Starting phenix.real_space_refine on Mon Aug 25 09:51:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vjh_8697/08_2025/5vjh_8697.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vjh_8697/08_2025/5vjh_8697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5vjh_8697/08_2025/5vjh_8697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vjh_8697/08_2025/5vjh_8697.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5vjh_8697/08_2025/5vjh_8697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vjh_8697/08_2025/5vjh_8697.map" } resolution = 4.0 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= 0.006 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: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 120 5.16 5 C 17230 2.51 5 N 4835 2.21 5 O 5356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27577 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4530 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain breaks: 2 Chain: "B" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4530 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain breaks: 2 Chain: "C" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4530 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain breaks: 2 Chain: "D" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4530 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain breaks: 2 Chain: "E" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4530 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain breaks: 2 Chain: "F" Number of atoms: 4424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4424 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 17, 'TRANS': 546} Chain breaks: 3 Chain: "P" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 131 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 25} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.17, per 1000 atoms: 0.26 Number of scatterers: 27577 At special positions: 0 Unit cell: (135, 143, 131, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 36 15.00 O 5356 8.00 N 4835 7.00 C 17230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 718 " - pdb=" SG CYS F 721 " distance=2.22 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6524 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 25 sheets defined 60.6% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 166 through 170 Processing helix chain 'A' and resid 174 through 180 Processing helix chain 'A' and resid 189 through 202 removed outlier: 3.583A pdb=" N ARG A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 231 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 247 through 253 Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 344 through 364 Proline residue: A 357 - end of helix Processing helix chain 'A' and resid 368 through 383 Processing helix chain 'A' and resid 387 through 410 removed outlier: 3.771A pdb=" N LEU A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 555 Processing helix chain 'A' and resid 562 through 569 Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 584 through 599 removed outlier: 3.542A pdb=" N LYS A 588 " --> pdb=" O MET A 584 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 633 Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 650 through 657 Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 730 through 735 Processing helix chain 'A' and resid 743 through 758 removed outlier: 5.272A pdb=" N LEU A 749 " --> pdb=" O SER A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 765 Processing helix chain 'A' and resid 776 through 795 Processing helix chain 'A' and resid 808 through 819 Processing helix chain 'A' and resid 825 through 835 Processing helix chain 'A' and resid 836 through 846 Processing helix chain 'B' and resid 166 through 170 Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 217 through 232 Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 285 through 291 removed outlier: 4.273A pdb=" N GLY B 291 " --> pdb=" O MET B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 298 Processing helix chain 'B' and resid 302 through 308 Processing helix chain 'B' and resid 317 through 329 removed outlier: 4.660A pdb=" N LYS B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 344 through 364 Proline residue: B 357 - end of helix Processing helix chain 'B' and resid 368 through 383 Processing helix chain 'B' and resid 387 through 409 Processing helix chain 'B' and resid 542 through 555 Processing helix chain 'B' and resid 556 through 560 Processing helix chain 'B' and resid 562 through 571 Processing helix chain 'B' and resid 571 through 578 Processing helix chain 'B' and resid 583 through 599 Processing helix chain 'B' and resid 619 through 633 Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 644 through 646 No H-bonds generated for 'chain 'B' and resid 644 through 646' Processing helix chain 'B' and resid 647 through 657 removed outlier: 4.553A pdb=" N VAL B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N SER B 653 " --> pdb=" O LYS B 649 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 678 removed outlier: 3.523A pdb=" N TYR B 677 " --> pdb=" O ASN B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 691 Processing helix chain 'B' and resid 692 through 704 Processing helix chain 'B' and resid 730 through 735 Processing helix chain 'B' and resid 745 through 758 Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 776 through 795 Processing helix chain 'B' and resid 808 through 818 Processing helix chain 'B' and resid 825 through 836 removed outlier: 3.898A pdb=" N ASN B 829 " --> pdb=" O ALA B 825 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 830 " --> pdb=" O ARG B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 846 Processing helix chain 'C' and resid 166 through 170 Processing