: 0.7756 (p90) REVERT: A 553 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6757 (tptp) REVERT: A 657 CYS cc_start: 0.6581 (t) cc_final: 0.5735 (t) REVERT: A 768 PHE cc_start: 0.7547 (t80) cc_final: 0.7202 (t80) REVERT: A 770 PHE cc_start: 0.7566 (t80) cc_final: 0.7049 (m-80) outliers start: 78 outliers final: 61 residues processed: 220 average time/residue: 0.0818 time to fit residues: 27.5106 Evaluate side-chains 215 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 149 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 604 CYS 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 633 ARG Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 812 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 155 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 0.0970 chunk 106 optimal weight: 0.0370 chunk 107 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.117937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098282 restraints weight = 24828.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.101095 restraints weight = 14681.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.102950 restraints weight = 10417.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.104140 restraints weight = 8282.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.105001 restraints weight = 7085.650| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12913 Z= 0.128 Angle : 0.646 17.626 17634 Z= 0.289 Chirality : 0.050 1.071 2042 Planarity : 0.004 0.045 2203 Dihedral : 7.099 59.012 2047 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.50 % Allowed : 26.49 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.22), residues: 1551 helix: 1.70 (0.19), residues: 749 sheet: -1.46 (0.36), residues: 198 loop : -0.30 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 757 TYR 0.016 0.001 TYR A 675 PHE 0.011 0.001 PHE B 730 TRP 0.011 0.001 TRP B 775 HIS 0.003 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00295 (12877) covalent geometry : angle 0.59128 (17546) SS BOND : bond 0.00276 ( 20) SS BOND : angle 1.06571 ( 40) hydrogen bonds : bond 0.03546 ( 628) hydrogen bonds : angle 4.07062 ( 1791) link_NAG-ASN : bond 0.01128 ( 16) link_NAG-ASN : angle 4.94697 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 160 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.5955 (ptm-80) REVERT: B 325 LEU cc_start: 0.8579 (tp) cc_final: 0.8352 (tp) REVERT: B 535 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: B 582 LEU cc_start: 0.5407 (OUTLIER) cc_final: 0.4929 (mp) REVERT: B 639 LEU cc_start: 0.7727 (mm) cc_final: 0.7299 (mp) REVERT: A 106 ASN cc_start: 0.7242 (t0) cc_final: 0.7031 (t0) REVERT: A 383 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7273 (mtt90) REVERT: A 515 PHE cc_start: 0.8965 (p90) cc_final: 0.8309 (p90) REVERT: A 552 PHE cc_start: 0.8175 (p90) cc_final: 0.7740 (p90) REVERT: A 553 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6741 (tptp) REVERT: A 657 CYS cc_start: 0.6663 (t) cc_final: 0.5778 (t) REVERT: A 682 MET cc_start: 0.6491 (mmp) cc_final: 0.6178 (mmp) REVERT: A 768 PHE cc_start: 0.7544 (t80) cc_final: 0.7203 (t80) REVERT: A 770 PHE cc_start: 0.7572 (t80) cc_final: 0.7015 (m-80) REVERT: A 776 LEU cc_start: 0.7892 (tp) cc_final: 0.7606 (tt) outliers start: 75 outliers final: 60 residues processed: 219 average time/residue: 0.0765 time to fit residues: 25.8637 Evaluate side-chains 217 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 152 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 604 CYS 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 633 ARG Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 812 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 45 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 449 ASN B 721 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.116919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.097187 restraints weight = 24646.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.099987 restraints weight = 14647.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.101809 restraints weight = 10438.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.103035 restraints weight = 8314.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.103792 restraints weight = 7120.721| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12913 Z= 0.168 Angle : 0.666 17.569 17634 Z= 0.306 Chirality : 0.045 0.386 2042 Planarity : 0.004 0.045 2203 Dihedral : 8.088 92.779 2047 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.43 % Allowed : 27.15 % Favored : 67.42 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.22), residues: 1551 helix: 1.63 (0.19), residues: 750 sheet: -1.45 (0.37), residues: 194 loop : -0.31 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 757 TYR 0.027 0.002 TYR A 675 PHE 0.013 0.001 PHE B 829 TRP 0.012 0.001 TRP B 775 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00401 (12877) covalent geometry : angle 0.60946 (17546) SS BOND : bond 0.00266 ( 20) SS BOND : angle 1.12426 ( 40) hydrogen bonds : bond 0.03731 ( 628) hydrogen bonds : angle 4.11203 ( 1791) link_NAG-ASN : bond 0.01183 ( 16) link_NAG-ASN : angle 5.12984 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 157 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.6087 (ptm-80) REVERT: B 325 LEU cc_start: 0.8602 (tp) cc_final: 0.8366 (tp) REVERT: B 535 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: B 558 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7045 (ptm-80) REVERT: B 582 LEU cc_start: 0.5526 (OUTLIER) cc_final: 0.5012 (mp) REVERT: B 639 LEU cc_start: 0.7712 (mm) cc_final: 0.7270 (mp) REVERT: A 106 ASN cc_start: 0.7280 (t0) cc_final: 0.7048 (t0) REVERT: A 383 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7316 (mtt90) REVERT: A 471 LEU cc_start: 0.8583 (mt) cc_final: 0.8265 (mp) REVERT: A 515 PHE cc_start: 0.8986 (p90) cc_final: 0.8357 (p90) REVERT: A 552 PHE cc_start: 0.8202 (p90) cc_final: 0.7786 (p90) REVERT: A 553 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6781 (tptp) REVERT: A 657 CYS cc_start: 0.6805 (t) cc_final: 0.5902 (t) REVERT: A 682 MET cc_start: 0.6609 (mmp) cc_final: 0.6381 (mmp) REVERT: A 768 PHE cc_start: 0.7543 (t80) cc_final: 0.7221 (t80) REVERT: A 770 PHE cc_start: 0.7599 (t80) cc_final: 0.7049 (m-80) REVERT: A 776 LEU cc_start: 0.7915 (tp) cc_final: 0.7625 (tt) outliers start: 74 outliers final: 60 residues processed: 214 average time/residue: 0.0761 time to fit residues: 24.7764 Evaluate side-chains 220 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 154 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 815 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 119 optimal weight: 0.0670 chunk 4 optimal weight: 0.5980 chunk 61 optimal weight: 0.0970 chunk 17 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 88 optimal weight: 0.0870 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.118941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.099655 restraints weight = 24956.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.102371 restraints weight = 15160.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.104166 restraints weight = 10899.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.105375 restraints weight = 8694.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.106198 restraints weight = 7432.696| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1404 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= 0.111 Angle : 0.604 17.412 17634 Z= 0.274 Chirality : 0.043 0.388 2042 Planarity : 0.004 0.045 2203 Dihedral : 6.854 59.090 2045 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.55 % Allowed : 28.39 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.22), residues: 1551 helix: 1.77 (0.19), residues: 746 sheet: -1.43 (0.36), residues: 200 loop : -0.28 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 443 TYR 0.016 0.001 TYR A 675 PHE 0.011 0.001 PHE B 730 TRP 0.008 0.001 TRP B 303 HIS 0.003 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00248 (12877) covalent geometry : angle 0.55069 (17546) SS BOND : bond 0.00247 ( 20) SS BOND : angle 1.04754 ( 40) hydrogen bonds : bond 0.03452 ( 628) hydrogen bonds : angle 4.04550 ( 1791) link_NAG-ASN : bond 0.00968 ( 16) link_NAG-ASN : angle 4.70996 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 159 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.5938 (ptm-80) REVERT: B 325 LEU cc_start: 0.8567 (tp) cc_final: 0.8354 (tp) REVERT: B 535 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: B 558 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7044 (ptm-80) REVERT: B 582 LEU cc_start: 0.5371 (OUTLIER) cc_final: 0.4880 (mp) REVERT: B 639 LEU cc_start: 0.7664 (mm) cc_final: 0.7249 (mp) REVERT: A 106 ASN cc_start: 0.7214 (t0) cc_final: 0.6998 (t0) REVERT: A 383 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7243 (mtt90) REVERT: A 471 LEU cc_start: 0.8533 (mt) cc_final: 0.8204 (mp) REVERT: A 515 PHE cc_start: 0.8928 (p90) cc_final: 0.8326 (p90) REVERT: A 552 PHE cc_start: 0.8187 (p90) cc_final: 0.7825 (p90) REVERT: A 553 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6775 (tptp) REVERT: A 657 CYS cc_start: 0.6706 (t) cc_final: 0.5787 (t) REVERT: A 682 MET cc_start: 0.6609 (mmp) cc_final: 0.6406 (mmp) REVERT: A 768 PHE cc_start: 0.7456 (t80) cc_final: 0.7189 (t80) REVERT: A 770 PHE cc_start: 0.7568 (t80) cc_final: 0.7024 (m-80) REVERT: A 776 LEU cc_start: 0.7911 (tp) cc_final: 0.7628 (tt) REVERT: A 814 MET cc_start: 0.7058 (mtt) cc_final: 0.6810 (mtt) outliers start: 62 outliers final: 51 residues processed: 209 average time/residue: 0.0810 time to fit residues: 25.7757 Evaluate side-chains 208 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 151 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 216 ASP 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 375 CYS Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 595 ILE 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 633 ARG Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 812 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 56 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 144 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.117834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.098495 restraints weight = 24879.