Starting phenix.real_space_refine on Wed Jun 11 07:03:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nos_49612/06_2025/9nos_49612.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nos_49612/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9nos_49612/06_2025/9nos_49612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nos_49612/06_2025/9nos_49612.map" model { file = "/net/cci-nas-00/data/ceres_data/9nos_49612/06_2025/9nos_49612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nos_49612/06_2025/9nos_49612.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12555 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6059 Classifications: {'peptide': 780} Link IDs: {'PTRANS': 45, 'TRANS': 734} Chain breaks: 3 Chain: "A" Number of atoms: 6272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6272 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 40, 'TRANS': 744} Chain breaks: 2 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 9.12, per 1000 atoms: 0.73 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: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 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: 1.58 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: 4.56 Time building geometry restraints manager: 3.89 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: 6.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 33.660 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.170 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.22), residues: 1551 helix: 1.51 (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 TRP 0.013 0.001 TRP B 775 HIS 0.007 0.001 HIS B 641 PHE 0.024 0.001 PHE A 659 TYR 0.017 0.001 TYR B 394 ARG 0.007 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.01063 ( 16) link_NAG-ASN : angle 5.97385 ( 48) hydrogen bonds : bond 0.14164 ( 628) hydrogen bonds : angle 5.68352 ( 1791) SS BOND : bond 0.00259 ( 20) SS BOND : angle 1.24481 ( 40) covalent geometry : bond 0.00278 (12877) covalent geometry : angle 0.58487 (17546) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8417 (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: 0.6973 (m-80) REVERT: A 776 LEU cc_start: 0.8065 (tp) cc_final: 0.7803 (tt) outliers start: 31 outliers final: 27 residues processed: 195 average time/residue: 0.2153 time to fit residues: 63.3319 Evaluate side-chains 192 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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 159 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 131 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.115430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.095900 restraints weight = 24823.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.098452 restraints weight = 15230.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.100164 restraints weight = 11158.079| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12913 Z= 0.237 Angle : 0.697 18.329 17634 Z= 0.327 Chirality : 0.047 0.595 2042 Planarity : 0.004 0.046 2203 Dihedral : 8.382 58.209 2088 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.80 % Allowed : 26.49 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1551 helix: 1.31 (0.19), residues: 752 sheet: -1.44 (0.39), residues: 182 loop : -0.60 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 564 HIS 0.009 0.001 HIS B 641 PHE 0.013 0.002 PHE A 591 TYR 0.023 0.002 TYR B 394 ARG 0.004 0.000 ARG B 757 Details of bonding type rmsd link_NAG-ASN : bond 0.01030 ( 16) link_NAG-ASN : angle 5.33012 ( 48) hydrogen bonds : bond 0.04597 ( 628) hydrogen bonds : angle 4.65080 ( 1791) SS BOND : bond 0.00385 ( 20) SS BOND : angle 1.36647 ( 40) covalent geometry : bond 0.00577 (12877) covalent geometry : angle 0.63685 (17546) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 163 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6377 (ptm-80) REVERT: B 325 LEU cc_start: 0.8702 (tp) cc_final: 0.8414 (tp) REVERT: B 582 LEU cc_start: 0.5731 (OUTLIER) cc_final: 0.5168 (mp) REVERT: B 639 LEU cc_start: 0.7612 (mm) cc_final: 0.7190 (mp) REVERT: A 106 ASN cc_start: 0.7490 (t0) cc_final: 0.7232 (t0) REVERT: A 553 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6859 (tptp) REVERT: A 676 GLN cc_start: 0.5045 (mm-40) cc_final: 0.4782 (mm-40) REVERT: A 770 PHE cc_start: 0.7607 (t80) cc_final: 0.7025 (m-80) REVERT: A 776 LEU cc_start: 0.7932 (tp) cc_final: 0.7696 (tt) outliers start: 79 outliers final: 58 residues processed: 229 average time/residue: 0.3097 time to fit residues: 109.1651 Evaluate side-chains 212 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 151 time to evaluate : 1.339 ------------------------------------------------------------------------------- 