helix chain 'C' and resid 174 through 180 Processing helix chain 'C' and resid 189 through 201 Processing helix chain 'C' and resid 217 through 231 Processing helix chain 'C' and resid 248 through 253 Processing helix chain 'C' and resid 259 through 274 Processing helix chain 'C' and resid 285 through 291 Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 301 through 307 Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 344 through 364 Proline residue: C 357 - end of helix Processing helix chain 'C' and resid 368 through 383 Processing helix chain 'C' and resid 387 through 407 removed outlier: 4.059A pdb=" N LEU C 393 " --> pdb=" O PRO C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 555 Processing helix chain 'C' and resid 556 through 560 Processing helix chain 'C' and resid 562 through 571 Processing helix chain 'C' and resid 571 through 580 Processing helix chain 'C' and resid 583 through 599 Processing helix chain 'C' and resid 619 through 633 Processing helix chain 'C' and resid 642 through 646 Processing helix chain 'C' and resid 647 through 657 removed outlier: 5.174A pdb=" N SER C 653 " --> pdb=" O LYS C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 676 Processing helix chain 'C' and resid 687 through 691 Processing helix chain 'C' and resid 695 through 703 removed outlier: 3.543A pdb=" N MET C 699 " --> pdb=" O VAL C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 759 through 764 Processing helix chain 'C' and resid 776 through 794 Processing helix chain 'C' and resid 809 through 818 Processing helix chain 'C' and resid 825 through 836 removed outlier: 3.831A pdb=" N ASN C 829 " --> pdb=" O ALA C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 846 Processing helix chain 'D' and resid 166 through 170 Processing helix chain 'D' and resid 174 through 180 Processing helix chain 'D' and resid 189 through 201 Processing helix chain 'D' and resid 217 through 231 Processing helix chain 'D' and resid 248 through 253 Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 285 through 291 Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 301 through 307 removed outlier: 3.570A pdb=" N ARG D 307 " --> pdb=" O PRO D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 329 removed outlier: 4.559A pdb=" N LYS D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 344 through 364 Proline residue: D 357 - end of helix Processing helix chain 'D' and resid 368 through 383 Processing helix chain 'D' and resid 387 through 409 removed outlier: 4.128A pdb=" N LEU D 393 " --> pdb=" O PRO D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 555 Processing helix chain 'D' and resid 556 through 560 Processing helix chain 'D' and resid 562 through 571 removed outlier: 3.736A pdb=" N ASN D 566 " --> pdb=" O SER D 562 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU D 567 " --> pdb=" O GLU D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 580 removed outlier: 3.500A pdb=" N GLU D 579 " --> pdb=" O ASP D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 599 Processing helix chain 'D' and resid 619 through 633 Processing helix chain 'D' and resid 634 through 638 Processing helix chain 'D' and resid 644 through 646 No H-bonds generated for 'chain 'D' and resid 644 through 646' Processing helix chain 'D' and resid 647 through 657 removed outlier: 4.472A pdb=" N VAL D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N SER D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 676 Processing helix chain 'D' and resid 687 through 691 Processing helix chain 'D' and resid 692 through 703 Processing helix chain 'D' and resid 730 through 735 Processing helix chain 'D' and resid 745 through 756 Processing helix chain 'D' and resid 759 through 764 Processing helix chain 'D' and resid 776 through 794 Processing helix chain 'D' and resid 808 through 819 Processing helix chain 'D' and resid 825 through 836 Processing helix chain 'D' and resid 836 through 846 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 174 through 180 Processing helix chain 'E' and resid 189 through 202 Processing helix chain 'E' and resid 217 through 231 Processing helix chain 'E' and resid 235 through 239 Processing helix chain 'E' and resid 248 through 253 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 286 through 291 Processing helix chain 'E' and resid 294 through 298 Processing helix chain 'E' and resid 301 through 307 Processing helix chain 'E' and resid 318 through 328 Processing helix chain 'E' and resid 329 through 335 Processing helix chain 'E' and resid 344 through 364 Proline residue: E 357 - end of helix Processing helix chain 'E' and resid 368 through 383 Processing helix chain 'E' and resid 387 through 407 Processing helix chain 'E' and resid 542 through 555 Processing helix chain 'E' and resid 556 through 560 Processing helix chain 'E' and resid 562 through 576 removed outlier: 4.704A pdb=" N GLU E 573 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG E 574 " --> pdb=" O ILE E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 579 No H-bonds generated for 'chain 'E' and resid 577 through 579' Processing helix chain 'E' and resid 583 through 599 Processing helix chain 'E' and resid 619 through 633 Processing helix chain 'E' and resid 634 through 638 removed outlier: 3.635A pdb=" N MET E 638 " --> pdb=" O GLU E 635 " (cutoff:3.500A) Processing helix chain 'E' and resid 642 through 646 Processing helix chain 'E' and resid 647 through 657 removed outlier: 5.743A pdb=" N SER E 653 " --> pdb=" O LYS E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 670 through 676 Processing helix chain 'E' and resid 687 through 691 Processing helix chain 'E' and resid 692 through 703 Processing helix chain 'E' and resid 730 through 735 Processing helix chain 