Starting phenix.real_space_refine on Sun Sep 29 14:16:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arh_43782/09_2024/9arh_43782.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arh_43782/09_2024/9arh_43782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arh_43782/09_2024/9arh_43782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arh_43782/09_2024/9arh_43782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arh_43782/09_2024/9arh_43782.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arh_43782/09_2024/9arh_43782.cif" } resolution = 3.69 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= 0.032 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 136 5.16 5 C 14690 2.51 5 N 3724 2.21 5 O 4242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22792 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 5695 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 36, 'TRANS': 765} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 659 Unresolved non-hydrogen angles: 805 Unresolved non-hydrogen dihedrals: 552 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 18, 'TRP:plan': 1, 'HIS:plan': 8, 'PHE:plan': 3, 'GLU:plan': 26, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 476 Chain: "B" Number of atoms: 5654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 5654 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PTRANS': 29, 'TRANS': 758} Chain breaks: 2 Unresolved non-hydrogen bonds: 587 Unresolved non-hydrogen angles: 712 Unresolved non-hydrogen dihedrals: 507 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 21, 'TYR:plan': 8, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 26, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 391 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: D, C, F Time building chain proxies: 22.35, per 1000 atoms: 0.98 Number of scatterers: 22792 At special positions: 0 Unit cell: (110.21, 145.52, 181.9, 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 136 16.00 O 4242 8.00 N 3724 7.00 C 14690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=1.33 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 901 " - " ASN B 542 " " NAG D 901 " - " ASN D 542 " " NAG E 1 " - " ASN A 224 " " NAG F 1 " - " ASN C 224 " Time building additional restraints: 6.51 Conformation dependent library (CDL) restraints added in 3.0 seconds 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 34 sheets defined 42.6% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 70 through 81 Processing helix chain 'A' and resid 103 through 114 removed outlier: 4.727A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 removed outlier: 3.813A pdb=" N GLN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 190 removed outlier: 3.667A pdb=" N LYS A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 245 through 260 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 297 through 317 Processing helix chain 'A' and resid 337 through 349 removed outlier: 4.019A pdb=" N LEU A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 492 Processing helix chain 'A' and resid 520 through 528 removed outlier: 3.516A pdb=" N GLY A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 601 removed outlier: 3.948A pdb=" N GLY A 588 " --> pdb=" O TRP A 584 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 636 Processing helix chain 'A' and resid 647 through 673 removed outlier: 3.795A pdb=" N GLY A 659 " --> pdb=" O MET A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 695 Processing helix chain 'A' and resid 708 through 717 Processing helix chain 'A' and resid 718 through 728 removed outlier: 3.572A pdb=" N THR A 722 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS A 726 " --> pdb=" O THR A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 744 removed outlier: 3.568A pdb=" N ARG A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A 744 " --> pdb=" O GLN A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 removed outlier: 4.056A pdb=" N LYS A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 803 removed outlier: 4.263A pdb=" N GLN A 791 " --> pdb=" O SER A 787 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 813 Processing helix chain 'A' and resid 835 through 861 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 105 through 120 removed outlier: 4.315A pdb=" N ALA B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.564A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 Processing helix chain 'B' and resid 209 through 224 removed outlier: 3.913A pdb=" N ASP B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 288 through 312 Processing helix chain 'B' and resid 323 through 330 removed outlier: 3.555A pdb=" N GLU B 326 " --> pdb=" O ASN B 323 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 460 through 472 removed outlier: 3.529A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 516 through 523 removed outlier: 4.237A pdb=" N VAL B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 576 removed outlier: 3.554A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 601 through 612 Processing helix chain 'B' and resid 625 through 657 removed outlier: 3.930A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 657 " --> pdb=" O PHE B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 699 through 708 Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 732 through 742 Processing helix chain 'B' and resid 772 through 787 Processing helix chain 'B' and resid 787 through 797 removed outlier: 4.001A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 843 Processing helix chain 'C' and resid 35 through 50 Processing helix chain 'C' and resid 70 through 81 Processing helix chain 'C' and resid 103 through 114 removed outlier: 