Starting phenix.real_space_refine on Wed Jul 30 17:56:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ut8_64484/07_2025/9ut8_64484.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ut8_64484/07_2025/9ut8_64484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ut8_64484/07_2025/9ut8_64484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ut8_64484/07_2025/9ut8_64484.map" model { file = "/net/cci-nas-00/data/ceres_data/9ut8_64484/07_2025/9ut8_64484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ut8_64484/07_2025/9ut8_64484.cif" } resolution = 3.41 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= 0.001 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 95 5.16 5 C 7890 2.51 5 N 2059 2.21 5 O 2170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12214 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6157 Classifications: {'peptide': 770} Link IDs: {'PTRANS': 39, 'TRANS': 730} Chain breaks: 2 Chain: "B" Number of atoms: 6057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 6057 Classifications: {'peptide': 782} Link IDs: {'PTRANS': 44, 'TRANS': 737} Chain breaks: 3 Time building chain proxies: 7.03, per 1000 atoms: 0.58 Number of scatterers: 12214 At special positions: 0 Unit cell: (95.04, 90.24, 190.08, 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 95 16.00 O 2170 8.00 N 2059 7.00 C 7890 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 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 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 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 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=2.28 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.4 seconds 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2930 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 13 sheets defined 51.3% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 65 through 85 removed outlier: 3.804A pdb=" N TYR A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 115 Processing helix chain 'A' and resid 143 through 155 removed outlier: 3.558A pdb=" N PHE A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.687A pdb=" N ASP A 173 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 removed outlier: 4.012A pdb=" N HIS A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 229 removed outlier: 3.996A pdb=" N ARG A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 280 through 291 removed outlier: 4.469A pdb=" N PHE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 320 removed outlier: 3.681A pdb=" N HIS A 318 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 319 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY A 320 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 384 through 404 removed outlier: 3.747A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 removed outlier: 3.751A pdb=" N LEU A 420 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 421 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU A 422 " --> pdb=" O TRP A 418 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 590 removed outlier: 3.704A pdb=" N HIS A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 601 through 617 removed outlier: 4.167A pdb=" N PHE A 605 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 626 through 665 removed outlier: 4.169A pdb=" N CYS A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N PHE A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) Proline residue: A 638 - end of helix removed outlier: 4.154A pdb=" N PHE A 641 " --> pdb=" O PHE A 637 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A 642 " --> pdb=" O PRO A 638 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 648 " --> pdb=" O CYS A 644 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 658 " --> pdb=" O GLN A 654 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N PHE A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 662 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 676 removed outlier: 3.749A pdb=" N ARG A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR A 675 " --> pdb=" O TYR A 671 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 700 removed outlier: 4.024A pdb=" N SER A 681 " --> pdb=" O GLY A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 723 Processing helix chain 'A' and resid 724 through 729 Processing helix chain 'A' and resid 733 through 749 Processing helix chain 'A' and resid 758 through 781 Processing helix chain 'A' and resid 787 through 805 removed outlier: 3.549A pdb=" N LEU A 800 " --> pdb=" O THR A 796 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE A 803 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 818 removed outlier: 3.548A pdb=" N ILE A 815 " --> pdb=" O LYS A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 833 removed outlier: 3.898A pdb=" N GLN A 832 " --> pdb=" O ASN A 828 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 833 " --> pdb=" O SER A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 66 through 86 removed outlier: 4.036A pdb=" N LEU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 removed outlier: 4.166A pdb=" N LYS B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Proline residue: B 112 - end of helix removed outlier: 3.767A pdb=" N LEU B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 160 removed outlier: 3.531A pdb=" N VAL B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 155 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.895A pdb=" N ALA B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 205 removed outlier: 4.577A pdb=" N GLN B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 232 removed outlier: 3.869A pdb=" N ALA B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 