'E' and resid 745 through 758 Processing helix chain 'E' and resid 759 through 764 Processing helix chain 'E' and resid 776 through 794 Processing helix chain 'E' and resid 808 through 818 Processing helix chain 'E' and resid 825 through 836 removed outlier: 3.588A pdb=" N ASN E 829 " --> pdb=" O ALA E 825 " (cutoff:3.500A) Processing helix chain 'E' and resid 836 through 846 Processing helix chain 'F' and resid 166 through 170 Processing helix chain 'F' and resid 174 through 180 Processing helix chain 'F' and resid 189 through 202 Processing helix chain 'F' and resid 217 through 232 Processing helix chain 'F' and resid 247 through 254 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.633A pdb=" N GLU F 274 " --> pdb=" O LYS F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 291 Processing helix chain 'F' and resid 295 through 300 Processing helix chain 'F' and resid 301 through 307 Processing helix chain 'F' and resid 318 through 328 Processing helix chain 'F' and resid 330 through 334 Processing helix chain 'F' and resid 344 through 364 Proline residue: F 357 - end of helix Processing helix chain 'F' and resid 368 through 383 Processing helix chain 'F' and resid 387 through 410 removed outlier: 4.663A pdb=" N LEU F 393 " --> pdb=" O PRO F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 555 Processing helix chain 'F' and resid 562 through 571 removed outlier: 3.646A pdb=" N ASN F 566 " --> pdb=" O SER F 562 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU F 569 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 577 Processing helix chain 'F' and resid 583 through 599 Processing helix chain 'F' and resid 619 through 633 Processing helix chain 'F' and resid 642 through 646 Processing helix chain 'F' and resid 647 through 655 removed outlier: 5.740A pdb=" N SER F 653 " --> pdb=" O LYS F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 678 removed outlier: 3.759A pdb=" N TYR F 677 " --> pdb=" O ASN F 673 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 691 Processing helix chain 'F' and resid 692 through 704 Processing helix chain 'F' and resid 730 through 735 Processing helix chain 'F' and resid 745 through 755 Processing helix chain 'F' and resid 759 through 764 Processing helix chain 'F' and resid 776 through 795 removed outlier: 3.551A pdb=" N LYS F 782 " --> pdb=" O LYS F 778 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE F 795 " --> pdb=" O ILE F 791 " (cutoff:3.500A) Processing helix chain 'F' and resid 806 through 817 Processing helix chain 'F' and resid 825 through 836 Processing helix chain 'F' and resid 836 through 846 Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 173 removed outlier: 6.174A pdb=" N LYS A 242 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N PHE A 282 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE A 244 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILE A 313 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU A 281 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ALA A 315 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE A 283 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N THR A 316 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 210 " --> pdb=" O THR A 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 366 through 367 removed outlier: 7.005A pdb=" N ARG A 366 " --> pdb=" O VAL A 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 638 through 642 removed outlier: 6.015A pdb=" N LEU A 683 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR A 726 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE A 685 " --> pdb=" O THR A 726 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER A 609 " --> pdb=" O SER A 768 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL A 770 " --> pdb=" O SER A 609 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU A 611 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N PHE A 772 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU A 613 " --> pdb=" O PHE A 772 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 802 through 804 removed outlier: 6.901A pdb=" N VAL A 855 " --> pdb=" O LYS A 803 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 173 removed outlier: 6.172A pdb=" N LYS B 242 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE B 282 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE B 244 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS B 311 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA B 315 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N THR B 316 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 210 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS B 209 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 366 through 367 removed outlier: 6.580A pdb=" N ARG B 366 " --> pdb=" O VAL B 541 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 639 through 642 removed outlier: 5.941A pdb=" N ALA B 608 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N MET B 725 " --> pdb=" O ALA B 608 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE B 610 " --> pdb=" O MET B 725 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N SER B 727 " --> pdb=" O PHE B 610 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE B 612 " --> pdb=" O SER B 727 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 802 through 804 removed outlier: 5.224A pdb=" N TYR B 802 " --> pdb=" O GLU B 853 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N VAL B 855 " --> pdb=" O TYR B 802 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU B 804 " --> pdb=" O VAL B 855 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N VAL B 857 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 171 through 173 removed outlier: 6.279A pdb=" N LYS C 242 