4.726A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 156 removed outlier: 3.813A pdb=" N GLN C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 190 removed outlier: 3.667A pdb=" N LYS C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 Processing helix chain 'C' and resid 245 through 260 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 297 through 317 Processing helix chain 'C' and resid 337 through 349 removed outlier: 4.019A pdb=" N LEU C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 492 Processing helix chain 'C' and resid 520 through 528 removed outlier: 3.516A pdb=" N GLY C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 601 removed outlier: 3.949A pdb=" N GLY C 588 " --> pdb=" O TRP C 584 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 594 " --> pdb=" O SER C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 636 Processing helix chain 'C' and resid 647 through 673 removed outlier: 3.795A pdb=" N GLY C 659 " --> pdb=" O MET C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 Processing helix chain 'C' and resid 708 through 717 Processing helix chain 'C' and resid 718 through 728 removed outlier: 3.572A pdb=" N THR C 722 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS C 726 " --> pdb=" O THR C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 744 removed outlier: 3.568A pdb=" N ARG C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP C 744 " --> pdb=" O GLN C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 764 removed outlier: 4.057A pdb=" N LYS C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 803 removed outlier: 4.264A pdb=" N GLN C 791 " --> pdb=" O SER C 787 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 795 " --> pdb=" O GLN C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 813 Processing helix chain 'C' and resid 835 through 861 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 51 through 56 Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 105 through 120 removed outlier: 4.316A pdb=" N ALA D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.564A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 209 through 224 removed outlier: 3.913A pdb=" N ASP D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 288 through 312 Processing helix chain 'D' and resid 323 through 330 removed outlier: 3.555A pdb=" N GLU D 326 " --> pdb=" O ASN D 323 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 460 through 472 removed outlier: 3.529A pdb=" N LYS D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 523 removed outlier: 4.237A pdb=" N VAL D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 576 removed outlier: 3.553A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 579 No H-bonds generated for 'chain 'D' and resid 577 through 579' Processing helix chain 'D' and resid 601 through 612 Processing helix chain 'D' and resid 625 through 657 removed outlier: 3.929A pdb=" N ALA D 648 " --> pdb=" O ALA D 644 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE D 655 " --> pdb=" O ALA D 651 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN D 656 " --> pdb=" O ALA D 652 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU D 657 " --> pdb=" O PHE D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 699 through 708 Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 732 through 742 Processing helix chain 'D' and resid 772 through 787 Processing helix chain 'D' and resid 787 through 797 removed outlier: 4.001A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 843 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 6.960A pdb=" N VAL A 27 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N THR A 63 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N VAL A 65 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 91 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 163 removed outlier: 3.868A pdb=" N ILE A 163 " --> pdb=" O LYS A 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 217 removed outlier: 7.393A pdb=" N LEU A 166 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 292 removed outlier: 6.556A pdb=" N TYR A 372 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 387 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 374 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 383 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 389 " --> pdb=" O HIS A 392 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 361 removed outlier: 4.151A pdb=" N GLU A 360 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 498 through 499 removed outlier: 6.426A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 430 through 432 removed outlier: 3.621A pdb=" N TYR A 477 " --> pdb=" O TYR A 431 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 509 through 510 removed outlier: 3.792A pdb=" N GLU A 509 " --> pdb=" O GLU A 518 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 518 " --> pdb=" O GLU A 509 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 548 through 550 removed outlier: 3.866A pdb=" N MET A 783 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 750 through 753 Processing sheet with id=AB2, first strand: chain 'B' and resid 67 through 69 removed outlier: 8.245A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 67 through 69 removed outlier: 5.974A pdb=" N GLY B 36 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 98 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA B 100 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE B 40 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LEU B 124 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 198 through 204 removed outlier: 7.723A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 229 