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 155 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 458 LEU 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 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 584 LEU Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 620 SER 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 719 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 183 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 430 THR Chi-restraints excluded: chain A residue 444 VAL 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 629 THR 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 754 THR Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 823 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 57 optimal weight: 0.0770 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 0.2980 chunk 15 optimal weight: 0.0980 chunk 145 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 A 447 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.117995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.098572 restraints weight = 24788.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101254 restraints weight = 15089.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103030 restraints weight = 10880.341| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.0880 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= 0.120 Angle : 0.595 18.059 17634 Z= 0.275 Chirality : 0.044 0.477 2042 Planarity : 0.004 0.045 2203 Dihedral : 7.543 59.788 2064 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.77 % Allowed : 28.10 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1551 helix: 1.61 (0.19), residues: 746 sheet: -1.45 (0.38), residues: 188 loop : -0.49 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 303 HIS 0.004 0.001 HIS B 405 PHE 0.014 0.001 PHE A 157 TYR 0.018 0.001 TYR B 394 ARG 0.005 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.01026 ( 16) link_NAG-ASN : angle 4.97342 ( 48) hydrogen bonds : bond 0.03787 ( 628) hydrogen bonds : angle 4.33584 ( 1791) SS BOND : bond 0.00275 ( 20) SS BOND : angle 1.09129 ( 40) covalent geometry : bond 0.00270 (12877) covalent geometry : angle 0.53438 (17546) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 161 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.5958 (ptm-80) REVERT: B 155 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8280 (mtmt) REVERT: B 325 LEU cc_start: 0.8670 (tp) cc_final: 0.8398 (tp) REVERT: B 535 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7397 (m-30) REVERT: B 639 LEU cc_start: 0.7605 (mm) cc_final: 0.7197 (mp) REVERT: A 106 ASN cc_start: 0.7383 (t0) cc_final: 0.7147 (t0) REVERT: A 113 TYR cc_start: 0.8708 (t80) cc_final: 0.8303 (t80) REVERT: A 476 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7941 (ptmm) REVERT: A 553 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6882 (tptp) REVERT: A 676 GLN cc_start: 0.4954 (mm-40) cc_final: 0.4719 (mm-40) REVERT: A 768 PHE cc_start: 0.7492 (t80) cc_final: 0.7164 (t80) REVERT: A 770 PHE cc_start: 0.7545 (t80) cc_final: 0.6995 (m-80) REVERT: A 776 LEU cc_start: 0.7867 (tp) cc_final: 0.7650 (tt) outliers start: 65 outliers final: 44 residues processed: 213 average time/residue: 0.2375 time to fit residues: 76.5302 Evaluate side-chains 197 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 152 VAL Chi-restraints excluded: chain B residue 155 LYS 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 309 VAL 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 516 SER Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 578 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 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 787 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 302 GLU Chi-restraints excluded: chain A residue 476 LYS 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 663 SER Chi-restraints excluded: chain A residue 715 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 79 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.116605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.096790 restraints weight = 24717.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.099602 restraints weight = 14704.