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE C 282 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE C 244 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE C 313 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU C 281 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA C 315 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE C 283 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N THR C 317 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY C 212 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N CYS C 209 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 366 through 367 removed outlier: 6.485A pdb=" N ARG C 366 " --> pdb=" O VAL C 541 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 639 through 641 Processing sheet with id=AB3, first strand: chain 'C' and resid 855 through 857 Processing sheet with id=AB4, first strand: chain 'D' and resid 171 through 173 removed outlier: 6.303A pdb=" N LYS D 242 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE D 282 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE D 244 " --> pdb=" O PHE D 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 366 through 367 removed outlier: 7.107A pdb=" N ARG D 366 " --> pdb=" O VAL D 541 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 639 through 642 removed outlier: 6.155A pdb=" N LEU D 683 " --> pdb=" O ILE D 724 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR D 726 " --> pdb=" O LEU D 683 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE D 685 " --> pdb=" O THR D 726 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 802 through 804 removed outlier: 6.898A pdb=" N VAL D 855 " --> pdb=" O LYS D 803 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 171 through 173 removed outlier: 6.311A pdb=" N LYS E 242 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE E 282 " --> pdb=" O LYS E 242 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE E 244 " --> pdb=" O PHE E 282 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP E 284 " --> pdb=" O PHE E 244 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU E 246 " --> pdb=" O ASP E 284 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ILE E 313 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU E 281 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA E 315 " --> pdb=" O LEU E 281 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE E 283 " --> pdb=" O ALA E 315 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N THR E 317 " --> pdb=" O ILE E 283 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 365 through 367 removed outlier: 6.241A pdb=" N ARG E 366 " --> pdb=" O VAL E 541 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 639 through 641 Processing sheet with id=AC2, first strand: chain 'E' and resid 802 through 804 removed outlier: 6.699A pdb=" N VAL E 855 " --> pdb=" O LYS E 803 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 171 through 173 removed outlier: 6.157A pdb=" N LYS F 242 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N PHE F 282 " --> pdb=" O LYS F 242 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE F 244 " --> pdb=" O PHE F 282 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE F 313 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU F 281 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA F 315 " --> pdb=" O LEU F 281 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE F 283 " --> pdb=" O ALA F 315 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N THR F 317 " --> pdb=" O ILE F 283 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 366 through 367 removed outlier: 6.841A pdb=" N ARG F 366 " --> pdb=" O VAL F 541 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 638 through 641 removed outlier: 6.190A pdb=" N ILE F 639 " --> pdb=" O LEU F 684 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER F 609 " --> pdb=" O SER F 768 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL F 770 " --> pdb=" O SER F 609 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU F 611 " --> pdb=" O VAL F 770 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 709 through 710 Processing sheet with id=AC7, first strand: chain 'F' and resid 802 through 804 1432 hydrogen bonds defined for protein. 4035 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: 6.25 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 9739 1.36 - 1.54: 17333 1.54 - 1.72: 677 1.72 - 1.90: 171 1.90 - 2.08: 12 Bond restraints: 27932 Sorted by residual: bond pdb=" C4 AGS F1002 " pdb=" C5 AGS F1002 " ideal model delta sigma weight residual 1.386 1.477 -0.091 1.00e-02 1.00e+04 8.28e+01 bond pdb=" C4 AGS A1001 " pdb=" C5 AGS A1001 " ideal model delta sigma weight residual 1.386 1.473 -0.087 1.00e-02 1.00e+04 7.50e+01 bond pdb=" C5 AGS C1002 " pdb=" N7 AGS C1002 " ideal model delta sigma weight residual 1.387 1.302 0.085 1.00e-02 1.00e+04 7.27e+01 bond pdb=" CB LEU F 383 " pdb=" CG LEU F 383 " ideal model delta sigma weight residual 1.530 1.360 0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" C4 AGS A1002 " pdb=" C5 AGS A1002 " ideal model delta sigma weight residual 1.386 1.468 -0.082 1.00e-02 1.00e+04 6.75e+01 ... (remaining 27927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 35407 3.68 - 7.37: 2051 7.37 - 11.05: 172 11.05 - 14.74: 35 14.74 - 18.42: 15 Bond angle restraints: 37680 Sorted by residual: angle pdb=" C5 AGS E1001 " pdb=" C4 AGS E1001 " pdb=" N3 AGS E1001 " ideal model delta sigma weight residual 126.80 117.37 9.43 7.41e-01 1.82e+00 1.62e+02 angle pdb=" N ASP D 799 " pdb=" CA ASP D 799 " pdb=" C ASP D 799 " ideal model delta sigma weight residual 113.41 97.95 15.46 1.22e+00 6.72e-01 1.61e+02 angle pdb=" N ASN B 882 " pdb=" CA ASN B 882 " pdb=" C ASN B 882 " ideal model delta sigma weight residual 113.88 98.57 