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 231 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 341 through 344 removed outlier: 4.361A pdb=" N VAL B 342 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 349 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 344 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 406 through 408 removed outlier: 3.770A pdb=" N ASP B 477 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 408 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU B 478 " --> pdb=" O PRO B 435 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 420 " --> pdb=" O CYS B 456 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 458 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AB8, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.771A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 59 through 65 removed outlier: 6.959A pdb=" N VAL C 27 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N THR C 63 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE C 29 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 91 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 162 through 163 removed outlier: 3.868A pdb=" N ILE C 163 " --> pdb=" O LYS C 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 216 through 217 removed outlier: 7.394A pdb=" N LEU C 166 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 289 through 292 removed outlier: 6.557A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE C 374 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 383 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN C 389 " --> pdb=" O HIS C 392 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 360 through 361 removed outlier: 4.150A pdb=" N GLU C 360 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 498 through 499 removed outlier: 6.426A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 430 through 432 removed outlier: 3.621A pdb=" N TYR C 477 " --> pdb=" O TYR C 431 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 509 through 510 removed outlier: 3.792A pdb=" N GLU C 509 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C 518 " --> pdb=" O GLU C 509 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 548 through 550 removed outlier: 3.866A pdb=" N MET C 783 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 750 through 753 Processing sheet with id=AD1, first strand: chain 'D' and resid 67 through 69 removed outlier: 8.246A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 67 through 69 removed outlier: 5.974A pdb=" N GLY D 36 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA D 100 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 198 through 204 removed outlier: 7.723A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 229 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR D 231 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY D 377 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 341 through 344 removed outlier: 4.361A pdb=" N VAL D 342 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 349 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE D 344 " --> pdb=" O ARG D 347 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 406 through 408 removed outlier: 3.770A pdb=" N ASP D 477 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE D 408 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU D 478 " --> pdb=" O PRO D 435 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU D 420 " --> pdb=" O CYS D 456 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS D 458 " --> pdb=" O ILE D 418 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 508 through 509 Processing sheet with id=AD7, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.771A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE D 530 " --> pdb=" O TYR D 762 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 1016 hydrogen bonds defined for protein. 2964 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: 8.64 Time building geometry restraints manager: 7.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.20: 268 1.20 - 1.36: 7195 1.36 - 1.51: 7095 1.51 - 1.67: 8494 1.67 - 1.82: 228 Bond restraints: 23280 Sorted by residual: bond pdb=" C PRO C 553 " pdb=" O PRO C 553 " ideal model delta sigma weight residual 1.233 1.047 0.186 1.23e-02 6.61e+03 2.29e+02 bond pdb=" C PRO A 553 " pdb=" O PRO A 553 " ideal model delta sigma weight residual 1.233 1.048 0.185 1.23e-02 6.61e+03 2.27e+02 bond pdb=" C LYS C 555 " pdb=" O LYS C 555 " ideal model delta sigma weight residual 1.234 1.059 0.175 1.22e-02 6.72e+03 2.05e+02 bond pdb=" C LYS A 555 " pdb=" O LYS A 555 " ideal model delta sigma weight residual 1.234 1.060 0.174 1.22e-02 6.72e+03 2.05e+02 bond pdb=" C ALA D 636 " pdb=" O ALA D 636 " ideal model delta sigma weight residual 1.236 1.064 0.172 1.25e-02 6.40e+03 1.90e+02 ... (remaining 23275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.71: 31335 5.71 - 11.42: 469 11.42 - 17.13: 40 17.13 - 22.84: 14 22.84 - 28.55: 4 Bond angle restraints: 31862 Sorted by residual: angle pdb=" C PHE D 653 " pdb=" CA PHE D 653 " pdb=" CB PHE D 653 " ideal model delta sigma weight residual 110.79 82.24 28.55 1.68e+00 3.54e-01 2.89e+02 angle pdb=" C PHE B 653 " pdb=" CA PHE B 653 " pdb=" CB PHE B 653 " ideal model delta sigma weight residual 110.79 82.27 28.52 1.68e+00 3.54e-01 2.88e+02 angle pdb=" C TYR A 668 " pdb=" CA TYR A 668 " pdb=" CB TYR A 668 " ideal model delta sigma weight residual 110.88 89.71 21.17 1.57e+00 4.06e-01 1.82e+02 angle pdb=" C TYR C 668 " pdb=" CA TYR C 668 " pdb=" CB TYR C 668 " ideal model delta sigma weight residual 110.88 89.72 21.16 1.57e+00 4.06e-01 1.82e+02 angle pdb=" CA PHE C 630 " pdb=" C PHE C 630 " pdb=" O PHE C 630 " ideal