Starting phenix.real_space_refine on Fri Sep 19 03:18:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9arh_43782/09_2025/9arh_43782.cif Found real_map, /net/cci-nas-00/data/ceres_data/9arh_43782/09_2025/9arh_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/cci-nas-00/data/ceres_data/9arh_43782/09_2025/9arh_43782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9arh_43782/09_2025/9arh_43782.map" model { file = "/net/cci-nas-00/data/ceres_data/9arh_43782/09_2025/9arh_43782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9arh_43782/09_2025/9arh_43782.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASN:plan1': 18, 'ARG:plan': 27, 'HIS:plan': 8, 'GLU:plan': 26, 'GLN:plan1': 11, 'PHE:plan': 3, 'ASP:plan': 17, 'TYR:plan': 3, 'TRP:plan': 1} 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: {'ASP:plan': 21, 'GLU:plan': 26, 'HIS:plan': 3, 'ARG:plan': 12, 'GLN:plan1': 9, 'TYR:plan': 8, 'PHE:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 1} 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: C, D, F Time building chain proxies: 8.51, per 1000 atoms: 0.37 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=18, 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 A 831 " - pdb=" SG CYS D 557 " distance=2.01 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 557 " - pdb=" SG CYS C 831 " distance=2.04 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=1.33 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.03 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 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: 1.73 Conformation dependent library (CDL) restraints added in 919.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.85 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: 4.75 Time building geometry restraints manager: 2.33 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: 12738 17.63 - 35.27: 696 35.27 - 52.90: 207 52.90 - 70.54: 81 70.54 - 88.17: 10 Dihedral angle restraints: 13732 sinusoidal: 4536 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 13729 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: 1.74 - 2.37: 50 2.37 - 3.00: 13160 3.00 - 3.63: 32473 3.63 - 4.27: 46024 4.27 - 4.90: 76699 Nonbonded interactions: 168406 Sorted by model distance: 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 nonbonded pdb=" O TRP B 391 " pdb=" N ARG B 393 " model vdw 1.826 3.120 ... (remaining 168401 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: 0.05 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.690 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.330 ------------------------------------------------------------------------------- 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 : 0.015 0.696 23304 Z= 1.005 Angle : 1.644 44.435 31916 Z= 1.098 Chirality : 0.114 1.392 3884 Planarity : 0.010 0.078 4022 Dihedral : 12.971 88.170 7738 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 19.14 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.008 0.001 ARG C 743 TYR 0.071 0.002 TYR C 732 PHE 0.071 0.003 PHE D 642 TRP 0.050 0.003 TRP B 610 HIS 0.021 0.002 HIS C 801 Details of bonding type rmsd covalent geometry : bond 0.01349 (23280) covalent geometry : angle 1.58252 (31862) SS BOND : bond 0.23217 ( 18) SS BOND : angle 11.22464 ( 36) hydrogen bonds : bond 0.19079 ( 1010) hydrogen bonds : angle 7.68136 ( 2964) link_BETA1-4 : bond 0.06427 ( 2) link_BETA1-4 : angle 17.92924 ( 6) link_NAG-ASN : bond 0.00099 ( 4) link_NAG-ASN : angle 1.01149 ( 12) *********************** 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 to be fit. rotamer outliers: 196 poor density : 471 time to evaluate : 0.697 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: 0.1298 time to fit residues: 136.5132 Evaluate side-chains 454 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 323 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.0670 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.0040 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.2980 overall best weight: 0.3730 ------------------------------------------------------------------------------- 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 B 615 ASN B 703 HIS ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN 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 D 615 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.225888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.208173 restraints weight = 26567.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.207610 restraints weight = 48298.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.199785 restraints weight = 43568.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.194343 restraints weight = 36177.