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.101434 restraints weight = 10465.256| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12913 Z= 0.159 Angle : 0.636 18.165 17634 Z= 0.294 Chirality : 0.044 0.361 2042 Planarity : 0.004 0.045 2203 Dihedral : 8.179 80.472 2059 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 6.31 % Allowed : 26.71 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1551 helix: 1.60 (0.19), residues: 746 sheet: -1.51 (0.37), residues: 200 loop : -0.42 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 775 HIS 0.005 0.001 HIS B 734 PHE 0.012 0.001 PHE B 829 TYR 0.019 0.001 TYR B 394 ARG 0.005 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.01156 ( 16) link_NAG-ASN : angle 4.94820 ( 48) hydrogen bonds : bond 0.03861 ( 628) hydrogen bonds : angle 4.25837 ( 1791) SS BOND : bond 0.00280 ( 20) SS BOND : angle 1.11973 ( 40) covalent geometry : bond 0.00377 (12877) covalent geometry : angle 0.58028 (17546) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 154 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6081 (ptm-80) REVERT: B 185 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8608 (ptp-170) REVERT: B 325 LEU cc_start: 0.8604 (tp) cc_final: 0.8360 (tp) REVERT: B 535 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: B 582 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5057 (mp) REVERT: B 639 LEU cc_start: 0.7650 (mm) cc_final: 0.7212 (mp) REVERT: B 734 HIS cc_start: 0.6683 (m170) cc_final: 0.5976 (m170) REVERT: A 106 ASN cc_start: 0.7401 (t0) cc_final: 0.7157 (t0) REVERT: A 476 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7889 (ptmm) REVERT: A 553 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6873 (tptp) REVERT: A 664 ARG cc_start: 0.3446 (ttt180) cc_final: 0.3232 (ttt180) REVERT: A 770 PHE cc_start: 0.7590 (t80) cc_final: 0.7010 (m-80) REVERT: A 776 LEU cc_start: 0.7878 (tp) cc_final: 0.7671 (tt) outliers start: 86 outliers final: 57 residues processed: 224 average time/residue: 0.2192 time to fit residues: 73.8877 Evaluate side-chains 214 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 151 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 173 LEU Chi-restraints excluded: chain B residue 185 ARG 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 309 VAL 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 489 THR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 516 SER 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 619 LEU 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 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 476 LYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 138 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.116730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.097003 restraints weight = 24610.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.099819 restraints weight = 14585.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.101674 restraints weight = 10368.687| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12913 Z= 0.148 Angle : 0.614 18.010 17634 Z= 0.281 Chirality : 0.043 0.366 2042 Planarity : 0.004 0.046 2203 Dihedral : 7.358 59.061 2058 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.53 % Allowed : 25.97 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1551 helix: 1.59 (0.19), residues: 749 sheet: -1.49 (0.37), residues: 200 loop : -0.42 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 775 HIS 0.004 0.001 HIS B 405 PHE 0.014 0.001 PHE A 157 TYR 0.019 0.001 TYR B 394 ARG 0.004 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00988 ( 16) link_NAG-ASN : angle 5.00112 ( 48) hydrogen bonds : bond 0.03781 ( 628) hydrogen bonds : angle 4.19088 ( 1791) SS BOND : bond 0.00308 ( 20) SS BOND : angle 1.12336 ( 40) covalent geometry : bond 0.00351 (12877) covalent geometry : angle 0.55498 (17546) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 156 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6087 (ptm-80) REVERT: B 185 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8672 (ptp-170) REVERT: B 325 LEU cc_start: 0.8606 (tp) cc_final: 0.8358 (tp) REVERT: B 535 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: B 558 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7110 (ptm-80) REVERT: B 582 LEU cc_start: 0.5502 (OUTLIER) cc_final: 0.4972 (mp) REVERT: B 639 LEU cc_start: 0.7677 (mm) cc_final: 0.7251 (mp) REVERT: A 106 ASN cc_start: 0.7400 (t0) cc_final: 0.7161 (t0) REVERT: A 476 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7826 (ptmm) REVERT: A 552 PHE cc_start: 0.8179 (p90) cc_final: 0.7714 (p90) REVERT: A 553 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6743 (tptp) REVERT: A 664 ARG cc_start: 0.3549 (ttt180) cc_final: 0.3257 (ttt180) REVERT: A 768 PHE cc_start: 0.7566 (t80) cc_final: 0.7201 (t80) REVERT: A 770 PHE cc_start: 0.7577 (t80) cc_final: 0.6997 (m-80) outliers start: 89 outliers final: 63 residues processed: 230 average time/residue: 0.2178 time to fit residues: 75.6543 Evaluate side-chains 217 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 147 time to evaluate : 1.431 ------------------------------------------------------------------------------- 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 185 ARG 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 309 VAL 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 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 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 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 754 GLN 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 802 VAL 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 146 SER 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 476 LYS 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 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 755 ASN Chi-restraints excluded: chain A residue 798 LEU 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 89 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 119 optimal weight: 0.0070 overall best weight: 0.7600 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.116540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.096736 restraints weight = 24984.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.099556 restraints weight = 14728.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.101414 restraints weight = 10470.624| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12913 Z= 0.155 Angle : 0.618 17.937 17634 Z= 0.283 Chirality : 0.043 0.373 2042 Planarity : 0.004 0.045 2203 Dihedral : 7.346 59.149 2058 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 6.02 % Allowed : 26.41 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.22), residues: 1551 helix: 1.59 (0.19), residues: 749 sheet: -1.48 (0.37), residues: 190 loop : -0.42 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 775 HIS 0.004 0.001 HIS B 734 PHE 0.015 0.001 PHE A 659 TYR 0.026 0.001 TYR A 675 ARG 0.004 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00974 ( 16) link_NAG-ASN : angle 4.79229 ( 48) hydrogen bonds : bond 0.03815 ( 628) hydrogen bonds : angle 4.16554 ( 1791) SS BOND : bond 0.00271 ( 20) SS BOND : angle 1.18108 ( 40) covalent geometry : bond 0.00371 (12877) covalent geometry : angle 0.56365 (17546) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 154 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.6033 (ptm-80) REVERT: B 185 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8650 (ptp-170) REVERT: B 325 LEU cc_start: 0.8600 (tp) cc_final: 0.8369 (tp) REVERT: B 535 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: B 558 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7118 (ptm-80) REVERT: B 582 LEU cc_start: 0.5569 (OUTLIER) cc_final: 0.5035 (mp) REVERT: A 106 ASN cc_start: 0.7388 (t0) cc_final: 0.7133 (t0) REVERT: A 231 ASP cc_start: 0.7829 (t70) cc_final: 0.7441 (t0) REVERT: A 383 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7335 (mtt90) REVERT: A 476 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7805 (ptmm) REVERT: A 552 PHE cc_start: 0.8217 (p90) cc_final: 0.7768 (p90) REVERT: A 553 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.6762 (tptp) REVERT: A 768 PHE cc_start: 0.7539 (t80) cc_final: 0.7190 (t80) REVERT: A 770 PHE cc_start: 0.7591 (t80) cc_final: 0.7014 (m-80) outliers start: 82 outliers final: 65 residues processed: 220 average time/residue: 0.2303 time to fit residues: 77.1192 Evaluate side-chains 220 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 147 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 185 ARG 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 309 VAL 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 754 GLN 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 802 VAL 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 146 SER 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 476 LYS 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 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 812 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 11 optimal weight: 0.0770 chunk 100 optimal weight: 2.9990 chunk 112 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 HIS ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.117525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.098255 restraints weight = 24825.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.100919 restraints weight = 15199.