15.31 1.23e+00 6.61e-01 1.55e+02 angle pdb=" N ASP E 799 " pdb=" CA ASP E 799 " pdb=" C ASP E 799 " ideal model delta sigma weight residual 113.88 98.67 15.21 1.23e+00 6.61e-01 1.53e+02 angle pdb=" C5 AGS F1002 " pdb=" C4 AGS F1002 " pdb=" N3 AGS F1002 " ideal model delta sigma weight residual 126.80 117.65 9.15 7.41e-01 1.82e+00 1.53e+02 ... (remaining 37675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.06: 16939 30.06 - 60.11: 381 60.11 - 90.17: 51 90.17 - 120.22: 0 120.22 - 150.28: 1 Dihedral angle restraints: 17372 sinusoidal: 7295 harmonic: 10077 Sorted by residual: dihedral pdb=" CB CYS F 718 " pdb=" SG CYS F 718 " pdb=" SG CYS F 721 " pdb=" CB CYS F 721 " ideal model delta sinusoidal sigma weight residual 93.00 40.15 52.85 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CA LYS A 302 " pdb=" C LYS A 302 " pdb=" N PRO A 303 " pdb=" CA PRO A 303 " ideal model delta harmonic sigma weight residual -180.00 -156.26 -23.74 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLU E 274 " pdb=" C GLU E 274 " pdb=" N SER E 275 " pdb=" CA SER E 275 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 17369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3159 0.108 - 0.215: 1013 0.215 - 0.323: 177 0.323 - 0.430: 16 0.430 - 0.538: 3 Chirality restraints: 4368 Sorted by residual: chirality pdb=" CG LEU C 700 " pdb=" CB LEU C 700 " pdb=" CD1 LEU C 700 " pdb=" CD2 LEU C 700 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.23e+00 chirality pdb=" CB ILE F 216 " pdb=" CA ILE F 216 " pdb=" CG1 ILE F 216 " pdb=" CG2 ILE F 216 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CB VAL D 695 " pdb=" CA VAL D 695 " pdb=" CG1 VAL D 695 " pdb=" CG2 VAL D 695 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.45 2.00e-01 2.50e+01 5.16e+00 ... (remaining 4365 not shown) Planarity restraints: 4817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 680 " -0.073 2.00e-02 2.50e+03 3.92e-02 3.08e+01 pdb=" CG TYR F 680 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR F 680 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR F 680 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR F 680 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR F 680 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR F 680 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 680 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 302 " -0.089 5.00e-02 4.00e+02 1.36e-01 2.94e+01 pdb=" N PRO A 303 " 0.234 5.00e-02 4.00e+02 pdb=" CA PRO A 303 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 303 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 650 " 0.066 2.00e-02 2.50e+03 3.36e-02 2.25e+01 pdb=" CG TYR E 650 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR E 650 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 650 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR E 650 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E 650 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR E 650 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 650 " 0.044 2.00e-02 2.50e+03 ... (remaining 4814 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 17 1.94 - 2.68: 2095 2.68 - 3.42: 41795 3.42 - 4.16: 71614 4.16 - 4.90: 125675 Nonbonded interactions: 241196 Sorted by model distance: nonbonded pdb=" OE2 GLU C 326 " pdb=" OE1 GLN D 712 " model vdw 1.198 3.040 nonbonded pdb=" NZ LYS C 205 " pdb=" NH1 ARG C 333 " model vdw 1.355 3.200 nonbonded pdb=" OE2 GLU C 326 " pdb=" CD GLN D 712 " model vdw 1.356 3.270 nonbonded pdb=" CE2 TYR E 662 " pdb=" OH TYR F 650 " model vdw 1.400 3.340 nonbonded pdb=" OE2 GLU C 326 " pdb=" NE2 GLN D 712 " model vdw 1.632 3.120 ... (remaining 241191 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 165 through 656 or resid 672 through 1002)) selection = (chain 'B' and (resid 165 through 656 or resid 672 through 1002)) selection = (chain 'C' and (resid 165 through 656 or resid 672 through 1002)) selection = (chain 'D' and (resid 165 through 656 or resid 672 through 1002)) selection = (chain 'E' and (resid 165 through 656 or resid 672 through 1002)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.510 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 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 : 0.025 0.548 27943 Z= 1.465 Angle : 1.941 18.420 37682 Z= 1.315 Chirality : 0.104 0.538 4368 Planarity : 0.010 0.136 4817 Dihedral : 12.364 150.281 10845 Min Nonbonded Distance : 1.198 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.96 % Allowed : 3.77 % Favored : 95.26 % Rotamer: Outliers : 0.94 % Allowed : 0.81 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.14), residues: 3421 helix: -0.60 (0.11), residues: 1760 sheet: 0.38 (0.25), residues: 358 loop : -0.20 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 595 TYR 0.073 0.009 TYR F 680 PHE 0.040 0.007 PHE A 685 HIS 0.014 0.003 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.02369 (27932) covalent geometry : angle 1.94035 (37680) SS BOND : bond 0.18680 ( 1) SS BOND : angle 4.46398 ( 2) hydrogen bonds : bond 0.17155 ( 1432) hydrogen bonds : angle 8.21674 ( 4035) Misc. bond : bond 0.35583 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 1156 time to evaluate : 1.235 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: 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: 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: symmetry clash REVERT: A 206 SER cc_start: 0.9386 (m) cc_final: 0.8774 (p) REVERT: A 216 ILE cc_start: 0.8662 (pt) cc_final: 0.8456 (mt) REVERT: A 352 LEU cc_start: 0.8439 (mt) cc_final: 0.8151 (mp) REVERT: B 238 LEU cc_start: 0.8348 (mt) cc_final: 0.8112 (mt) REVERT: B 320 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7139 (mt-10) REVERT: B 580 VAL cc_start: 0.8397 (t) cc_final: 0.7942 (p) REVERT: B 791 ILE cc_start: 