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.193873 restraints weight = 37764.688| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23304 Z= 0.136 Angle : 0.652 8.590 31916 Z= 0.345 Chirality : 0.045 0.250 3884 Planarity : 0.005 0.053 4022 Dihedral : 9.512 74.819 3694 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.39 % Favored : 92.42 % Rotamer: Outliers : 7.01 % Allowed : 17.00 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.14), residues: 3152 helix: 0.34 (0.14), residues: 1324 sheet: -2.86 (0.22), residues: 372 loop : -2.88 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 694 TYR 0.023 0.001 TYR A 668 PHE 0.029 0.002 PHE A 575 TRP 0.019 0.001 TRP D 391 HIS 0.009 0.001 HIS D 61 Details of bonding type rmsd covalent geometry : bond 0.00283 (23280) covalent geometry : angle 0.64946 (31862) SS BOND : bond 0.00304 ( 18) SS BOND : angle 1.47194 ( 36) hydrogen bonds : bond 0.04625 ( 1010) hydrogen bonds : angle 5.31234 ( 2964) link_BETA1-4 : bond 0.00656 ( 2) link_BETA1-4 : angle 1.33684 ( 6) link_NAG-ASN : bond 0.00413 ( 4) link_NAG-ASN : angle 1.63582 ( 12) *********************** 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 473 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 320 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 MET cc_start: 0.7915 (ptp) cc_final: 0.7601 (ptp) REVERT: A 675 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8357 (t80) REVERT: A 730 HIS cc_start: 0.8428 (OUTLIER) cc_final: 0.7999 (p-80) REVERT: A 743 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.8018 (mtm180) REVERT: A 801 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.7701 (t-90) REVERT: B 358 MET cc_start: 0.7596 (mmm) cc_final: 0.7297 (mmt) REVERT: B 563 PHE cc_start: 0.7712 (t80) cc_final: 0.7049 (m-10) REVERT: B 796 TRP cc_start: 0.8748 (m100) cc_final: 0.8479 (m100) REVERT: C 342 PHE cc_start: 0.6981 (t80) cc_final: 0.6494 (t80) REVERT: C 723 MET cc_start: 0.7809 (tmm) cc_final: 0.7471 (tmm) REVERT: C 730 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.8041 (p-80) REVERT: C 743 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7895 (mtm180) REVERT: D 207 MET cc_start: 0.5330 (mmm) cc_final: 0.4733 (mmt) REVERT: D 358 MET cc_start: 0.7633 (mmm) cc_final: 0.7260 (mmt) REVERT: D 563 PHE cc_start: 0.7931 (t80) cc_final: 0.7246 (m-10) outliers start: 153 outliers final: 81 residues processed: 449 average time/residue: 0.1224 time to fit residues: 92.4223 Evaluate side-chains 390 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 303 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 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 490 THR Chi-restraints excluded: chain A residue 494 THR 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 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 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 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 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 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 800 ILE Chi-restraints excluded: chain B residue 840 HIS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 CYS 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 316 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 494 THR 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 629 TRP Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 669 THR 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 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 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 422 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 3 optimal weight: 50.0000 chunk 15 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 240 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 282 optimal weight: 0.2980 chunk 135 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 GLN ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN 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 D 491 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.232728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.195997 restraints weight = 29581.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.189867 restraints weight = 31402.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.191659 restraints weight = 45066.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.193351 restraints weight = 24733.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.196415 restraints weight = 17824.675| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23304 Z= 0.169 Angle : 0.645 9.124 31916 Z= 0.340 Chirality : 0.045 0.218 3884 Planarity : 0.004 0.053 4022 Dihedral : 8.082 67.325 3553 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.22 % Favored : 91.72 % Rotamer: Outliers : 6.60 % Allowed : 17.19 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.15), residues: 3152 helix: 0.91 (0.15), residues: 1314 sheet: -2.62 (0.25), residues: 322 loop : -2.73 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 694 TYR 0.015 0.001 TYR B 239 PHE 0.026 0.002 PHE C 554 TRP 0.012 0.001 TRP B 391 HIS 0.006 0.001 HIS B 703 Details of bonding type rmsd covalent geometry : bond 0.00395 (23280) covalent geometry : angle 0.64141 (31862) SS BOND : bond 0.00473 ( 18) SS BOND : angle 2.00163 ( 36) hydrogen bonds : bond 0.04452 ( 1010) hydrogen bonds : angle 4.86008 ( 2964) link_BETA1-4 : bond 0.00546 ( 2) link_BETA1-4 : angle 1.17844 ( 6) link_NAG-ASN : bond 0.00094 ( 4) link_NAG-ASN : angle 1.30236 ( 12) *********************** 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 466 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 322 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.7987 (mmp) cc_final: 0.7771 (mmt) REVERT: A 557 GLN cc_start: 0.9206 (pp30) cc_final: 0.8955 (pp30) REVERT: A 730 HIS cc_start: 0.8338 (OUTLIER) cc_final: 0.8036 (p-80) REVERT: A 743 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7998 (mtm180) REVERT: B 358 MET cc_start: 0.8144 (mmm) cc_final: 0.7897 (mpp) REVERT: B 618 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7707 (m) REVERT: B 664 SER cc_start: 0.7891 (t) cc_final: 0.7526 (p) REVERT: C 723 MET cc_start: 0.7792 (tmm) cc_final: 0.7483 (tmm) REVERT: C 743 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7901 (mtm180) REVERT: D 207 MET cc_start: 0.5493 (mmm) cc_final: 0.4928 (mmt) REVERT: D 563 PHE cc_start: 0.8201 (t80) cc_final: 0.7005 (m-10) REVERT: D 616 ASN cc_start: 0.5801 (OUTLIER) cc_final: 0.5585 (p0) REVERT: D 664 SER cc_start: 0.7673 (t) cc_final: 0.7343 (p) REVERT: D 796 TRP cc_start: 0.8763 (m100) cc_final: 0.8434 (m100) outliers start: 144 outliers final: 110 residues processed: 438 average time/residue: 0.1162 time to fit residues: 86.0518 Evaluate side-chains 410 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 295 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 800 SER 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 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 425 LEU 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 618 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 749 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 79 CYS 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 329 CYS 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 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 784 ARG Chi-restraints excluded: chain C residue 787 SER 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 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 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 561 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 36 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 287 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 192 optimal weight: 0.2980 chunk 113 optimal weight: 0.5980 chunk 165 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS B 491 ASN B 703 HIS ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN D 491 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.234274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.206190 restraints weight = 29600.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.203718 restraints weight = 50705.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.204590 restraints weight = 51638.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.205057 restraints weight = 28093.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.206134 restraints weight = 22776.118| |-----------------------------------------------------------------------------| r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23304 Z= 0.126 Angle : 0.600 8.221 31916 Z= 0.315 Chirality : 0.044 0.228 3884 Planarity : 0.004 0.057 4022 Dihedral : 7.556 61.688 3535 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.65 % Favored : 92.26 % Rotamer: Outliers : 6.69 % Allowed : 18.65 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.15), residues: 3152 helix: 1.16 (0.15), residues: 1314 sheet: -2.51 (0.24), residues: 358 loop : -2.53 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 694 TYR 0.016 0.001 TYR B 239 PHE 0.020 0.001 PHE B 351 TRP 0.011 0.001 TRP A 789 HIS 0.006 0.001 HIS B 703 Details of bonding type rmsd covalent geometry : bond 0.00278 (23280) covalent geometry : angle 0.59750 (31862) SS BOND : bond 0.00484 ( 18) SS BOND : angle 1.48443 ( 36) hydrogen bonds : bond 0.03884 ( 1010) hydrogen bonds : angle 4.61981 ( 2964) link_BETA1-4 : bond 0.00580 ( 2) link_BETA1-4 : angle 1.16305 ( 6) link_NAG-ASN : bond 0.00099 ( 4) link_NAG-ASN : angle 1.29035 ( 12) *********************** 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 474 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 328 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 MET cc_start: 0.7922 (ptp) cc_final: 0.7720 (ptp) REVERT: A 557 GLN cc_start: 0.9239 (pp30) cc_final: 0.8931 (pp30) REVERT: A 730 HIS cc_start: 0.8241 (OUTLIER) cc_final: 0.7828 (p-80) REVERT: B 563 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.6864 (m-10) REVERT: C 261 MET cc_start: 0.7242 (tpp) cc_final: 0.6853 (tpp) REVERT: C 342 PHE cc_start: 0.6592 (t80) cc_final: 0.6237 (t80) REVERT: C 723 MET cc_start: 0.7806 (tmm) cc_final: 0.7534 (tmm) REVERT: D 207 MET cc_start: 0.5459 (mmm) cc_final: 0.4942 (mmt) REVERT: D 563 PHE cc_start: 0.8163 (t80) cc_final: 0.7168 (m-10) REVERT: D 796 TRP cc_start: 0.8825 (m100) cc_final: 0.8521 (m100) outliers start: 146 outliers final: 97 residues processed: 442 average time/residue: 0.1089 time to fit residues: 82.5619 Evaluate side-chains 391 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 292 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 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 316 LEU Chi-restraints excluded: chain A residue 335 ILE 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 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 773 LEU 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 851 LEU Chi-restraints excluded: chain B residue 61 HIS 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 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 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 563 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 641 ILE Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 702 MET 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 C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 79 CYS 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 329 CYS Chi-restraints excluded: chain C residue 335 ILE 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 629 TRP Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 669 THR 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 765 CYS 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 