model delta sigma weight residual 120.55 106.78 13.77 1.06e+00 8.90e-01 1.69e+02 ... (remaining 31857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 12721 17.63 - 35.27: 688 35.27 - 52.90: 204 52.90 - 70.54: 80 70.54 - 88.17: 9 Dihedral angle restraints: 13702 sinusoidal: 4506 harmonic: 9196 Sorted by residual: dihedral pdb=" C PHE A 759 " pdb=" N PHE A 759 " pdb=" CA PHE A 759 " pdb=" CB PHE A 759 " ideal model delta harmonic sigma weight residual -122.60 -157.99 35.39 0 2.50e+00 1.60e-01 2.00e+02 dihedral pdb=" C PHE C 759 " pdb=" N PHE C 759 " pdb=" CA PHE C 759 " pdb=" CB PHE C 759 " ideal model delta harmonic sigma weight residual -122.60 -157.98 35.38 0 2.50e+00 1.60e-01 2.00e+02 dihedral pdb=" N THR C 669 " pdb=" C THR C 669 " pdb=" CA THR C 669 " pdb=" CB THR C 669 " ideal model delta harmonic sigma weight residual 123.40 155.96 -32.56 0 2.50e+00 1.60e-01 1.70e+02 ... (remaining 13699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.278: 3755 0.278 - 0.557: 107 0.557 - 0.835: 6 0.835 - 1.113: 8 1.113 - 1.392: 8 Chirality restraints: 3884 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.24 -1.16 2.00e-02 2.50e+03 3.39e+03 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.24 -1.16 2.00e-02 2.50e+03 3.38e+03 chirality pdb=" CA PHE A 759 " pdb=" N PHE A 759 " pdb=" C PHE A 759 " pdb=" CB PHE A 759 " both_signs ideal model delta sigma weight residual False 2.51 1.12 1.39 2.00e-01 2.50e+01 4.84e+01 ... (remaining 3881 not shown) Planarity restraints: 4026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 580 " -0.040 2.00e-02 2.50e+03 7.71e-02 5.95e+01 pdb=" C GLN A 580 " 0.134 2.00e-02 2.50e+03 pdb=" O GLN A 580 " -0.048 2.00e-02 2.50e+03 pdb=" N SER A 581 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 580 " 0.040 2.00e-02 2.50e+03 7.71e-02 5.95e+01 pdb=" C GLN C 580 " -0.133 2.00e-02 2.50e+03 pdb=" O GLN C 580 " 0.048 2.00e-02 2.50e+03 pdb=" N SER C 581 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 800 " -0.035 2.00e-02 2.50e+03 7.37e-02 5.43e+01 pdb=" C SER A 800 " 0.127 2.00e-02 2.50e+03 pdb=" O SER A 800 " -0.048 2.00e-02 2.50e+03 pdb=" N HIS A 801 " -0.045 2.00e-02 2.50e+03 ... (remaining 4023 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.05: 18 2.05 - 2.76: 4178 2.76 - 3.47: 31590 3.47 - 4.19: 47927 4.19 - 4.90: 84723 Nonbonded interactions: 168436 Sorted by model distance: nonbonded pdb=" SG CYS D 746 " pdb=" SG CYS D 801 " model vdw 1.335 3.760 nonbonded pdb=" O SER B 469 " pdb=" O VAL B 472 " model vdw 1.736 3.040 nonbonded pdb=" O SER D 469 " pdb=" O VAL D 472 " model vdw 1.737 3.040 nonbonded pdb=" O VAL B 538 " pdb=" CG1 VAL B 749 " model vdw 1.739 3.460 nonbonded pdb=" O VAL D 538 " pdb=" CG1 VAL D 749 " model vdw 1.740 3.460 ... (remaining 168431 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 61.570 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.100 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 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 : 0.013 0.186 23280 Z= 0.905 Angle : 1.583 28.545 31862 Z= 1.081 Chirality : 0.114 1.392 3884 Planarity : 0.010 0.078 4022 Dihedral : 12.971 88.170 7738 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.36 % Favored : 92.26 % Rotamer: Outliers : 8.98 % Allowed : 10.36 % Favored : 80.66 % Cbeta Deviations : 2.49 % 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: -3.17 (0.13), residues: 3152 helix: -0.48 (0.13), residues: 1280 sheet: -3.06 (0.23), residues: 334 loop : -3.42 (0.13), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP B 610 HIS 0.021 0.002 HIS C 801 PHE 0.071 0.003 PHE D 642 TYR 0.071 0.002 TYR C 732 ARG 0.008 0.001 ARG C 743 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 471 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8654 (tp) REVERT: A 660 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.7614 (t80) REVERT: A 662 MET cc_start: 0.8701 (tmt) cc_final: 0.7306 (tmm) REVERT: B 358 MET cc_start: 0.7283 (mmm) cc_final: 0.7016 (mmt) REVERT: B 563 PHE cc_start: 0.7574 (t80) cc_final: 0.6750 (m-10) REVERT: B 796 TRP cc_start: 0.8651 (m100) cc_final: 0.8325 (m100) REVERT: C 342 PHE cc_start: 0.6547 (t80) cc_final: 0.6117 (t80) REVERT: C 628 MET cc_start: 0.8692 (tmm) cc_final: 0.7785 (tmm) REVERT: C 635 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8694 (tp) REVERT: C 660 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.7611 (t80) REVERT: C 662 MET cc_start: 0.8589 (tmt) cc_final: 0.7145 (tmm) REVERT: C 806 MET cc_start: 0.8759 (mmm) cc_final: 0.7229 (mmt) REVERT: D 358 MET cc_start: 0.7011 (mmm) cc_final: 0.6790 (mmt) REVERT: D 563 PHE cc_start: 0.7829 (t80) cc_final: 0.6824 (m-10) REVERT: D 631 MET cc_start: 0.7278 (tpt) cc_final: 0.6958 (tpp) REVERT: D 796 TRP cc_start: 0.8579 (m100) cc_final: 0.8101 (m100) outliers start: 196 outliers final: 127 residues processed: 646 average time/residue: 0.2982 time to fit residues: 309.5574 Evaluate side-chains 454 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 323 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 629 TRP Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 784 ARG Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 392 PRO Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 578 PRO Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 630 PHE Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 660 PHE Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain C residue 730 HIS Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 784 ARG Chi-restraints excluded: chain C residue 787 SER Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 392 PRO Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 795 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 40.0000 chunk 