0.7953 (mm) cc_final: 0.7660 (mm) REVERT: C 271 GLU cc_start: 0.6042 (tt0) cc_final: 0.5757 (tm-30) REVERT: C 280 VAL cc_start: 0.8614 (t) cc_final: 0.8296 (m) REVERT: C 310 LEU cc_start: 0.7109 (mt) cc_final: 0.6626 (mt) REVERT: C 349 VAL cc_start: 0.9105 (t) cc_final: 0.8873 (t) REVERT: C 680 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.7103 (p90) REVERT: C 765 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7750 (mtt-85) REVERT: D 183 LEU cc_start: 0.7379 (mt) cc_final: 0.6630 (mt) REVERT: D 269 LEU cc_start: 0.8373 (mt) cc_final: 0.8016 (tp) REVERT: D 271 GLU cc_start: 0.6471 (tt0) cc_final: 0.6034 (tp30) REVERT: D 310 LEU cc_start: 0.8552 (mt) cc_final: 0.8026 (mt) REVERT: D 333 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6972 (ttp-110) REVERT: D 626 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8104 (mmmt) REVERT: D 686 ASP cc_start: 0.7380 (m-30) cc_final: 0.7179 (m-30) REVERT: D 727 SER cc_start: 0.8332 (t) cc_final: 0.7771 (t) REVERT: D 746 THR cc_start: 0.8202 (m) cc_final: 0.7886 (m) REVERT: D 783 ILE cc_start: 0.8749 (mt) cc_final: 0.8523 (mt) REVERT: E 238 LEU cc_start: 0.6015 (pt) cc_final: 0.5682 (tp) REVERT: E 348 THR cc_start: 0.7797 (m) cc_final: 0.7554 (m) REVERT: E 359 TYR cc_start: 0.8072 (m-80) cc_final: 0.7612 (m-10) REVERT: E 578 SER cc_start: 0.8169 (p) cc_final: 0.7771 (t) REVERT: E 587 ILE cc_start: 0.8554 (mt) cc_final: 0.7886 (mt) REVERT: E 708 ILE cc_start: 0.7631 (mm) cc_final: 0.7113 (tt) REVERT: E 826 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8244 (mmt180) REVERT: F 174 MET cc_start: 0.6244 (mmm) cc_final: 0.5761 (tpp) REVERT: F 216 ILE cc_start: 0.5154 (tt) cc_final: 0.4425 (tt) REVERT: F 310 LEU cc_start: 0.7852 (tp) cc_final: 0.7521 (tt) REVERT: F 361 ILE cc_start: 0.7177 (mt) cc_final: 0.6943 (mt) REVERT: F 615 LEU cc_start: 0.7599 (mt) cc_final: 0.7359 (mt) outliers start: 28 outliers final: 18 residues processed: 1178 average time/residue: 0.2338 time to fit residues: 407.7202 Evaluate side-chains 637 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 615 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 643 CYS Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 680 TYR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 826 ARG Chi-restraints excluded: chain F residue 334 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 347 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN B 239 GLN B 299 ASN B 377 GLN B 743 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 HIS ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 673 ASN ** D 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 781 HIS E 363 HIS E 764 ASN F 177 GLN ** F 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.154900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.132207 restraints weight = 51734.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.134053 restraints weight = 33129.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135496 restraints weight = 22573.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.136141 restraints weight = 16917.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136375 restraints weight = 14255.120| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 27943 Z= 0.226 Angle : 0.909 14.654 37682 Z= 0.477 Chirality : 0.051 0.262 4368 Planarity : 0.006 0.102 4817 Dihedral : 11.218 139.724 4068 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.74 % Favored : 94.83 % Rotamer: Outliers : 3.77 % Allowed : 12.31 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.24 % 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: -0.59 (0.14), residues: 3421 helix: -0.09 (0.11), residues: 1791 sheet: -0.32 (0.25), residues: 384 loop : -0.63 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 202 TYR 0.036 0.003 TYR B 802 PHE 0.036 0.003 PHE A 630 HIS 0.017 0.003 HIS A 781 Details of bonding type rmsd covalent geometry : bond 0.00505 (27932) covalent geometry : angle 0.90860 (37680) SS BOND : bond 0.00138 ( 1) SS BOND : angle 1.84542 ( 2) hydrogen bonds : bond 0.06070 ( 1432) hydrogen bonds : angle 6.61666 ( 4035) Misc. bond : bond 0.00391 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 785 time to evaluate : 1.174 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8796 (mm) cc_final: 0.8431 (mm) REVERT: A 173 ASP cc_start: 0.7815 (t0) cc_final: 0.7542 (t70) REVERT: A 287 HIS cc_start: 0.7223 (p-80) cc_final: 0.4822 (p-80) REVERT: A 332 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8058 (pp20) REVERT: A 397 ASP cc_start: 0.7851 (t70) cc_final: 0.7321 (t70) REVERT: A 588 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7370 (tptm) REVERT: A 613 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6009 (mm) REVERT: A 622 GLU cc_start: 0.7439 (tp30) cc_final: 0.7105 (tp30) REVERT: A 635 GLU cc_start: 0.7153 (mp0) cc_final: 0.6831 (mt-10) REVERT: A 638 MET cc_start: 0.8133 (tpp) cc_final: 0.7096 (ttp) REVERT: A 743 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.6537 (mp10) REVERT: A 781 HIS cc_start: 0.6034 (m-70) cc_final: 0.5807 (m-70) REVERT: A 783 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8452 (tp) REVERT: B 192 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8334 (mm-30) REVERT: B 236 THR cc_start: 0.7775 (m) cc_final: 0.7362 (p) REVERT: B 333 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7995 (ttp80) REVERT: B 355 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8917 (tp) REVERT: B 580 VAL cc_start: 0.8906 (t) cc_final: 0.8547 (p) REVERT: B 584 MET cc_start: 0.8325 (mmm) cc_final: 0.8075 (mmm) REVERT: B 605 ARG cc_start: 0.7139 (mtp180) cc_final: 0.6914 (mtp180) REVERT: B 616 SER cc_start: 0.8059 (m) cc_final: 0.7484 (p) REVERT: B 702 MET cc_start: 0.8340 (tmm) cc_final: 0.8120 (tmm) REVERT: C 174 MET