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 440 ILE 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 599 SER Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL 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 800 ILE Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 123 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 309 optimal weight: 0.0470 chunk 210 optimal weight: 0.0370 chunk 127 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 chunk 243 optimal weight: 9.9990 chunk 297 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.5956 ------------------------------------------------------------------------------- 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 491 ASN B 703 HIS C 426 GLN C 730 HIS D 127 HIS D 145 GLN D 491 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.225972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.204336 restraints weight = 28853.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.197578 restraints weight = 33730.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.195788 restraints weight = 37553.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.195921 restraints weight = 35385.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.195130 restraints weight = 31595.672| |-----------------------------------------------------------------------------| r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23304 Z= 0.122 Angle : 0.601 7.843 31916 Z= 0.315 Chirality : 0.044 0.198 3884 Planarity : 0.004 0.058 4022 Dihedral : 7.065 59.464 3517 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.90 % Favored : 92.01 % Rotamer: Outliers : 6.05 % Allowed : 19.48 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.15), residues: 3152 helix: 1.28 (0.15), residues: 1318 sheet: -2.37 (0.24), residues: 358 loop : -2.42 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 694 TYR 0.015 0.001 TYR B 239 PHE 0.021 0.001 PHE B 351 TRP 0.009 0.001 TRP A 584 HIS 0.007 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00267 (23280) covalent geometry : angle 0.59740 (31862) SS BOND : bond 0.00526 ( 18) SS BOND : angle 1.94893 ( 36) hydrogen bonds : bond 0.03676 ( 1010) hydrogen bonds : angle 4.50603 ( 2964) link_BETA1-4 : bond 0.00579 ( 2) link_BETA1-4 : angle 1.25779 ( 6) link_NAG-ASN : bond 0.00121 ( 4) link_NAG-ASN : angle 1.30233 ( 12) *********************** 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 432 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 300 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 GLN cc_start: 0.9100 (pp30) cc_final: 0.8736 (pp30) REVERT: A 723 MET cc_start: 0.7782 (tmm) cc_final: 0.7397 (tmm) REVERT: A 730 HIS cc_start: 0.8241 (OUTLIER) cc_final: 0.7763 (p-80) REVERT: B 563 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.6962 (m-10) REVERT: C 557 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7555 (pp30) REVERT: C 723 MET cc_start: 0.7786 (tmm) cc_final: 0.7516 (tmm) REVERT: C 839 MET cc_start: 0.7046 (ppp) cc_final: 0.6717 (ppp) REVERT: D 112 LEU cc_start: 0.8123 (tp) cc_final: 0.7824 (tp) REVERT: D 207 MET cc_start: 0.5492 (mmm) cc_final: 0.5037 (mmt) REVERT: D 563 PHE cc_start: 0.8276 (t80) cc_final: 0.7078 (m-10) REVERT: D 796 TRP cc_start: 0.8802 (m100) cc_final: 0.8559 (m100) outliers start: 132 outliers final: 106 residues processed: 401 average time/residue: 0.1124 time to fit residues: 77.3855 Evaluate side-chains 398 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 289 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 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 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 773 LEU Chi-restraints excluded: chain A residue 787 SER 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 851 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 127 HIS 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 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 563 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 574 VAL 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 79 CYS 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 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 557 GLN Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 632 TRP 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 765 CYS Chi-restraints excluded: chain C residue 787 SER 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 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 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 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 653 PHE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 791 GLU 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 141 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 174 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 chunk 232 optimal weight: 0.9980 chunk 229 optimal weight: 0.8980 chunk 276 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS B 703 HIS D 127 HIS D 491 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.233118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.195772 restraints weight = 29339.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.192084 restraints weight = 33042.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.193910 restraints weight = 39562.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.195011 restraints weight = 21352.