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.101156 restraints weight = 15219.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.102949 restraints weight = 10996.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.104157 restraints weight = 8817.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.104960 restraints weight = 7546.876| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12913 Z= 0.141 Angle : 0.622 17.222 17634 Z= 0.283 Chirality : 0.044 0.390 2042 Planarity : 0.004 0.045 2203 Dihedral : 6.906 59.232 2045 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.40 % Allowed : 28.32 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.22), residues: 1551 helix: 1.73 (0.19), residues: 746 sheet: -1.45 (0.36), residues: 201 loop : -0.27 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.022 0.001 TYR A 675 PHE 0.013 0.001 PHE B 829 TRP 0.036 0.001 TRP B 461 HIS 0.003 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00333 (12877) covalent geometry : angle 0.57119 (17546) SS BOND : bond 0.00246 ( 20) SS BOND : angle 1.06908 ( 40) hydrogen bonds : bond 0.03608 ( 628) hydrogen bonds : angle 4.07356 ( 1791) link_NAG-ASN : bond 0.00946 ( 16) link_NAG-ASN : angle 4.66988 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 159 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6052 (ptm-80) REVERT: B 325 LEU cc_start: 0.8580 (tp) cc_final: 0.8347 (tp) REVERT: B 535 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7422 (m-30) REVERT: B 558 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7037 (ptm-80) REVERT: B 582 LEU cc_start: 0.5421 (OUTLIER) cc_final: 0.4896 (mp) REVERT: B 639 LEU cc_start: 0.7695 (mm) cc_final: 0.7275 (mp) REVERT: A 106 ASN cc_start: 0.7249 (t0) cc_final: 0.7021 (t0) REVERT: A 383 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7286 (mtt90) REVERT: A 515 PHE cc_start: 0.8967 (p90) cc_final: 0.8429 (p90) REVERT: A 552 PHE cc_start: 0.8201 (p90) cc_final: 0.7866 (p90) REVERT: A 553 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6773 (tptp) REVERT: A 657 CYS cc_start: 0.6806 (t) cc_final: 0.5884 (t) REVERT: A 676 GLN cc_start: 0.4986 (mm110) cc_final: 0.4540 (mm-40) REVERT: A 682 MET cc_start: 0.6662 (mmp) cc_final: 0.6347 (mmp) REVERT: A 768 PHE cc_start: 0.7505 (t80) cc_final: 0.7228 (t80) REVERT: A 770 PHE cc_start: 0.7607 (t80) cc_final: 0.7027 (m-80) REVERT: A 776 LEU cc_start: 0.7910 (tp) cc_final: 0.7617 (tt) outliers start: 60 outliers final: 52 residues processed: 207 average time/residue: 0.0797 time to fit residues: 25.1864 Evaluate side-chains 212 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 154 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 216 ASP 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 375 CYS Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 812 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 48 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 118 optimal weight: 0.0980 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 117 optimal weight: 0.0670 chunk 112 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.118432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.099211 restraints weight = 24941.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.101850 restraints weight = 15210.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.103672 restraints weight = 11016.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.104871 restraints weight = 8782.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.105690 restraints weight = 7496.151| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1523 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= 0.122 Angle : 0.607 17.053 17634 Z= 0.278 Chirality : 0.043 0.395 2042 Planarity : 0.004 0.045 2203 Dihedral : 6.848 59.406 2045 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.48 % Allowed : 28.47 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.22), residues: 1551 helix: 1.74 (0.19), residues: 747 sheet: -1.44 (0.36), residues: 201 loop : -0.26 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.020 0.001 TYR A 675 PHE 0.012 0.001 PHE B 829 TRP 0.030 0.001 TRP B 461 HIS 0.003 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00282 (12877) covalent geometry : angle 0.55871 (17546) SS BOND : bond 0.00243 ( 20) SS BOND : angle 1.05225 ( 40) hydrogen bonds : bond 0.03519 ( 628) hydrogen bonds : angle 4.05228 ( 1791) link_NAG-ASN : bond 0.00923 ( 16) link_NAG-ASN : angle 4.49532 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1811.83 seconds wall clock time: 32 minutes 1.43 seconds (1921.43 seconds total)