cc_start: 0.8318 (mmm) cc_final: 0.7828 (ttt) REVERT: C 200 LEU cc_start: 0.9450 (mt) cc_final: 0.9198 (mt) REVERT: C 231 ASP cc_start: 0.7113 (p0) cc_final: 0.6792 (m-30) REVERT: C 328 ASP cc_start: 0.7060 (t70) cc_final: 0.6657 (m-30) REVERT: C 553 LEU cc_start: 0.9193 (tp) cc_final: 0.8988 (tp) REVERT: C 605 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.7462 (mmt-90) REVERT: C 636 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7399 (t0) REVERT: C 705 ASP cc_start: 0.7531 (t0) cc_final: 0.7242 (t0) REVERT: C 819 TYR cc_start: 0.7848 (t80) cc_final: 0.7501 (t80) REVERT: C 848 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7177 (tp30) REVERT: D 183 LEU cc_start: 0.8395 (mt) cc_final: 0.8150 (mt) REVERT: D 192 GLU cc_start: 0.7733 (mp0) cc_final: 0.6910 (mp0) REVERT: D 260 ASP cc_start: 0.7655 (t0) cc_final: 0.7429 (t0) REVERT: D 269 LEU cc_start: 0.8674 (mt) cc_final: 0.8370 (tp) REVERT: D 310 LEU cc_start: 0.8759 (mt) cc_final: 0.8245 (mt) REVERT: D 626 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8758 (mmmt) REVERT: D 720 ASN cc_start: 0.8279 (t0) cc_final: 0.7893 (t0) REVERT: D 766 ILE cc_start: 0.8946 (mm) cc_final: 0.8356 (tp) REVERT: D 795 PHE cc_start: 0.6868 (m-10) cc_final: 0.6455 (m-10) REVERT: E 170 TYR cc_start: 0.8618 (m-80) cc_final: 0.8215 (m-80) REVERT: E 183 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.6729 (mm) REVERT: E 189 ARG cc_start: 0.8649 (mmt180) cc_final: 0.8045 (mmt-90) REVERT: E 192 GLU cc_start: 0.7727 (mp0) cc_final: 0.7185 (mp0) REVERT: E 238 LEU cc_start: 0.8303 (pt) cc_final: 0.7772 (tp) REVERT: E 284 ASP cc_start: 0.5817 (t70) cc_final: 0.5523 (t70) REVERT: E 290 MET cc_start: 0.8010 (mmp) cc_final: 0.7085 (mmm) REVERT: E 578 SER cc_start: 0.8456 (p) cc_final: 0.7903 (t) REVERT: E 587 ILE cc_start: 0.8743 (mt) cc_final: 0.8281 (mt) REVERT: E 591 SER cc_start: 0.8761 (m) cc_final: 0.7804 (m) REVERT: E 763 LEU cc_start: 0.8029 (mt) cc_final: 0.7224 (tp) REVERT: E 806 LEU cc_start: 0.6445 (mp) cc_final: 0.6197 (mt) REVERT: E 838 ASN cc_start: 0.8074 (m-40) cc_final: 0.7615 (m110) REVERT: F 166 TYR cc_start: 0.6133 (m-80) cc_final: 0.5838 (m-80) REVERT: F 218 LYS cc_start: 0.7648 (tppp) cc_final: 0.7372 (tppt) REVERT: F 219 THR cc_start: 0.8311 (m) cc_final: 0.8091 (p) REVERT: F 290 MET cc_start: 0.6013 (mmt) cc_final: 0.4842 (tmm) REVERT: F 338 ILE cc_start: 0.8491 (mt) cc_final: 0.8286 (mt) REVERT: F 544 ASP cc_start: 0.7514 (m-30) cc_final: 0.7135 (p0) REVERT: F 585 ASP cc_start: 0.6518 (m-30) cc_final: 0.5551 (t0) REVERT: F 678 LYS cc_start: 0.6082 (ttmt) cc_final: 0.5815 (tppp) REVERT: F 737 GLN cc_start: 0.6410 (mm-40) cc_final: 0.6114 (mp10) REVERT: F 747 LYS cc_start: 0.7051 (pttt) cc_final: 0.6244 (tptt) REVERT: F 801 HIS cc_start: 0.8033 (OUTLIER) cc_final: 0.7315 (m-70) outliers start: 112 outliers final: 61 residues processed: 860 average time/residue: 0.2036 time to fit residues: 271.0431 Evaluate side-chains 645 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 573 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 743 GLN Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 643 CYS Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 710 SER Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 777 ARG Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 680 TYR Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 762 PHE Chi-restraints excluded: chain F residue 801 HIS Chi-restraints excluded: chain F residue 816 LYS Chi-restraints excluded: chain F residue 857 VAL Chi-restraints excluded: chain F residue 877 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 121 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 217 optimal weight: 0.0470 chunk 270 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS A 336 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN B 673 ASN ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS C 363 HIS C 781 HIS D 743 GLN F 606 GLN F 756 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.149390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.124745 restraints weight = 52275.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.127492 restraints weight = 31722.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.129281 restraints weight = 21665.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130470 restraints weight = 16360.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.131349 restraints weight = 13421.882| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 27943 Z= 0.232 Angle : 0.817 15.631 37682 Z= 0.429 Chirality : 0.050 0.282 4368 Planarity : 0.006 0.098 4817 Dihedral : 10.585 146.227 4031 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.20 % Favored : 94.39 % Rotamer: Outliers : 4.88 % Allowed : 15.41 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.15 % 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: -0.58 (0.14), residues: 3421 helix: 0.11 (0.12), residues: 1794 sheet: -0.58 (0.24), residues: 401 loop : -0.86 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 598 TYR 0.044 0.002 TYR E 665 PHE 0.035 0.003 PHE E 685 HIS 0.016 0.002 HIS C 287 Details of bonding type rmsd covalent geometry : bond 0.00511 (27932) covalent geometry : angle 0.81619 (37680) SS BOND : bond 0.04962 ( 1) SS BOND : angle 3.83241 ( 2) hydrogen bonds : bond 0.05209 ( 1432) hydrogen bonds : angle 6.29129 ( 4035) Misc. bond : bond 0.00400 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 639 time to evaluate : 1.137 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8876 (mm) cc_final: 0.8526 (mm) REVERT: A 274 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6694 (pp20) REVERT: A 285 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: A 287 HIS cc_start: 0.7595 (p90) cc_final: 0.5827 (p90) REVERT: A 397 ASP