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.195885 restraints weight = 16920.502| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23304 Z= 0.137 Angle : 0.608 8.457 31916 Z= 0.318 Chirality : 0.044 0.239 3884 Planarity : 0.004 0.060 4022 Dihedral : 6.949 59.855 3512 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.93 % Favored : 92.01 % Rotamer: Outliers : 6.87 % Allowed : 19.43 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.15), residues: 3152 helix: 1.36 (0.15), residues: 1310 sheet: -2.37 (0.24), residues: 358 loop : -2.36 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 694 TYR 0.028 0.001 TYR C 266 PHE 0.025 0.001 PHE B 351 TRP 0.009 0.001 TRP A 584 HIS 0.023 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00316 (23280) covalent geometry : angle 0.60531 (31862) SS BOND : bond 0.00481 ( 18) SS BOND : angle 1.74400 ( 36) hydrogen bonds : bond 0.03774 ( 1010) hydrogen bonds : angle 4.48456 ( 2964) link_BETA1-4 : bond 0.00510 ( 2) link_BETA1-4 : angle 1.28838 ( 6) link_NAG-ASN : bond 0.00073 ( 4) link_NAG-ASN : angle 1.33097 ( 12) *********************** 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 447 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 297 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.6637 (m-70) cc_final: 0.6436 (m-70) REVERT: A 723 MET cc_start: 0.7697 (tmm) cc_final: 0.7324 (tmm) REVERT: A 730 HIS cc_start: 0.8246 (OUTLIER) cc_final: 0.7814 (p-80) REVERT: B 563 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6946 (m-10) REVERT: C 430 VAL cc_start: 0.8654 (OUTLIER) cc_final: 0.8451 (t) REVERT: C 557 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7701 (pp30) REVERT: C 723 MET cc_start: 0.7705 (tmm) cc_final: 0.7359 (tmm) REVERT: C 766 ASP cc_start: 0.7949 (p0) cc_final: 0.7369 (t0) REVERT: C 839 MET cc_start: 0.7033 (ppp) cc_final: 0.6726 (ppp) REVERT: D 112 LEU cc_start: 0.8520 (tp) cc_final: 0.8300 (tp) REVERT: D 207 MET cc_start: 0.5701 (mmm) cc_final: 0.5261 (mmt) REVERT: D 563 PHE cc_start: 0.8298 (t80) cc_final: 0.7216 (m-10) REVERT: D 631 MET cc_start: 0.6719 (tpt) cc_final: 0.6485 (tpt) REVERT: D 778 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8145 (tt) REVERT: D 789 MET cc_start: 0.8290 (tpp) cc_final: 0.7931 (tpp) REVERT: D 796 TRP cc_start: 0.8751 (m100) cc_final: 0.8541 (m100) outliers start: 150 outliers final: 123 residues processed: 415 average time/residue: 0.1079 time to fit residues: 77.7971 Evaluate side-chains 416 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 288 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 321 ASN 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 773 LEU Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 793 VAL 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 851 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 127 HIS 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 418 ILE Chi-restraints excluded: chain B residue 420 GLU 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 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 567 LEU 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 79 CYS 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 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 557 GLN 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 632 TRP 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 765 CYS Chi-restraints excluded: chain C residue 787 SER 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 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 307 MET Chi-restraints excluded: chain D residue 321 CYS Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 440 ILE 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 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 653 PHE Chi-restraints excluded: chain D residue 709 PHE 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 815 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 283 optimal weight: 0.0970 chunk 297 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 199 optimal weight: 0.8980 chunk 252 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 245 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.7778 ------------------------------------------------------------------------------- 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 = 0.4647 r_free = 0.4647 target = 0.233932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.204441 restraints weight = 29438.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.201148 restraints weight = 52339.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.202296 restraints weight = 54097.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.202476 restraints weight = 33614.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.205261 restraints weight = 27831.536| |-----------------------------------------------------------------------------| r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23304 Z= 0.129 Angle : 0.607 9.005 31916 Z= 0.316 Chirality : 0.044 0.206 3884 Planarity : 0.004 0.062 4022 Dihedral : 6.785 59.882 3509 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.06 % Favored : 91.88 % Rotamer: Outliers : 6.60 % Allowed : 20.35 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.15), residues: 3152 helix: 1.49 (0.15), residues: 1296 sheet: -2.30 (0.24), residues: 358 loop : -2.33 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 238 TYR 0.021 0.001 TYR C 266 PHE 0.028 0.001 PHE D 351 TRP 0.008 0.001 TRP A 584 HIS 0.012 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00292 (23280) covalent geometry : angle 0.60355 (31862) SS BOND : bond 0.00547 ( 18) SS BOND : angle 1.79853 ( 36) hydrogen bonds : bond 0.03694 ( 1010) hydrogen bonds : angle 4.42770 ( 2964) link_BETA1-4 : bond 0.00595 ( 2) link_BETA1-4 : angle 1.30227 ( 6) link_NAG-ASN : bond 0.00086 ( 4) link_NAG-ASN : angle 1.34752 ( 12) *********************** 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 437 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 293 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 MET cc_start: 0.7677 (tmm) cc_final: 0.7343 (tmm) REVERT: A 730 HIS cc_start: 0.8200 (OUTLIER) cc_final: 0.7674 (p-80) REVERT: B 563 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.7007 (m-10) REVERT: B 778 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8152 (tt) REVERT: C 766 ASP cc_start: 0.7844 (p0) cc_final: 0.7429 (t0) REVERT: C 839 MET cc_start: 0.7030 (ppp) cc_final: 0.6720 (ppp) REVERT: D 112 LEU cc_start: 0.8179 (tp) cc_final: 0.7956 (tp) REVERT: D 207 MET cc_start: 0.5800 (mmm) cc_final: 0.5392 (mmt) REVERT: D 563 PHE cc_start: 0.8232 (t80) cc_final: 0.7162 (m-10) REVERT: D 643 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8005 (tt) REVERT: D 778 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8036 (tt) REVERT: D 789 MET cc_start: 0.8256 (tpp) cc_final: 0.7894 (tpp) outliers start: 144 outliers final: 118 residues processed: 407 average time/residue: 0.1038 time to fit residues: 73.8085 Evaluate side-chains 411 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 288 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 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 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 800 SER 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 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 434 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 563 PHE Chi-restraints excluded: chain B residue 567 LEU 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 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 79 CYS 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 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 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 765 CYS Chi-restraints excluded: chain C residue 787 SER 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 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 321 CYS 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 440 ILE 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 815 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 158 optimal weight: 20.0000 chunk 218 optimal weight: 0.6980 chunk 266 optimal weight: 6.9990 chunk 227 optimal weight: 0.5980 chunk 72 optimal weight: 0.0770 chunk 41 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 203 optimal weight: 1.9990 chunk 305 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 HIS D 145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.225507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.203787 restraints weight = 28742.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.196554 restraints weight = 33625.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.194876 restraints weight = 38912.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.194453 restraints weight = 34534.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.194031 restraints weight = 32297.509| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23304 Z= 0.120 Angle : 0.601 8.694 31916 Z= 0.312 Chirality : 0.044 0.193 3884 Planarity : 0.004 0.064 4022 Dihedral : 6.462 59.424 3500 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.19 % Favored : 91.75 % Rotamer: Outliers : 5.87 % Allowed : 20.90 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.15), residues: 3152 helix: 1.51 (0.15), residues: 1308 sheet: -2.24 (0.24), residues: 358 loop : -2.30 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 238 TYR 0.024 0.001 TYR C 266 PHE 0.026 0.001 PHE D 351 TRP 0.009 0.001 TRP D 197 HIS 0.007 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00264 (23280) covalent geometry : angle 0.59926 (31862) SS BOND : bond 0.00374 ( 18) SS BOND : angle 1.29797 ( 36) hydrogen bonds : bond 0.03535 ( 1010) hydrogen bonds : angle 4.37027 ( 2964) link_BETA1-4 : bond 0.00557 ( 2) link_BETA1-4 : angle 1.31442 ( 6) link_NAG-ASN : bond 0.00098 ( 4) link_NAG-ASN : angle 1.34723 ( 12) *********************** 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 420 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 292 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 MET cc_start: 0.7812 (tmm) cc_final: 0.7504 (tmm) REVERT: A 730 HIS cc_start: 0.8148 (OUTLIER) cc_final: 0.7630 (p-80) REVERT: B 563 PHE cc_start: 0.7508 (t80) cc_final: 0.6859 (m-10) REVERT: B 778 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8209 (tt) REVERT: C 688 ILE cc_start: 0.7634 (tp) cc_final: 0.7398 (tp) REVERT: C 766 ASP cc_start: 0.7808 (p0) cc_final: 0.7550 (t0) REVERT: C 839 MET cc_start: 0.7074 (ppp) cc_final: 0.6793 (ppp) REVERT: D 112 LEU cc_start: 0.8113 (tp) cc_final: 0.7844 (tp) REVERT: D 207 MET cc_start: 0.5713 (mmm) cc_final: 0.5342 (mmt) REVERT: D 643 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8099 (tt) REVERT: D 778 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8068 (tt) REVERT: D 789 MET cc_start: 0.8231 (tpp) cc_final: 0.7867 (tpp) outliers start: 128 outliers final: 110 residues processed: 393 average time/residue: 0.1048 time to fit residues: 71.5610 Evaluate side-chains 399 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 