265 removed outlier: 3.751A pdb=" N ASP B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 290 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 356 removed outlier: 3.585A pdb=" N CYS B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.727A pdb=" N VAL B 381 " --> pdb=" O THR B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 389 through 409 Processing helix chain 'B' and resid 422 through 425 Processing helix chain 'B' and resid 426 through 431 removed outlier: 4.137A pdb=" N TYR B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 591 removed outlier: 3.539A pdb=" N VAL B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 603 removed outlier: 3.515A pdb=" N SER B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 620 removed outlier: 3.516A pdb=" N GLY B 615 " --> pdb=" O LEU B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 635 Processing helix chain 'B' and resid 637 through 664 removed outlier: 3.819A pdb=" N LEU B 642 " --> pdb=" O PRO B 638 " (cutoff:3.500A) Proline residue: B 643 - end of helix removed outlier: 3.647A pdb=" N SER B 649 " --> pdb=" O THR B 645 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THR B 650 " --> pdb=" O GLY B 646 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 654 " --> pdb=" O THR B 650 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 677 removed outlier: 3.554A pdb=" N ARG B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 677 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 703 Processing helix chain 'B' and resid 727 through 734 Processing helix chain 'B' and resid 734 through 747 removed outlier: 3.879A pdb=" N GLY B 747 " --> pdb=" O LEU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 783 removed outlier: 3.512A pdb=" N ALA B 770 " --> pdb=" O PHE B 766 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 779 " --> pdb=" O TRP B 775 " (cutoff:3.500A) Proline residue: B 780 - end of helix removed outlier: 3.543A pdb=" N ALA B 783 " --> pdb=" O VAL B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 807 removed outlier: 3.737A pdb=" N GLN B 794 " --> pdb=" O ARG B 790 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET B 795 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY B 796 " --> pdb=" O ALA B 792 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B 798 " --> pdb=" O GLN B 794 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 799 " --> pdb=" O MET B 795 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 805 " --> pdb=" O CYS B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 824 Proline residue: B 821 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.625A pdb=" N LEU A 29 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 96 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY A 37 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 38 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL A 138 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN A 161 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 123 Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 239 removed outlier: 7.922A pdb=" N ILE A 206 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLN A 237 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL A 208 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N THR A 239 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 210 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL A 271 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 272 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N PHE A 322 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU A 448 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N SER A 467 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 450 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 429 through 430 removed outlier: 3.742A pdb=" N PHE A 429 " --> pdb=" O ILE A 436 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 525 Processing sheet with id=AA7, first strand: chain 'A' and resid 555 through 557 removed outlier: 3.860A pdb=" N VAL A 718 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.588A pdb=" N TYR B 97 " --> pdb=" O MET B 31 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA B 140 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN B 164 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AB1, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.711A pdb=" N VAL B 209 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N GLY B 241 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA B 211 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL B 243 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY B 213 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL B 270 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP B 297 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N PHE B 324 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL B 321 " --> pdb=" O TRP B 459 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TYR B 454 " --> pdb=" O ARG B 473 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ARG B 473 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU B 456 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN B 462 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL B 465 " --> pdb=" O GLN B 462 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 434 through 437 removed outlier: 3.653A pdb=" N VAL B 437 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 508 through 512 Processing sheet with id=AB4, first strand: chain 'B' and resid 559 through 560 removed outlier: 3.827A pdb=" N GLU B 706 " --> pdb=" O ARG B 723 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1605 