239 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 81 optimal weight: 0.0670 chunk 161 optimal weight: 30.0000 chunk 127 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 184 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 414 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN A 542 ASN A 803 ASN A 824 ASN B 180 GLN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN B 703 HIS ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 171 HIS C 414 GLN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 GLN C 671 ASN C 803 ASN C 824 ASN ** D 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23280 Z= 0.236 Angle : 0.668 8.799 31862 Z= 0.355 Chirality : 0.046 0.253 3884 Planarity : 0.005 0.058 4022 Dihedral : 9.544 74.668 3694 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.27 % Favored : 92.54 % Rotamer: Outliers : 7.20 % Allowed : 17.00 % Favored : 75.80 % 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: -2.26 (0.14), residues: 3152 helix: 0.32 (0.14), residues: 1320 sheet: -2.95 (0.22), residues: 370 loop : -2.92 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 391 HIS 0.010 0.001 HIS D 61 PHE 0.030 0.002 PHE C 554 TYR 0.022 0.001 TYR A 668 ARG 0.009 0.001 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 324 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 GLN cc_start: 0.9127 (pp30) cc_final: 0.8897 (pp30) REVERT: A 675 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8456 (t80) REVERT: A 730 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.7974 (p-80) REVERT: A 743 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.8054 (mtm180) REVERT: B 358 MET cc_start: 0.7734 (mmm) cc_final: 0.7453 (mmt) REVERT: B 563 PHE cc_start: 0.7896 (t80) cc_final: 0.7127 (m-10) REVERT: B 796 TRP cc_start: 0.8782 (m100) cc_final: 0.8514 (m100) REVERT: C 342 PHE cc_start: 0.6485 (t80) cc_final: 0.6079 (t80) REVERT: C 557 GLN cc_start: 0.9090 (pp30) cc_final: 0.8855 (pp30) REVERT: C 675 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8352 (t80) REVERT: C 723 MET cc_start: 0.7838 (tmm) cc_final: 0.7487 (tmm) REVERT: C 730 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.7949 (p-80) REVERT: C 743 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7891 (mtm180) REVERT: D 123 ILE cc_start: 0.7722 (pt) cc_final: 0.7514 (mt) REVERT: D 207 MET cc_start: 0.5369 (mmm) cc_final: 0.4762 (mmt) REVERT: D 358 MET cc_start: 0.7504 (mmm) cc_final: 0.7050 (mmt) REVERT: D 563 PHE cc_start: 0.8059 (t80) cc_final: 0.7198 (m-10) outliers start: 157 outliers final: 97 residues processed: 459 average time/residue: 0.2860 time to fit residues: 219.8345 Evaluate side-chains 409 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 306 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 629 TRP Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 784 ARG Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 840 HIS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 730 HIS Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 784 ARG Chi-restraints excluded: chain C residue 787 SER Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 786 ASP Chi-restraints excluded: chain D residue 800 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 195 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 310 optimal weight: 0.5980 chunk 256 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 230 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 GLN ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 HIS ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C 792 GLN ** D 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23280 Z= 0.224 Angle : 0.619 8.766 31862 Z= 0.327 Chirality : 0.045 0.200 3884 Planarity : 0.004 0.057 4022 Dihedral : 8.149 66.856 3560 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.96 % Favored : 91.94 % Rotamer: Outliers : 6.78 % Allowed : 17.60 % Favored : 75.62 % 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: -1.68 (0.15), residues: 3152 helix: 0.90 (0.15), residues: 1314 sheet: -2.62 (0.25), residues: 322 loop : -2.72 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 391 HIS 0.006 0.001 HIS B 703 PHE 0.021 0.002 PHE B 351 TYR 0.015 0.001 TYR B 239 ARG 0.006 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 320 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 GLN cc_start: 0.9116 (pp30) cc_final: 0.8864 (pp30) REVERT: A 730 HIS cc_start: 0.8239 (OUTLIER) cc_final: 0.7880 (p-80) REVERT: A 743 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8022 (mtm180) REVERT: B 664 SER cc_start: 0.7524 (t) cc_final: 0.7314 (p) REVERT: C 557 GLN cc_start: 0.9125 (pp30) cc_final: 0.8831 (pp30) REVERT: C 723 MET cc_start: 0.7818 (tmm) cc_final: 0.7535 (tmm) REVERT: C 743 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7971 (mtm180) REVERT: D 207 MET cc_start: 0.5345 (mmm) cc_final: 0.4772 (mmt) REVERT: D 358 MET cc_start: 0.7673 (mmm) cc_final: 0.7382 (mmt) REVERT: D 563 PHE cc_start: 0.8195 (t80) cc_final: 0.7152 (m-10) REVERT: D 796 TRP cc_start: 0.8817 (m100) cc_final: 0.8496 (m100) outliers start: 148 outliers final: 109 residues processed: 439 average time/residue: 0.2800 time to fit residues: 204.7622 Evaluate side-chains 407 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 295 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 629 TRP Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 784 ARG Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 784 ARG Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 786 ASP Chi-restraints excluded: chain D residue 793 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 193 optimal weight: 5.9990 chunk 288 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 273 