285 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 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 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 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 350 SER Chi-restraints excluded: chain B residue 418 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 567 LEU 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 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 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 79 CYS 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 329 CYS Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 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 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 787 SER 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 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 321 CYS 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 433 THR Chi-restraints excluded: chain D residue 440 ILE 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 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 815 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 270 optimal weight: 6.9990 chunk 288 optimal weight: 0.0870 chunk 272 optimal weight: 2.9990 chunk 262 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 ASN B 127 HIS D 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.234332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.206384 restraints weight = 29296.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.203581 restraints weight = 51656.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.204563 restraints weight = 52223.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.204673 restraints weight = 31454.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.205658 restraints weight = 27317.070| |-----------------------------------------------------------------------------| r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23304 Z= 0.122 Angle : 0.603 9.473 31916 Z= 0.312 Chirality : 0.044 0.275 3884 Planarity : 0.004 0.065 4022 Dihedral : 6.360 59.920 3495 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.06 % Favored : 91.88 % Rotamer: Outliers : 5.64 % Allowed : 21.72 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.15), residues: 3152 helix: 1.62 (0.15), residues: 1296 sheet: -2.19 (0.24), residues: 358 loop : -2.27 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 238 TYR 0.021 0.001 TYR A 266 PHE 0.026 0.001 PHE D 351 TRP 0.008 0.001 TRP B 197 HIS 0.011 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00273 (23280) covalent geometry : angle 0.60083 (31862) SS BOND : bond 0.00343 ( 18) SS BOND : angle 1.25234 ( 36) hydrogen bonds : bond 0.03485 ( 1010) hydrogen bonds : angle 4.33377 ( 2964) link_BETA1-4 : bond 0.00538 ( 2) link_BETA1-4 : angle 1.32921 ( 6) link_NAG-ASN : bond 0.00094 ( 4) link_NAG-ASN : angle 1.36894 ( 12) *********************** 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 412 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 289 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 MET cc_start: 0.7745 (tmm) cc_final: 0.7442 (tmm) REVERT: A 730 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7635 (p-80) REVERT: B 563 PHE cc_start: 0.7464 (t80) cc_final: 0.6905 (m-10) REVERT: C 557 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.7920 (pp30) REVERT: C 839 MET cc_start: 0.7020 (ppp) cc_final: 0.6780 (ppp) REVERT: D 112 LEU cc_start: 0.8163 (tp) cc_final: 0.7895 (tp) REVERT: D 207 MET cc_start: 0.5738 (mmm) cc_final: 0.5366 (mmt) REVERT: D 643 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7908 (tt) REVERT: D 778 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8134 (tt) REVERT: D 789 MET cc_start: 0.8291 (tpp) cc_final: 0.7931 (tpp) outliers start: 123 outliers final: 109 residues processed: 383 average time/residue: 0.1113 time to fit residues: 73.8445 Evaluate side-chains 398 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 285 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 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 803 ASN Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 127 HIS 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 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 567 LEU 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 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 79 CYS Chi-restraints excluded: chain C residue 127 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 266 TYR Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 557 GLN 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 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 787 SER 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 D residue 61 HIS Chi-restraints excluded: chain D residue 126 ILE 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 321 CYS Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 433 THR 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 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 815 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 60 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 112 optimal weight: 0.4980 chunk 263 optimal weight: 6.9990 chunk 262 optimal weight: 0.5980 chunk 217 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 216 optimal weight: 0.6980 chunk 248 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.225399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.204211 restraints weight = 28894.