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: 4.03 Time building geometry restraints manager: 3.18 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: 3900 1.34 - 1.47: 3086 1.47 - 1.59: 5411 1.59 - 1.71: 0 1.71 - 1.84: 134 Bond restraints: 12531 Sorted by residual: bond pdb=" N ARG A 554 " pdb=" CA ARG A 554 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.09e-02 8.42e+03 1.39e+01 bond pdb=" N ARG B 556 " pdb=" CA ARG B 556 " ideal model delta sigma weight residual 1.453 1.504 -0.051 1.41e-02 5.03e+03 1.33e+01 bond pdb=" N LYS A 553 " pdb=" CA LYS A 553 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.29e-02 6.01e+03 1.31e+01 bond pdb=" N ARG B 557 " pdb=" CA ARG B 557 " ideal model delta sigma weight residual 1.457 1.503 -0.045 1.29e-02 6.01e+03 1.24e+01 bond pdb=" CA LYS A 553 " pdb=" C LYS A 553 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.34e-02 5.57e+03 4.13e+00 ... (remaining 12526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 16901 2.45 - 4.91: 162 4.91 - 7.36: 9 7.36 - 9.82: 1 9.82 - 12.27: 1 Bond angle restraints: 17074 Sorted by residual: angle pdb=" O PHE B 555 " pdb=" C PHE B 555 " pdb=" N ARG B 556 " ideal model delta sigma weight residual 123.03 118.33 4.70 1.13e+00 7.83e-01 1.73e+01 angle pdb=" CB PRO B 638 " pdb=" CG PRO B 638 " pdb=" CD PRO B 638 " ideal model delta sigma weight residual 106.10 93.83 12.27 3.20e+00 9.77e-02 1.47e+01 angle pdb=" CA PRO B 638 " pdb=" N PRO B 638 " pdb=" CD PRO B 638 " ideal model delta sigma weight residual 112.00 106.69 5.31 1.40e+00 5.10e-01 1.44e+01 angle pdb=" N PRO B 638 " pdb=" CD PRO B 638 " pdb=" CG PRO B 638 " ideal model delta sigma weight residual 103.20 97.77 5.43 1.50e+00 4.44e-01 1.31e+01 angle pdb=" CA PRO B 638 " pdb=" CB PRO B 638 " pdb=" CG PRO B 638 " ideal model delta sigma weight residual 104.50 98.02 6.48 1.90e+00 2.77e-01 1.16e+01 ... (remaining 17069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6455 17.91 - 35.82: 721 35.82 - 53.73: 210 53.73 - 71.64: 54 71.64 - 89.55: 13 Dihedral angle restraints: 7453 sinusoidal: 2924 harmonic: 4529 Sorted by residual: dihedral pdb=" CB CYS B 370 " pdb=" SG CYS B 370 " pdb=" SG CYS B 373 " pdb=" CB CYS B 373 " ideal model delta sinusoidal sigma weight residual -86.00 -173.25 87.25 1 1.00e+01 1.00e-02 9.14e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 551 " pdb=" CB CYS A 551 " ideal model delta sinusoidal sigma weight residual 93.00 160.73 -67.73 1 1.00e+01 1.00e-02 5.96e+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 -148.43 62.43 1 1.00e+01 1.00e-02 5.16e+01 ... (remaining 7450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1166 0.026 - 0.051: 482 0.051 - 0.077: 167 0.077 - 0.103: 84 0.103 - 0.128: 45 Chirality restraints: 1944 Sorted by residual: chirality pdb=" CA VAL A 271 " pdb=" N VAL A 271 " pdb=" C VAL A 271 " pdb=" CB VAL A 271 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE B 235 " pdb=" N ILE B 235 " pdb=" C ILE B 235 " pdb=" CB ILE B 235 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA ILE A 332 " pdb=" N ILE A 332 " pdb=" C ILE A 332 " pdb=" CB ILE A 332 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1941 not shown) Planarity restraints: 2164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 556 " 0.592 9.50e-02 1.11e+02 2.65e-01 4.30e+01 pdb=" NE ARG B 556 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG B 556 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 556 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 556 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 555 " 0.020 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C PHE B 555 " -0.067 2.00e-02 2.50e+03 pdb=" O PHE B 555 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG B 556 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 557 " -0.345 9.50e-02 1.11e+02 1.55e-01 1.47e+01 pdb=" NE ARG B 557 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 557 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 557 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 557 " -0.012 2.00e-02 2.50e+03 ... (remaining 2161 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 115 2.60 - 3.18: 10704 3.18 - 3.75: 17548 3.75 - 4.33: 23619 4.33 - 4.90: 39776 Nonbonded interactions: 91762 Sorted by model distance: nonbonded pdb=" OG SER B 227 " pdb=" OE2 GLU B 240 " model vdw 2.029 3.040 nonbonded pdb=" OG1 THR B 645 " pdb=" OG1 THR B 736 " model vdw 2.093 3.040 nonbonded pdb=" OE1 GLU A 81 " pdb=" OH TYR A 389 " model vdw 2.108 3.040 nonbonded pdb=" NH2 ARG B 54 " pdb=" O SER B 58 " model vdw 2.169 3.120 nonbonded pdb=" O ALA A 683 " pdb=" OG1 THR A 686 " model vdw 2.221 3.040 ... (remaining 91757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.110 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 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 0.249 12549 Z= 0.177 Angle : 0.612 23.570 17110 Z= 0.319 Chirality : 0.038 0.128 1944 Planarity : 0.008 0.265 2164 Dihedral : 16.771 89.552 4469 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.07 % Favored : 94.86 % Rotamer: Outliers : 0.15 % Allowed : 21.23 % Favored : 78.62 % 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: -0.85 (0.22), residues: 1538 helix: 0.55 (0.20), residues: 722 sheet: -1.15 (0.36), residues: 212 loop : -1.68 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 698 HIS 0.003 0.001 HIS A 397 PHE 0.010 0.001 PHE A 558 TYR 0.018 0.001 TYR B 529 ARG 0.014 0.000 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.22584 ( 556) hydrogen bonds : angle 7.22724 ( 1605) SS BOND : bond 0.05872 ( 18) SS BOND : angle 5.37353 ( 36) covalent geometry : bond 0.00265 (12531) covalent geometry : angle 0.56104 (17074) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 245 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8457 (tp) cc_final: 0.8218 (tt) REVERT: A 238 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7744 (tp30) REVERT: A 315 GLU cc_start: 0.8053 (tp30) cc_final: 0.7468 (tp30) REVERT: A 473 ARG cc_start: 0.8401 (mtp85) cc_final: 0.8156 (mmm-85) REVERT: A 479 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7273 (mm-40) REVERT: A 644 CYS cc_start: 0.6771 (t) cc_final: 0.6328 (p) REVERT: A 788 VAL cc_start: 0.6314 (t) cc_final: 0.6025 (m) REVERT: A 792 ASP cc_start: 0.6724 (m-30) cc_final: 0.6236 (m-30) REVERT: B 193 GLN cc_start: 0.7826 (tt0) cc_final: 0.7596 (tt0) REVERT: B 443 ARG cc_start: 0.7812 (ttp80) cc_final: 0.7520 (ptm-80) REVERT: B 699 TYR cc_start: 0.6387 (OUTLIER) cc_final: 0.5894 (p90) REVERT: B 744 CYS cc_start: 0.7865 (m) cc_final: 0.7642 (t) outliers start: 2 outliers final: 1 residues processed: 246 average time/residue: 0.2880 time to fit residues: 97.1198 Evaluate side-chains 232 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 230 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 TYR Chi-restraints excluded: chain B residue 699 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 140 optimal weight: 30.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS A 283 HIS A 434 HIS A 755 ASN B 207 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 HIS B 543 GLN ** B 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.172832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.130690 restraints weight = 17757.850| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.53 r_work: 0.3411 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 12549 Z= 0.278 Angle : 0.720 12.012 17110 Z= 0.373 Chirality : 0.046 0.146 1944 Planarity : 0.006 0.063 2164 Dihedral : 5.039 55.878 1681 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.64 % Allowed : 19.90 % Favored : 76.47 % 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: -0.86 (0.21), residues: 1538 helix: 0.56 (0.20), residues: 719 sheet: -0.98 (0.35), residues: 216 loop : -1.78 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 208 HIS 0.015 0.002 HIS B 734 PHE 0.027 0.002 PHE B 435 TYR 0.030 0.002 TYR B 529 ARG 0.007 0.001 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.07294 ( 556) hydrogen bonds : angle 5.09750 ( 1605) SS BOND : bond 0.00386 ( 18) SS BOND : angle 1.80106 ( 36) covalent geometry : bond 0.00669 (12531) covalent geometry : angle 0.71636 (17074) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7265 (mm-30) REVERT: A 100 ASP cc_start: 0.7519 (t0) cc_final: 0.7310 (t0) REVERT: A 136 VAL cc_start: 0.8671 (t) cc_final: 0.8331 (p) REVERT: A 315 GLU cc_start: 0.8054 (tp30) cc_final: 0.7347 (tp30) REVERT: A 479 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7320 (mm-40) REVERT: A 644 CYS cc_start: 0.6937 (t) cc_final: 0.6323 (p) REVERT: A 750 LYS cc_start: 0.7990 (tttp) cc_final: 0.7727 (tttm) REVERT: B 148 GLU cc_start: 0.7436 (mp0) cc_final: 0.6767 (mp0) REVERT: B 647 CYS cc_start: 0.4626 (OUTLIER) cc_final: 0.2025 (m) REVERT: B 699 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.6084 (p90) REVERT: B 732 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6905 (tm) REVERT: B 768 MET cc_start: 0.7988 (mmt) cc_final: 0.7109 (mmt) outliers start: 49 outliers final: 28 residues processed: 257 average time/residue: 0.2605 time to fit residues: 92.8603 Evaluate side-chains 253 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 397 HIS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 529 TYR Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 793 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 108 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 60 optimal weight: 50.0000 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 112 optimal weight: 0.0980 chunk 36 optimal weight: 0.1980 chunk 128 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS A 441 GLN B 207 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.174787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.132688 restraints weight = 18057.219| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.57 r_work: 0.3437 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12549 Z= 0.154 Angle : 0.617 12.156 17110 Z= 0.315 Chirality : 0.041 0.156 1944 Planarity : 0.005 0.063 2164 Dihedral : 4.919 55.152 1681 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.90 % Allowed : 22.05 % Favored : 75.06 % 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: -0.61 (0.21), residues: 1538 helix: 0.77 (0.20), residues: 718 sheet: -0.83 (0.35), residues: 218 loop : -1.66 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 424 HIS 0.011 0.001 HIS B 734 PHE 0.017 0.001 PHE B 435 TYR 0.028 0.002 TYR B 529 ARG 0.010 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.05399 ( 556) hydrogen bonds : angle 4.59794 ( 1605) SS BOND : bond 0.00328 ( 18) SS BOND : angle 1.62531 ( 36) covalent geometry : bond 0.00354 (12531) covalent geometry : angle 0.61295 (17074) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7225 (mm-30) REVERT: A 100 ASP cc_start: 0.7531 (t0) cc_final: 0.7267 (t0) REVERT: A 136 VAL cc_start: 0.8671 (t) cc_final: 0.8333 (p) REVERT: A 226 ARG cc_start: 0.8306 (tpp80) cc_final: 0.7777 (tpp-160) REVERT: A 290 ARG cc_start: 0.7435 (ttm110) cc_final: 0.6966 (ttm110) REVERT: A 315 GLU cc_start: 0.8096 (tp30) cc_final: 0.7467 (tp30) REVERT: A 644 CYS cc_start: 0.6980 (t) cc_final: 0.6350 (p) REVERT: B 148 GLU cc_start: 0.7444 (mp0) cc_final: 0.6859 (mp0) REVERT: B 699 TYR cc_start: 0.6694 (OUTLIER) cc_final: 0.6115 (p90) REVERT: B 732 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6970 (tm) REVERT: B 782 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8068 (tp) outliers start: 39 outliers final: 22 residues processed: 249 average time/residue: 0.2745 time to fit residues: 94.7385 Evaluate side-chains 243 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 397 HIS Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 529 TYR Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 618 CYS Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 712 HIS Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 782 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 60 optimal weight: 40.0000 chunk 145 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN B 207 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 HIS B 462 GLN B 627 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.173072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.131047 restraints weight = 17815.106| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.55 r_work: 0.3385 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12549 Z= 0.225 Angle : 0.646 12.891 17110 Z= 0.333 Chirality : 0.043 0.153 1944 Planarity : 0.005 0.066 2164 Dihedral : 5.097 58.218 1681 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.23 % Allowed : 21.97 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.75 (0.21), residues: 1538 helix: 0.62 (0.20), residues: 721 sheet: -0.83 (0.36), residues: 218 loop : -1.72 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 208 HIS 0.007 0.001 HIS B 734 PHE 0.025 0.002 PHE B 435 TYR 0.028 0.002 TYR B 529 ARG 0.010 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.05934 ( 556) hydrogen bonds : angle 4.59526 ( 1605) SS BOND : bond 0.00371 ( 18) SS BOND : angle 1.61798 ( 36) covalent geometry : bond 0.00541 (12531) covalent geometry : angle 0.64206 (17074) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 217 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7241 (mm-30) REVERT: A 100 ASP cc_start: 0.7540 (t0) cc_final: 0.7260 (t0) REVERT: A 136 VAL cc_start: 0.8700 (t) cc_final: 0.8357 (p) REVERT: A 226 ARG cc_start: 0.8368 (tpp80) cc_final: 0.7840 (tpp-160) REVERT: A 290 ARG cc_start: 0.7462 (ttm110) cc_final: 0.7042 (ttm110) REVERT: A 315 GLU cc_start: 0.8099 (tp30) cc_final: 0.7542 (tp30) REVERT: A 479 GLN cc_start: 0.7583 (mm-40) cc_final: 0.7317 (mm-40) REVERT: A 644 CYS cc_start: 0.7020 (t) cc_final: 0.6367 (p) REVERT: A 690 MET cc_start: 0.4264 (mpt) cc_final: 0.4032 (mpt) REVERT: B 148 GLU cc_start: 0.7466 (mp0) cc_final: 0.6903 (mp0) REVERT: B 256 VAL cc_start: 0.6757 (m) cc_final: 0.6134 (t) REVERT: B 260 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8297 (mm) REVERT: B 501 ARG cc_start: 0.6671 (mtp85) cc_final: 0.6459 (mtt-85) REVERT: B 699 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.6086 (p90) REVERT: B 732 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6929 (tm) REVERT: B 782 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8179 (tp) outliers start: 57 outliers final: 42 residues processed: 253 average time/residue: 0.2798 time to fit residues: 98.2432 Evaluate side-chains 260 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 213 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 397 HIS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 529 TYR Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 712 HIS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 801 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 28 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 265 GLN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.173284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.131616 restraints weight = 17922.176| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.55 r_work: 0.3419 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12549 Z= 0.178 Angle : 0.615 12.896 17110 Z= 0.314 Chirality : 0.042 0.145 1944 Planarity : 0.005 0.072 2164 Dihedral : 5.033 55.750 1681 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.38 % Allowed : 22.05 % Favored : 73.57 % 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: -0.66 (0.21), residues: 1538 helix: 0.72 (0.20), residues: 721 sheet: -0.80 (0.36), residues: 218 loop : -1.70 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 208 HIS 0.006 0.001 HIS A 117 PHE 0.021 0.002 PHE B 435 TYR 0.025 0.002 TYR B 529 ARG 0.009 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.05354 ( 556) hydrogen bonds : angle 4.45837 ( 1605) SS BOND : bond 0.00315 ( 18) SS BOND : angle 1.55403 ( 36) covalent geometry : bond 0.00423 (12531) covalent geometry : angle 0.61139 (17074) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7233 (mm-30) REVERT: A 100 ASP cc_start: 0.7529 (t0) cc_final: 0.7239 (t0) REVERT: A 226 ARG cc_start: 0.8358 (tpp80) cc_final: 0.7843 (tpp-160) REVERT: A 263 LYS cc_start: 0.7872 (mttt) cc_final: 0.7659 (mttt) REVERT: A 315 GLU cc_start: 0.8086 (tp30) cc_final: 0.7539 (tp30) REVERT: A 644 CYS cc_start: 0.7066 (t) cc_final: 0.6476 (p) REVERT: B 148 GLU cc_start: 0.7453 (mp0) cc_final: 0.6882 (mp0) REVERT: B 260 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8281 (mm) REVERT: B 520 ASP cc_start: 0.7595 (t0) cc_final: 0.7326 (t0) REVERT: B 616 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6347 (mt) REVERT: B 654 GLN cc_start: 0.5611 (OUTLIER) cc_final: 0.4355 (mt0) REVERT: B 699 TYR cc_start: 0.6860 (OUTLIER) cc_final: 0.6129 (p90) REVERT: B 732 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6900 (tm) REVERT: B 782 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8166 (tp) outliers start: 59 outliers final: 44 residues processed: 255 average time/residue: 0.2950 time to fit residues: 