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN B 703 HIS ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS D 145 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23280 Z= 0.228 Angle : 0.613 8.148 31862 Z= 0.323 Chirality : 0.045 0.227 3884 Planarity : 0.004 0.054 4022 Dihedral : 7.689 61.256 3539 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.15 % Favored : 91.75 % Rotamer: Outliers : 7.47 % Allowed : 17.74 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.15), residues: 3152 helix: 1.12 (0.15), residues: 1306 sheet: -2.51 (0.25), residues: 322 loop : -2.58 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 391 HIS 0.006 0.001 HIS B 703 PHE 0.022 0.002 PHE A 554 TYR 0.016 0.001 TYR B 239 ARG 0.007 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 326 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 730 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.7796 (p-80) REVERT: B 563 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.6608 (m-10) REVERT: B 643 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7922 (tt) REVERT: C 261 MET cc_start: 0.7173 (tpp) cc_final: 0.6901 (tpp) REVERT: C 342 PHE cc_start: 0.6432 (t80) cc_final: 0.6114 (t80) REVERT: C 723 MET cc_start: 0.7779 (tmm) cc_final: 0.7511 (tmm) REVERT: C 743 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7981 (mtm180) REVERT: D 112 LEU cc_start: 0.8326 (mm) cc_final: 0.8061 (tp) REVERT: D 207 MET cc_start: 0.5557 (mmm) cc_final: 0.5017 (mmt) REVERT: D 563 PHE cc_start: 0.8279 (t80) cc_final: 0.7182 (m-10) REVERT: D 643 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8179 (tt) REVERT: D 789 MET cc_start: 0.8225 (tpp) cc_final: 0.7890 (tpp) REVERT: D 796 TRP cc_start: 0.8871 (m100) cc_final: 0.8603 (m100) REVERT: D 818 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7600 (ptm) outliers start: 163 outliers final: 116 residues processed: 446 average time/residue: 0.2674 time to fit residues: 202.9158 Evaluate side-chains 419 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 297 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 629 TRP Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 786 ASP Chi-restraints excluded: chain D residue 793 GLU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 818 MET Chi-restraints excluded: chain D residue 835 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 260 optimal weight: 0.9980 chunk 211 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 77 optimal weight: 0.0010 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN B 127 HIS B 703 HIS C 426 GLN ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS D 145 GLN D 491 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23280 Z= 0.185 Angle : 0.593 7.889 31862 Z= 0.312 Chirality : 0.044 0.199 3884 Planarity : 0.004 0.061 4022 Dihedral : 7.242 59.597 3523 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.96 % Favored : 91.94 % Rotamer: Outliers : 6.78 % Allowed : 18.84 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.22 (0.15), residues: 3152 helix: 1.30 (0.15), residues: 1306 sheet: -2.46 (0.24), residues: 358 loop : -2.43 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 197 HIS 0.008 0.001 HIS B 703 PHE 0.023 0.001 PHE B 351 TYR 0.017 0.001 TYR B 239 ARG 0.004 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 296 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 MET cc_start: 0.7798 (tmm) cc_final: 0.7431 (tmm) REVERT: A 730 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7738 (p-80) REVERT: B 157 MET cc_start: 0.8526 (mtm) cc_final: 0.8192 (mtt) REVERT: B 207 MET cc_start: 0.5600 (mmm) cc_final: 0.4973 (mmt) REVERT: B 491 ASN cc_start: 0.5426 (t0) cc_final: 0.5223 (t0) REVERT: B 508 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7606 (tpt) REVERT: C 723 MET cc_start: 0.7770 (tmm) cc_final: 0.7511 (tmm) REVERT: C 743 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7951 (mtm180) REVERT: D 112 LEU cc_start: 0.8352 (mm) cc_final: 0.7914 (tp) REVERT: D 207 MET cc_start: 0.5491 (mmm) cc_final: 0.5045 (mmt) REVERT: D 563 PHE cc_start: 0.8350 (t80) cc_final: 0.7119 (m-10) REVERT: D 631 MET cc_start: 0.6813 (tpt) cc_final: 0.6459 (tpt) REVERT: D 643 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8030 (tt) REVERT: D 778 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8112 (tt) REVERT: D 789 MET cc_start: 0.8199 (tpp) cc_final: 0.7840 (tpp) REVERT: D 796 TRP cc_start: 0.8887 (m100) cc_final: 0.8625 (m100) REVERT: D 818 MET cc_start: 0.8078 (ptm) cc_final: 0.7811 (ptm) outliers start: 148 outliers final: 120 residues processed: 408 average time/residue: 0.2678 time to fit residues: 187.1672 Evaluate side-chains 409 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 284 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 629 TRP Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 793 GLU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 0.9990 chunk 275 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 305 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 chunk 141 optimal weight: 0.3980 chunk 25 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 160 optimal weight: 30.