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.102675 restraints weight = 10983.827| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1346 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= 0.130 Angle : 0.649 17.799 17634 Z= 0.289 Chirality : 0.050 1.088 2042 Planarity : 0.004 0.046 2203 Dihedral : 7.256 59.635 2054 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.87 % Allowed : 26.34 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.22), residues: 1551 helix: 1.65 (0.19), residues: 749 sheet: -1.47 (0.37), residues: 188 loop : -0.39 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 775 HIS 0.004 0.001 HIS B 734 PHE 0.013 0.001 PHE B 730 TYR 0.019 0.001 TYR A 675 ARG 0.003 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.01063 ( 16) link_NAG-ASN : angle 5.04903 ( 48) hydrogen bonds : bond 0.03631 ( 628) hydrogen bonds : angle 4.11953 ( 1791) SS BOND : bond 0.00266 ( 20) SS BOND : angle 1.09826 ( 40) covalent geometry : bond 0.00299 (12877) covalent geometry : angle 0.59274 (17546) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 160 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6034 (ptm-80) REVERT: B 185 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8662 (ptp-170) REVERT: B 325 LEU cc_start: 0.8589 (tp) cc_final: 0.8367 (tp) REVERT: B 535 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7350 (m-30) REVERT: B 582 LEU cc_start: 0.5426 (OUTLIER) cc_final: 0.4928 (mp) REVERT: A 106 ASN cc_start: 0.7345 (t0) cc_final: 0.7115 (t0) REVERT: A 383 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7370 (mtt90) REVERT: A 476 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7756 (ptmm) REVERT: A 515 PHE cc_start: 0.8943 (p90) cc_final: 0.8379 (p90) REVERT: A 552 PHE cc_start: 0.8168 (p90) cc_final: 0.7746 (p90) REVERT: A 553 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6745 (tptp) REVERT: A 682 MET cc_start: 0.6555 (mmp) cc_final: 0.6257 (mmp) REVERT: A 768 PHE cc_start: 0.7483 (t80) cc_final: 0.7204 (t80) REVERT: A 770 PHE cc_start: 0.7579 (t80) cc_final: 0.7038 (m-80) REVERT: A 776 LEU cc_start: 0.7869 (tp) cc_final: 0.7589 (tt) outliers start: 80 outliers final: 59 residues processed: 225 average time/residue: 0.2193 time to fit residues: 75.8900 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 : 1.165 ------------------------------------------------------------------------------- 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 152 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 309 VAL 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 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 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 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 146 SER 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 476 LYS 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 663 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 0.4980 chunk 142 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 HIS ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.116788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.097529 restraints weight = 24921.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.100169 restraints weight = 15187.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.101905 restraints weight = 10994.200| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12913 Z= 0.161 Angle : 0.641 17.621 17634 Z= 0.294 Chirality : 0.047 0.729 2042 Planarity : 0.004 0.046 2203 Dihedral : 7.188 59.361 2048 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.80 % Allowed : 26.71 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1551 helix: 1.59 (0.19), residues: 749 sheet: -1.52 (0.36), residues: 193 loop : -0.34 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 775 HIS 0.004 0.001 HIS B 405 PHE 0.027 0.001 PHE A 779 TYR 0.024 0.002 TYR A 675 ARG 0.003 0.000 ARG B 757 Details of bonding type rmsd link_NAG-ASN : bond 0.00953 ( 16) link_NAG-ASN : angle 4.70879 ( 48) hydrogen bonds : bond 0.03794 ( 628) hydrogen bonds : angle 4.14170 ( 1791) SS BOND : bond 0.00268 ( 20) SS BOND : angle 1.15109 ( 40) covalent geometry : bond 0.00383 (12877) covalent geometry : angle 0.59121 (17546) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 155 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6061 (ptm-80) REVERT: B 325 LEU cc_start: 0.8607 (tp) cc_final: 0.8377 (tp) REVERT: B 535 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: B 582 LEU cc_start: 0.5567 (OUTLIER) cc_final: 0.5021 (mp) REVERT: A 106 ASN cc_start: 0.7392 (t0) cc_final: 0.7142 (t0) REVERT: A 194 MET cc_start: 0.8436 (mtt) cc_final: 0.8218 (mtt) REVERT: A 383 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7387 (mtt90) REVERT: A 476 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7735 (ptmm) REVERT: A 515 PHE cc_start: 0.8982 (p90) cc_final: 0.8374 (p90) REVERT: A 552 PHE cc_start: 0.8177 (p90) cc_final: 0.7772 (p90) REVERT: A 553 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6738 (tptp) REVERT: A 682 MET cc_start: 0.6634 (mmp) cc_final: 0.6419 (mmp) REVERT: A 768 PHE cc_start: 0.7516 (t80) cc_final: 0.7191 (t80) REVERT: A 770 PHE cc_start: 0.7607 (t80) cc_final: 0.7053 (m-80) REVERT: A 776 LEU cc_start: 0.7881 (tp) cc_final: 0.7595 (tt) outliers start: 79 outliers final: 62 residues processed: 221 average time/residue: 0.2151 time to fit residues: 72.9378 Evaluate side-chains 216 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 148 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 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 309 VAL 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 538 CYS Chi-restraints excluded: chain B residue 552 THR 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 617 VAL 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 146 SER 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 476 LYS 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 579 SER 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 632 CYS Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 812 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 33 optimal weight: 0.2980 chunk 94 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.117108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.097531 restraints weight = 24853.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.100364 restraints weight = 14747.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.102218 restraints weight = 10444.824| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1468 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= 0.140 Angle : 0.629 17.481 17634 Z= 0.289 Chirality : 0.045 0.570 2042 Planarity : 0.004 0.046 2203 Dihedral : 7.137 59.501 2048 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.58 % Allowed : 27.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.22), residues: 1551 helix: 1.65 (0.19), residues: 740 sheet: -1.49 (0.37), residues: 193 loop : -0.32 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 775 HIS 0.009 0.001 HIS B 734 PHE 0.027 0.001 PHE A 779 TYR 0.019 0.001 TYR A 675 ARG 0.003 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00944 ( 16) link_NAG-ASN : angle 4.54242 ( 48) hydrogen bonds : bond 0.03731 ( 628) hydrogen bonds : angle 4.14005 ( 1791) SS BOND : bond 0.00252 ( 20) SS BOND : angle 1.17945 ( 40) covalent geometry : bond 0.00331 (12877) covalent geometry : angle 0.58156 (17546) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 156 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6040 (ptm-80) REVERT: B 325 LEU cc_start: 0.8604 (tp) cc_final: 0.8368 (tp) REVERT: B 535 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: B 582 LEU cc_start: 0.5469 (OUTLIER) cc_final: 0.4935 (mp) REVERT: A 106 ASN cc_start: 0.7356 (t0) cc_final: 0.7119 (t0) REVERT: A 194 MET cc_start: 0.8420 (mtt) cc_final: 0.8203 (mtt) REVERT: A 383 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7408 (mtt90) REVERT: A 476 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7687 (ptmm) REVERT: A 515 PHE cc_start: 0.8957 (p90) cc_final: 0.8381 (p90) REVERT: A 552 PHE cc_start: 0.8172 (p90) cc_final: 0.7805 (p90) REVERT: A 553 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6769 (tptp) REVERT: A 642 THR cc_start: 0.7109 (t) cc_final: 0.6897 (m) REVERT: A 682 MET cc_start: 0.6602 (mmp) cc_final: 0.6168 (mmt) REVERT: A 768 PHE cc_start: 0.7462 (t80) cc_final: 0.7201 (t80) REVERT: A 770 PHE cc_start: 0.7601 (t80) cc_final: 0.7024 (m-80) REVERT: A 776 LEU cc_start: 0.7920 (tp) cc_final: 0.7630 (tt) outliers start: 76 outliers final: 70 residues processed: 218 average time/residue: 0.2060 time to fit residues: 68.5357 Evaluate side-chains 228 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 152 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 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 272 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 309 VAL 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 538 CYS Chi-restraints excluded: chain B residue 552 THR 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 617 VAL 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 146 SER 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 476 LYS 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 579 SER 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 632 CYS Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 663 SER 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 804 SER Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 815 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 31 optimal weight: 3.9990 chunk 155 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.117369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097789 restraints weight = 24582.