106.3290 Evaluate side-chains 256 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 397 HIS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 529 TYR Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 654 GLN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 712 HIS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 788 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 77 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 124 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 chunk 123 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 119 optimal weight: 0.0000 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 207 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.173484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132763 restraints weight = 18084.988| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.46 r_work: 0.3451 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12549 Z= 0.152 Angle : 0.597 11.254 17110 Z= 0.302 Chirality : 0.041 0.140 1944 Planarity : 0.005 0.061 2164 Dihedral : 4.907 53.906 1681 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.31 % Allowed : 22.57 % Favored : 73.13 % 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 (0.21), residues: 1538 helix: 0.79 (0.20), residues: 725 sheet: -0.75 (0.36), residues: 218 loop : -1.66 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 588 HIS 0.006 0.001 HIS B 405 PHE 0.017 0.001 PHE B 435 TYR 0.021 0.002 TYR B 529 ARG 0.009 0.001 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.04867 ( 556) hydrogen bonds : angle 4.29955 ( 1605) SS BOND : bond 0.00250 ( 18) SS BOND : angle 1.51665 ( 36) covalent geometry : bond 0.00356 (12531) covalent geometry : angle 0.59315 (17074) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 215 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7108 (mm-30) REVERT: A 100 ASP cc_start: 0.7460 (t0) cc_final: 0.7192 (t0) REVERT: A 126 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7205 (tp30) REVERT: A 136 VAL cc_start: 0.8699 (t) cc_final: 0.8357 (p) REVERT: A 315 GLU cc_start: 0.8073 (tp30) cc_final: 0.7503 (tp30) REVERT: A 479 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7299 (mm-40) REVERT: A 644 CYS cc_start: 0.7126 (t) cc_final: 0.6240 (p) REVERT: B 30 ARG cc_start: 0.7205 (ttp80) cc_final: 0.6953 (ttp80) REVERT: B 148 GLU cc_start: 0.7418 (mp0) cc_final: 0.6857 (mp0) REVERT: B 260 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8310 (mm) REVERT: B 520 ASP cc_start: 0.7641 (t0) cc_final: 0.7329 (t0) REVERT: B 616 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6308 (mt) REVERT: B 699 TYR cc_start: 0.6783 (OUTLIER) cc_final: 0.6040 (p90) REVERT: B 732 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6906 (tm) REVERT: B 782 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8194 (tp) outliers start: 58 outliers final: 42 residues processed: 255 average time/residue: 0.2656 time to fit residues: 94.7067 Evaluate side-chains 255 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 397 HIS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 529 TYR Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 618 CYS Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 712 HIS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 801 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 112 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 45 optimal weight: 0.0030 chunk 136 optimal weight: 0.9990 chunk 60 optimal weight: 50.0000 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS A 291 GLN A 441 GLN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 HIS B 462 GLN B 627 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.173316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.135071 restraints weight = 17893.307| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.55 r_work: 0.3460 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12549 Z= 0.141 Angle : 0.600 15.844 17110 Z= 0.302 Chirality : 0.041 0.142 1944 Planarity : 0.005 0.059 2164 Dihedral : 4.760 53.756 1681 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.45 % Allowed : 22.49 % Favored : 73.05 % 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: -0.44 (0.21), residues: 1538 helix: 0.88 (0.20), residues: 720 sheet: -0.67 (0.36), residues: 216 loop : -1.57 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 208 HIS 0.006 0.001 HIS B 405 PHE 0.016 0.001 PHE B 435 TYR 0.018 0.001 TYR B 394 ARG 0.009 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04575 ( 556) hydrogen bonds : angle 4.20921 ( 1605) SS BOND : bond 0.00258 ( 18) SS BOND : angle 1.36070 ( 36) covalent geometry : bond 0.00328 (12531) covalent geometry : angle 0.59756 (17074) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 209 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7105 (mm-30) REVERT: A 100 ASP cc_start: 0.7429 (t0) cc_final: 0.7215 (t0) REVERT: A 126 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7135 (tp30) REVERT: A 315 GLU cc_start: 0.8068 (tp30) cc_final: 0.7516 (tp30) REVERT: A 479 GLN cc_start: 0.7527 (mm-40) cc_final: 0.7316 (mm-40) REVERT: A 644 CYS cc_start: 0.7075 (t) cc_final: 0.6191 (p) REVERT: B 30 ARG cc_start: 0.7211 (ttp80) cc_final: 0.6923 (ttp80) REVERT: B 148 GLU cc_start: 0.7406 (mp0) cc_final: 0.6852 (mp0) REVERT: B 260 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8338 (mm) REVERT: B 398 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7675 (m-80) REVERT: B 520 ASP cc_start: 0.7574 (t0) cc_final: 0.7209 (t0) REVERT: B 616 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6287 (mt) REVERT: B 654 GLN cc_start: 0.5523 (OUTLIER) cc_final: 0.4220 (mt0) REVERT: B 699 TYR cc_start: 0.6825 (OUTLIER) cc_final: 0.6027 (p90) REVERT: B 732 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6855 (tm) REVERT: B 768 MET cc_start: 0.7675 (tpp) cc_final: 0.7111 (mmt) REVERT: B 775 TRP cc_start: 0.7563 (m100) cc_final: 0.7352 (m100) REVERT: B 782 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8156 (tp) REVERT: B 818 MET cc_start: 0.3032 (mmt) cc_final: 0.2784 (mmt) outliers start: 60 outliers final: 45 residues processed: 253 average time/residue: 0.2625 time to fit residues: 92.1695 Evaluate side-chains 256 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 397 HIS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 398 TYR Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 529 TYR Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 618 CYS Chi-restraints excluded: chain B residue 654 GLN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 712 HIS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 801 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 32 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 151 optimal weight: 0.4980 chunk 92 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 123 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.172775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.134450 restraints weight = 18041.011| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.58 r_work: 0.3457 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12549 Z= 0.158 Angle : 0.603 12.141 17110 Z= 0.304 Chirality : 0.041 0.144 1944 Planarity : 0.005 0.059 2164 Dihedral : 4.688 53.582 1681 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.68 % Allowed : 21.90 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.21), residues: 1538 helix: 0.87 (0.20), residues: 721 sheet: -0.70 (0.36), residues: 218 loop : -1.57 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 208 HIS 0.008 0.001 HIS A 117 PHE 0.018 0.001 PHE B 435 TYR 0.018 0.002 TYR B 394 ARG 0.006 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 556) hydrogen bonds : angle 4.22906 ( 1605) SS BOND : bond 0.00289 ( 18) SS BOND : angle 1.31722 ( 36) covalent geometry : bond 0.00373 (12531) covalent geometry : angle 0.60073 (17074) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 207 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7115 (mm-30) REVERT: A 100 ASP cc_start: 0.7416 (t0) cc_final: 0.7202 (t0) REVERT: A 126 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7098 (tp30) REVERT: A 315 GLU cc_start: 0.8068 (tp30) cc_final: 0.7491 (tp30) REVERT: A 479 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7306 (mm-40) REVERT: A 644 CYS cc_start: 0.7025 (t) cc_final: 0.6177 (p) REVERT: B 30 ARG cc_start: 0.7264 (ttp80) cc_final: 0.6923 (ttp80) REVERT: B 148 GLU cc_start: 0.7396 (mp0) cc_final: 0.6843 (mp0) REVERT: B 260 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8351 (mm) REVERT: B 398 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: B 520 ASP cc_start: 0.7555 (t0) cc_final: 0.7172 (t0) REVERT: B 616 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6278 (mt) REVERT: B 654 GLN cc_start: 0.5506 (OUTLIER) cc_final: 0.4271 (mt0) REVERT: B 699 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.6035 (p90) REVERT: B 732 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6808 (tm) REVERT: B 768 MET cc_start: 0.7669 (tpp) cc_final: 0.7117 (mmt) REVERT: B 775 TRP cc_start: 0.7585 (m100) cc_final: 0.7361 (m100) REVERT: B 782 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8153 (tp) outliers start: 63 outliers final: 47 residues processed: 253 average time/residue: 0.2654 time to fit residues: 94.2703 Evaluate side-chains 256 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 397 HIS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 398 TYR Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 529 TYR Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 618 CYS Chi-restraints excluded: chain B residue 654 GLN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 712 HIS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 801 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 112 optimal weight: 0.7980 chunk 29 optimal weight: 0.0570 chunk 108 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 133 optimal weight: 0.0980 chunk 142 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN A 441 GLN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.173123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.134379 restraints weight = 17824.015| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.48 r_work: 0.3461 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12549 Z= 0.138 Angle : 0.599 12.095 17110 Z= 0.303 Chirality : 0.041 0.272 1944 Planarity : 0.005 0.058 2164 Dihedral : 4.600 53.373 1681 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.16 % Allowed : 22.64 % Favored : 73.20 % 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: -0.32 (0.22), residues: 1538 helix: 1.01 (0.20), residues: 715 sheet: -0.62 (0.36), residues: 216 loop : -1.53 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 424 HIS 0.006 0.001 HIS A 117 PHE 0.015 0.001 PHE B 435 TYR 0.017 0.001 TYR B 394 ARG 0.007 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 556) hydrogen bonds : angle 4.15810 ( 1605) SS BOND : bond 0.00295 ( 18) SS BOND : angle 1.55076 ( 36) covalent geometry : bond 0.00320 (12531) covalent geometry : angle 0.59491 (17074) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7085 (mm-30) REVERT: A 100 ASP cc_start: 0.7455 (t0) cc_final: 0.7245 (t0) REVERT: A 126 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7110 (tp30) REVERT: A 315 GLU cc_start: 0.8066 (tp30) cc_final: 0.7597 (tp30) REVERT: A 479 