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS B 180 GLN C 730 HIS D 127 HIS D 491 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23280 Z= 0.252 Angle : 0.620 8.485 31862 Z= 0.325 Chirality : 0.045 0.208 3884 Planarity : 0.004 0.058 4022 Dihedral : 7.162 59.368 3517 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.47 % Favored : 91.47 % Rotamer: Outliers : 7.79 % Allowed : 19.29 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.17 (0.15), residues: 3152 helix: 1.38 (0.15), residues: 1294 sheet: -2.35 (0.25), residues: 322 loop : -2.45 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 391 HIS 0.011 0.001 HIS D 127 PHE 0.026 0.002 PHE D 351 TYR 0.026 0.001 TYR C 266 ARG 0.004 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 301 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8428 (t) REVERT: A 723 MET cc_start: 0.7739 (tmm) cc_final: 0.7414 (tmm) REVERT: A 730 HIS cc_start: 0.8233 (OUTLIER) cc_final: 0.7791 (p-80) REVERT: B 207 MET cc_start: 0.5577 (mmm) cc_final: 0.4994 (mmt) REVERT: B 358 MET cc_start: 0.7513 (mmm) cc_final: 0.7210 (mmt) REVERT: B 491 ASN cc_start: 0.5517 (t0) cc_final: 0.5298 (t0) REVERT: B 563 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.6755 (m-10) REVERT: B 778 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8374 (tt) REVERT: C 430 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8431 (t) REVERT: C 723 MET cc_start: 0.7825 (tmm) cc_final: 0.7568 (tmm) REVERT: C 743 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7976 (mtm180) REVERT: C 839 MET cc_start: 0.7115 (ppp) cc_final: 0.6835 (ppp) REVERT: D 112 LEU cc_start: 0.8452 (mm) cc_final: 0.8098 (tp) REVERT: D 207 MET cc_start: 0.5504 (mmm) cc_final: 0.5041 (mmt) REVERT: D 631 MET cc_start: 0.6780 (tpt) cc_final: 0.6473 (tpt) REVERT: D 643 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8049 (tt) REVERT: D 778 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8244 (tt) REVERT: D 796 TRP cc_start: 0.8894 (m100) cc_final: 0.8676 (m100) REVERT: D 818 MET cc_start: 0.8280 (ptm) cc_final: 0.8057 (ptm) outliers start: 170 outliers final: 139 residues processed: 427 average time/residue: 0.2653 time to fit residues: 193.5077 Evaluate side-chains 442 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 295 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 629 TRP Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 127 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 563 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 793 GLU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 835 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 0.4980 chunk 34 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 223 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 257 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 304 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 chunk 185 optimal weight: 40.0000 chunk 140 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS B 127 HIS D 127 HIS D 491 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23280 Z= 0.197 Angle : 0.603 7.938 31862 Z= 0.315 Chirality : 0.044 0.202 3884 Planarity : 0.004 0.063 4022 Dihedral : 7.048 59.989 3517 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.06 % Favored : 91.88 % Rotamer: Outliers : 7.20 % Allowed : 20.12 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.10 (0.15), residues: 3152 helix: 1.46 (0.15), residues: 1292 sheet: -2.41 (0.24), residues: 358 loop : -2.38 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 197 HIS 0.008 0.001 HIS B 127 PHE 0.026 0.001 PHE D 351 TYR 0.028 0.001 TYR A 266 ARG 0.007 0.000 ARG C 694 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 304 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8395 (t) REVERT: A 723 MET cc_start: 0.7773 (tmm) cc_final: 0.7452 (tmm) REVERT: A 730 HIS cc_start: 0.8204 (OUTLIER) cc_final: 0.7679 (p-80) REVERT: B 207 MET cc_start: 0.5571 (mmm) cc_final: 0.5069 (mmt) REVERT: B 358 MET cc_start: 0.7515 (mmm) cc_final: 0.7176 (mmt) REVERT: B 491 ASN cc_start: 0.5594 (t0) cc_final: 0.5362 (t0) REVERT: C 839 MET cc_start: 0.7082 (ppp) cc_final: 0.6772 (ppp) REVERT: D 112 LEU cc_start: 0.8490 (mm) cc_final: 0.8143 (tp) REVERT: D 207 MET cc_start: 0.5483 (mmm) cc_final: 0.5075 (mmt) REVERT: D 643 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8023 (tt) REVERT: D 778 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8207 (tt) outliers start: 157 outliers final: 129 residues processed: 422 average time/residue: 0.2662 time to fit residues: 193.2200 Evaluate side-chains 425 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 292 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 629 TRP Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 127 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 793 GLU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 181 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 193 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 chunk 277 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS C 498 HIS D 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23280 Z= 0.261 Angle : 0.636 9.096 31862 Z= 0.331 Chirality : 0.045 0.193 3884 Planarity : 0.004 0.063 4022 Dihedral : 6.795 59.652 3506 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.88 % Favored : 91.05 % Rotamer: Outliers : 7.15 % Allowed : 20.71 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.12 (0.15), residues: 3152 helix: 1.44 (0.15), residues: 1290 sheet: -2.31 (0.26), residues: 322 loop : -2.43 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 197 HIS 0.013 0.001 HIS B 127 PHE 0.026 0.002 PHE A 554 TYR 0.018 0.001 TYR D 239 ARG 0.005 0.000 ARG C 694 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 296 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8463 (t) REVERT: A 723 MET cc_start: 0.7756 (tmm) cc_final: 0.7455 (tmm) REVERT: A 730 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7644 (p-80) REVERT: B 207 MET cc_start: 0.5598 (mmm) cc_final: 0.5071 (mmt) REVERT: B 491 ASN cc_start: 0.5628 (t0) cc_final: 0.5388 (t0) REVERT: C 839 MET cc_start: 0.7158 (ppp) cc_final: 0.6873 (ppp) REVERT: D 207 MET cc_start: 0.5479 (mmm) cc_final: 0.5063 (mmt) REVERT: D 643 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8059 (tt) REVERT: D 778 