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.100568 restraints weight = 14606.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102397 restraints weight = 10426.129| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1587 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= 0.146 Angle : 0.627 17.279 17634 Z= 0.289 Chirality : 0.044 0.422 2042 Planarity : 0.004 0.046 2203 Dihedral : 7.105 59.677 2048 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.87 % Allowed : 27.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1551 helix: 1.63 (0.19), residues: 747 sheet: -1.49 (0.36), residues: 193 loop : -0.38 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 303 HIS 0.005 0.001 HIS B 734 PHE 0.027 0.001 PHE A 779 TYR 0.021 0.001 TYR A 675 ARG 0.003 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00930 ( 16) link_NAG-ASN : angle 4.40029 ( 48) hydrogen bonds : bond 0.03719 ( 628) hydrogen bonds : angle 4.12448 ( 1791) SS BOND : bond 0.00294 ( 20) SS BOND : angle 1.13518 ( 40) covalent geometry : bond 0.00348 (12877) covalent geometry : angle 0.58228 (17546) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 156 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6008 (ptm-80) REVERT: B 325 LEU cc_start: 0.8592 (tp) cc_final: 0.8371 (tp) REVERT: B 535 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: B 582 LEU cc_start: 0.5475 (OUTLIER) cc_final: 0.4941 (mp) REVERT: A 106 ASN cc_start: 0.7355 (t0) cc_final: 0.7109 (t0) REVERT: A 194 MET cc_start: 0.8398 (mtt) cc_final: 0.8182 (mtt) REVERT: A 383 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7389 (mtt90) REVERT: A 476 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7654 (ptmm) REVERT: A 515 PHE cc_start: 0.8972 (p90) cc_final: 0.8402 (p90) REVERT: A 552 PHE cc_start: 0.8180 (p90) cc_final: 0.7852 (p90) REVERT: A 553 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6747 (tptp) REVERT: A 642 THR cc_start: 0.7158 (t) cc_final: 0.6937 (m) REVERT: A 676 GLN cc_start: 0.4971 (mm110) cc_final: 0.4567 (mm-40) REVERT: A 682 MET cc_start: 0.6632 (mmp) cc_final: 0.6198 (mmt) REVERT: A 768 PHE cc_start: 0.7457 (t80) cc_final: 0.7177 (t80) REVERT: A 770 PHE cc_start: 0.7633 (t80) cc_final: 0.7056 (m-80) REVERT: A 776 LEU cc_start: 0.7884 (tp) cc_final: 0.7583 (tt) outliers start: 80 outliers final: 71 residues processed: 222 average time/residue: 0.2181 time to fit residues: 74.1295 Evaluate side-chains 226 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 149 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 125 ILE 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 288 ILE Chi-restraints excluded: chain B residue 309 VAL 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 538 CYS Chi-restraints excluded: chain B residue 552 THR 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 617 VAL 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 146 SER 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 476 LYS Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 535 CYS 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 579 SER 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 632 CYS Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 663 SER 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 804 SER Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 815 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.116467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.096872 restraints weight = 24828.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.099646 restraints weight = 14756.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.101459 restraints weight = 10547.791| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12913 Z= 0.171 Angle : 0.642 17.153 17634 Z= 0.297 Chirality : 0.045 0.388 2042 Planarity : 0.004 0.046 2203 Dihedral : 7.136 59.835 2048 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.94 % Allowed : 26.93 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.22), residues: 1551 helix: 1.54 (0.19), residues: 746 sheet: -1.50 (0.36), residues: 193 loop : -0.41 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 303 HIS 0.005 0.001 HIS B 734 PHE 0.027 0.001 PHE A 779 TYR 0.024 0.001 TYR A 675 ARG 0.003 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00920 ( 16) link_NAG-ASN : angle 4.34603 ( 48) hydrogen bonds : bond 0.03837 ( 628) hydrogen bonds : angle 4.18243 ( 1791) SS BOND : bond 0.00289 ( 20) SS BOND : angle 1.19593 ( 40) covalent geometry : bond 0.00413 (12877) covalent geometry : angle 0.59889 (17546) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4229.33 seconds wall clock time: 76 minutes 5.72 seconds (4565.72 seconds total)