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7340 (mm-40) REVERT: A 644 CYS cc_start: 0.7052 (t) cc_final: 0.6211 (p) REVERT: B 148 GLU cc_start: 0.7366 (mp0) cc_final: 0.6839 (mp0) REVERT: B 260 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8288 (mm) REVERT: B 398 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: B 520 ASP cc_start: 0.7582 (t0) cc_final: 0.7198 (t0) REVERT: B 616 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6270 (mm) REVERT: B 654 GLN cc_start: 0.5538 (OUTLIER) cc_final: 0.4238 (mt0) REVERT: B 699 TYR cc_start: 0.6769 (OUTLIER) cc_final: 0.6021 (p90) REVERT: B 732 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6801 (tm) REVERT: B 768 MET cc_start: 0.7624 (tpp) cc_final: 0.7083 (mmt) REVERT: B 775 TRP cc_start: 0.7520 (m100) cc_final: 0.7275 (m100) REVERT: B 782 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8112 (tp) outliers start: 56 outliers final: 46 residues processed: 241 average time/residue: 0.2501 time to fit residues: 85.2205 Evaluate side-chains 252 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 198 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 397 HIS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 398 TYR Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 529 TYR Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 618 CYS Chi-restraints excluded: chain B residue 654 GLN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 712 HIS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 801 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 126 optimal weight: 0.9990 chunk 79 optimal weight: 0.0040 chunk 0 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.171868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133590 restraints weight = 17901.578| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.65 r_work: 0.3436 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12549 Z= 0.182 Angle : 0.639 16.132 17110 Z= 0.323 Chirality : 0.043 0.280 1944 Planarity : 0.005 0.057 2164 Dihedral : 4.681 52.977 1681 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.16 % Allowed : 22.79 % Favored : 73.05 % 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 (0.21), residues: 1538 helix: 0.79 (0.20), residues: 727 sheet: -0.66 (0.35), residues: 225 loop : -1.58 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 424 HIS 0.006 0.001 HIS B 405 PHE 0.021 0.002 PHE B 435 TYR 0.019 0.002 TYR B 286 ARG 0.009 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.05117 ( 556) hydrogen bonds : angle 4.27641 ( 1605) SS BOND : bond 0.00297 ( 18) SS BOND : angle 1.59907 ( 36) covalent geometry : bond 0.00436 (12531) covalent geometry : angle 0.63562 (17074) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7469 (t0) cc_final: 0.7260 (t0) REVERT: A 126 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7049 (tp30) REVERT: A 315 GLU cc_start: 0.8073 (tp30) cc_final: 0.7599 (tp30) REVERT: A 479 GLN cc_start: 0.7604 (mm-40) cc_final: 0.7351 (mm-40) REVERT: A 644 CYS cc_start: 0.7020 (t) cc_final: 0.6192 (p) REVERT: B 148 GLU cc_start: 0.7381 (mp0) cc_final: 0.6843 (mp0) REVERT: B 260 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8368 (mm) REVERT: B 398 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7696 (m-80) REVERT: B 520 ASP cc_start: 0.7596 (t0) cc_final: 0.7215 (t0) REVERT: B 616 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6285 (mt) REVERT: B 654 GLN cc_start: 0.5597 (OUTLIER) cc_final: 0.4351 (mt0) REVERT: B 699 TYR cc_start: 0.6838 (OUTLIER) cc_final: 0.6097 (p90) REVERT: B 732 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6817 (tm) REVERT: B 768 MET cc_start: 0.7633 (tpp) cc_final: 0.7165 (mmt) REVERT: B 775 TRP cc_start: 0.7573 (m100) cc_final: 0.7348 (m100) REVERT: B 782 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8152 (tp) outliers start: 56 outliers final: 46 residues processed: 238 average time/residue: 0.3334 time to fit residues: 115.0579 Evaluate side-chains 242 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 189 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 397 HIS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 398 TYR Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 529 TYR Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 618 CYS Chi-restraints excluded: chain B residue 654 GLN Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 712 HIS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 801 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 60 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.171100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130304 restraints weight = 17849.456| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.45 r_work: 0.3421 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12549 Z= 0.217 Angle : 0.666 13.024 17110 Z= 0.339 Chirality : 0.044 0.276 1944 Planarity : 0.005 0.056 2164 Dihedral : 4.796 52.565 1681 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.23 % Allowed : 22.57 % Favored : 73.20 % 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 (0.21), residues: 1538 helix: 0.70 (0.20), residues: 722 sheet: -0.65 (0.35), residues: 225 loop : -1.67 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 424 HIS 0.006 0.001 HIS B 405 PHE 0.024 0.002 PHE B 435 TYR 0.020 0.002 TYR B 394 ARG 0.009 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.05438 ( 556) hydrogen bonds : angle 4.37861 ( 1605) SS BOND : bond 0.00307 ( 18) SS BOND : angle 1.98545 ( 36) covalent geometry : bond 0.00524 (12531) covalent geometry : angle 0.66020 (17074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6275.96 seconds wall clock time: 109 minutes 23.70 seconds (6563.70 seconds total)