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8291 (tt) outliers start: 156 outliers final: 134 residues processed: 411 average time/residue: 0.2583 time to fit residues: 182.3084 Evaluate side-chains 431 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 293 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 127 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 793 GLU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 2.9990 chunk 266 optimal weight: 30.0000 chunk 283 optimal weight: 0.5980 chunk 170 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 222 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 256 optimal weight: 2.9990 chunk 268 optimal weight: 0.9980 chunk 282 optimal weight: 0.2980 chunk 186 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 23280 Z= 0.188 Angle : 0.617 8.999 31862 Z= 0.319 Chirality : 0.044 0.233 3884 Planarity : 0.004 0.067 4022 Dihedral : 6.638 59.034 3504 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.19 % Favored : 91.75 % Rotamer: Outliers : 6.05 % Allowed : 21.59 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.01 (0.15), residues: 3152 helix: 1.51 (0.15), residues: 1294 sheet: -2.23 (0.25), residues: 340 loop : -2.36 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 197 HIS 0.017 0.001 HIS B 127 PHE 0.026 0.001 PHE D 351 TYR 0.021 0.001 TYR D 239 ARG 0.005 0.000 ARG C 694 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 299 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 MET cc_start: 0.7723 (tmm) cc_final: 0.7434 (tmm) REVERT: A 730 HIS cc_start: 0.8145 (OUTLIER) cc_final: 0.7599 (p-80) REVERT: B 207 MET cc_start: 0.5691 (mmm) cc_final: 0.5184 (mmt) REVERT: B 340 ILE cc_start: 0.7985 (pt) cc_final: 0.7751 (pt) REVERT: C 839 MET cc_start: 0.7102 (ppp) cc_final: 0.6816 (ppp) REVERT: D 207 MET cc_start: 0.5459 (mmm) cc_final: 0.5094 (mmt) REVERT: D 643 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8012 (tt) REVERT: D 778 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8202 (tt) outliers start: 132 outliers final: 119 residues processed: 398 average time/residue: 0.2651 time to fit residues: 179.8204 Evaluate side-chains 413 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 291 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 127 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 793 GLU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 208 optimal weight: 0.4980 chunk 314 optimal weight: 0.9990 chunk 289 optimal weight: 0.9980 chunk 250 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 498 HIS B 127 HIS D 127 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23280 Z= 0.284 Angle : 0.658 8.805 31862 Z= 0.342 Chirality : 0.046 0.220 3884 Planarity : 0.005 0.069 4022 Dihedral : 6.669 59.965 3500 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.23 % Favored : 90.70 % Rotamer: Outliers : 5.87 % Allowed : 22.23 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.08 (0.15), residues: 3152 helix: 1.42 (0.15), residues: 1294 sheet: -2.29 (0.26), residues: 322 loop : -2.36 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 285 HIS 0.006 0.001 HIS B 127 PHE 0.030 0.002 PHE C 554 TYR 0.017 0.001 TYR D 239 ARG 0.007 0.000 ARG B 742 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 295 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 ASN cc_start: 0.6301 (t0) cc_final: 0.6088 (t0) REVERT: A 723 MET cc_start: 0.7725 (tmm) cc_final: 0.7456 (tmm) REVERT: A 730 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7567 (p-80) REVERT: B 207 MET cc_start: 0.5565 (mmm) cc_final: 0.5059 (mmt) REVERT: B 340 ILE cc_start: 0.8019 (pt) cc_final: 0.7787 (pt) REVERT: B 563 PHE cc_start: 0.7584 (t80) cc_final: 0.6819 (m-10) REVERT: C 839 MET cc_start: 0.7145 (ppp) cc_final: 0.6936 (ppp) REVERT: D 207 MET cc_start: 0.5480 (mmm) cc_final: 0.4902 (mmp) REVERT: D 643 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8062 (tt) outliers start: 128 outliers final: 115 residues processed: 390 average time/residue: 0.2704 time to fit residues: 179.1627 Evaluate side-chains 401 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 284 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 127 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 793 GLU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 0.3980 chunk 76 optimal weight: 0.0030 chunk 231 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 251 optimal weight: 2.9990 chunk 105 optimal weight: 0.0980 chunk 257 optimal weight: 0.4980 chunk 31 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS D 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.233815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.206640 restraints weight = 29238.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.204596 restraints weight = 54374.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.205501 restraints weight = 53394.967| |-----------------------------------------------------------------------------| r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23280 Z= 0.161 Angle : 0.625 9.186 31862 Z= 0.322 Chirality : 0.044 0.213 3884 Planarity : 0.004 0.067 4022 Dihedral : 6.518 59.338 3498 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.96 % Favored : 91.97 % Rotamer: Outliers : 4.63 % Allowed : 23.83 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.91 (0.15), residues: 3152 helix: 1.57 (0.15), residues: 1288 sheet: -2.17 (0.26), residues: 340 loop : -2.25 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 285 HIS 0.027 0.001 HIS D 127 PHE 0.025 0.001 PHE D 351 TYR 0.021 0.001 TYR D 239 ARG 0.011 0.000 ARG B 742 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4593.55 seconds wall clock time: 88 minutes 21.03 seconds (5301.03 seconds total)