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.194416 restraints weight = 30034.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.193144 restraints weight = 39555.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.192900 restraints weight = 33321.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.192652 restraints weight = 32372.585| |-----------------------------------------------------------------------------| r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 23304 Z= 0.191 Angle : 0.798 59.198 31916 Z= 0.463 Chirality : 0.045 0.667 3884 Planarity : 0.006 0.198 4022 Dihedral : 6.290 59.906 3490 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.12 % Favored : 91.81 % Rotamer: Outliers : 5.45 % Allowed : 21.95 % Favored : 72.59 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.15), residues: 3152 helix: 1.62 (0.15), residues: 1296 sheet: -2.18 (0.24), residues: 358 loop : -2.28 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG B 742 TYR 0.064 0.001 TYR C 266 PHE 0.024 0.001 PHE D 351 TRP 0.035 0.001 TRP D 285 HIS 0.282 0.007 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00372 (23280) covalent geometry : angle 0.79510 (31862) SS BOND : bond 0.00318 ( 18) SS BOND : angle 1.99863 ( 36) hydrogen bonds : bond 0.03491 ( 1010) hydrogen bonds : angle 4.34361 ( 2964) link_BETA1-4 : bond 0.00666 ( 2) link_BETA1-4 : angle 1.45280 ( 6) link_NAG-ASN : bond 0.00091 ( 4) link_NAG-ASN : angle 1.36754 ( 12) ********************** 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 406 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 287 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 MET cc_start: 0.7774 (tmm) cc_final: 0.7475 (tmm) REVERT: A 730 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7631 (p-80) REVERT: B 563 PHE cc_start: 0.7495 (t80) cc_final: 0.6855 (m-10) REVERT: C 557 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.7860 (pp30) REVERT: C 839 MET cc_start: 0.7072 (ppp) cc_final: 0.6797 (ppp) REVERT: D 112 LEU cc_start: 0.8125 (tp) cc_final: 0.7854 (tp) REVERT: D 207 MET cc_start: 0.5701 (mmm) cc_final: 0.5336 (mmt) REVERT: D 643 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8091 (tt) REVERT: D 778 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8108 (tt) REVERT: D 789 MET cc_start: 0.8259 (tpp) cc_final: 0.7893 (tpp) outliers start: 119 outliers final: 108 residues processed: 376 average time/residue: 0.1105 time to fit residues: 72.1118 Evaluate side-chains 394 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 282 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 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 B residue 61 HIS 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 440 ILE Chi-restraints excluded: chain B residue 462 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 567 LEU 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 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 79 CYS Chi-restraints excluded: chain C residue 127 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 266 TYR Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 557 GLN 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 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 787 SER 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 D residue 61 HIS Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 134 MET 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 321 CYS Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 433 THR 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 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 815 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 308 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 312 optimal weight: 0.3980 chunk 93 optimal weight: 0.8980 chunk 249 optimal weight: 0.8980 chunk 271 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.234317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.197546 restraints weight = 29276.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.190867 restraints weight = 39698.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.193042 restraints weight = 46426.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.194135 restraints weight = 28415.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.196154 restraints weight = 21665.519| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 23304 Z= 0.191 Angle : 0.798 59.198 31916 Z= 0.463 Chirality : 0.045 0.667 3884 Planarity : 0.006 0.198 4022 Dihedral : 6.290 59.906 3490 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.12 % Favored : 91.81 % Rotamer: Outliers : 5.13 % Allowed : 22.27 % Favored : 72.59 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.15), residues: 3152 helix: 1.62 (0.15), residues: 1296 sheet: -2.18 (0.24), residues: 358 loop : -2.28 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG B 742 TYR 0.064 0.001 TYR C 266 PHE 0.024 0.001 PHE D 351 TRP 0.035 0.001 TRP D 285 HIS 0.282 0.007 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00372 (23280) covalent geometry : angle 0.79511 (31862) SS BOND : bond 0.00318 ( 18) SS BOND : angle 1.99863 ( 36) hydrogen bonds : bond 0.03491 ( 1010) hydrogen bonds : angle 4.34361 ( 2964) link_BETA1-4 : bond 0.00666 ( 2) link_BETA1-4 : angle 1.45280 ( 6) link_NAG-ASN : bond 0.00091 ( 4) link_NAG-ASN : angle 1.36754 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3247.33 seconds wall clock time: 56 minutes 45.89 seconds (3405.89 seconds total)