cc_start: 0.7832 (t70) cc_final: 0.7254 (t70) REVERT: A 588 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7811 (ptpt) REVERT: A 781 HIS cc_start: 0.6279 (m-70) cc_final: 0.5597 (m90) REVERT: A 783 ILE cc_start: 0.8582 (mm) cc_final: 0.8231 (tt) REVERT: B 192 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8285 (mm-30) REVERT: B 243 LEU cc_start: 0.9463 (tp) cc_final: 0.9130 (tt) REVERT: B 278 LEU cc_start: 0.8315 (tp) cc_final: 0.8053 (mt) REVERT: B 572 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7906 (ptm) REVERT: B 680 TYR cc_start: 0.8604 (t80) cc_final: 0.8308 (t80) REVERT: B 699 MET cc_start: 0.7521 (tpp) cc_final: 0.7268 (ttt) REVERT: B 883 HIS cc_start: 0.2658 (OUTLIER) cc_final: -0.0084 (m90) REVERT: C 167 LEU cc_start: 0.8890 (tp) cc_final: 0.8546 (tp) REVERT: C 231 ASP cc_start: 0.7213 (p0) cc_final: 0.6902 (m-30) REVERT: C 233 ASP cc_start: 0.7201 (t0) cc_final: 0.6927 (t70) REVERT: C 271 GLU cc_start: 0.5958 (tt0) cc_final: 0.5661 (tm-30) REVERT: C 328 ASP cc_start: 0.7556 (t70) cc_final: 0.6781 (m-30) REVERT: C 333 ARG cc_start: 0.8417 (tmm160) cc_final: 0.7656 (tpt90) REVERT: C 385 TYR cc_start: 0.7718 (m-10) cc_final: 0.7496 (m-80) REVERT: C 579 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7288 (mm-30) REVERT: C 649 LYS cc_start: 0.6539 (tttt) cc_final: 0.6276 (tttt) REVERT: C 687 GLU cc_start: 0.7397 (mp0) cc_final: 0.7177 (mp0) REVERT: C 785 ASP cc_start: 0.7727 (t0) cc_final: 0.7295 (t0) REVERT: C 819 TYR cc_start: 0.7831 (t80) cc_final: 0.7588 (t80) REVERT: C 848 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7307 (tp30) REVERT: D 183 LEU cc_start: 0.8598 (mt) cc_final: 0.8388 (mt) REVERT: D 361 ILE cc_start: 0.8801 (mm) cc_final: 0.8540 (mm) REVERT: D 626 LYS cc_start: 0.9070 (mmtt) cc_final: 0.8779 (mmmt) REVERT: D 720 ASN cc_start: 0.8386 (t0) cc_final: 0.8053 (t0) REVERT: D 767 SER cc_start: 0.8908 (m) cc_final: 0.8707 (m) REVERT: E 170 TYR cc_start: 0.8752 (m-80) cc_final: 0.7964 (m-80) REVERT: E 183 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7300 (mm) REVERT: E 238 LEU cc_start: 0.8398 (pt) cc_final: 0.7785 (tp) REVERT: E 302 LYS cc_start: 0.7208 (mmtt) cc_final: 0.6946 (mmtt) REVERT: E 334 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7201 (ptp-110) REVERT: E 591 SER cc_start: 0.9122 (m) cc_final: 0.8250 (m) REVERT: E 808 GLN cc_start: 0.7346 (mm-40) cc_final: 0.6834 (tm-30) REVERT: E 838 ASN cc_start: 0.7867 (m-40) cc_final: 0.7507 (m110) REVERT: F 218 LYS cc_start: 0.7591 (tppp) cc_final: 0.7154 (mttt) REVERT: F 219 THR cc_start: 0.8223 (m) cc_final: 0.7934 (p) REVERT: F 221 ILE cc_start: 0.7440 (mt) cc_final: 0.7157 (mt) REVERT: F 290 MET cc_start: 0.5878 (mmt) cc_final: 0.4955 (tmm) REVERT: F 358 LYS cc_start: 0.6725 (mtpt) cc_final: 0.6328 (mttt) REVERT: F 544 ASP cc_start: 0.7351 (m-30) cc_final: 0.6987 (p0) REVERT: F 585 ASP cc_start: 0.6635 (m-30) cc_final: 0.5816 (t0) REVERT: F 678 LYS cc_start: 0.6115 (ttmt) cc_final: 0.5802 (tppp) REVERT: F 747 LYS cc_start: 0.6915 (pttt) cc_final: 0.6075 (tptt) REVERT: F 801 HIS cc_start: 0.7413 (OUTLIER) cc_final: 0.6970 (m-70) outliers start: 145 outliers final: 84 residues processed: 731 average time/residue: 0.1945 time to fit residues: 225.8280 Evaluate side-chains 633 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 540 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 777 ARG Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 680 TYR Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 703 LEU Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 719 SER Chi-restraints excluded: chain E residue 732 GLU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 801 HIS Chi-restraints excluded: chain F residue 816 LYS Chi-restraints excluded: chain F residue 857 VAL Chi-restraints excluded: chain F residue 877 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 175 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 277 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 338 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 264 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 GLN ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN C 781 HIS D 309 GLN E 764 ASN ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.149821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125172 restraints weight = 51240.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.128040 restraints weight = 30164.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129955 restraints weight = 20075.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131235 restraints weight = 14840.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.131928 restraints weight = 12082.726| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27943 Z= 0.184 Angle : 0.754 16.906 37682 Z= 0.389 Chirality : 0.047 0.260 4368 Planarity : 0.005 0.091 4817 Dihedral : 10.281 146.215 4025 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.17 % Favored : 94.39 % Rotamer: Outliers : 4.27 % Allowed : 17.83 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % 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: -0.53 (0.14), residues: 3421 helix: 0.21 (0.12), residues: 1782 sheet: -0.77 (0.24), residues: 408 loop : -0.86 (0.18), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 765 TYR 0.028 0.002 TYR E 665 PHE 0.027 0.002 PHE A 630 HIS 0.013 0.002 HIS C 287 Details of bonding type rmsd covalent geometry : bond 0.00413 (27932) covalent geometry : angle 0.75411 (37680) SS BOND : bond 0.00630 ( 1) SS BOND : angle 1.46476 ( 2) hydrogen bonds : bond 0.04674 ( 1432) hydrogen bonds : angle 6.11831 ( 4035) Misc. bond : bond 0.00729 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 621 time to evaluate : 1.111 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8823 (mm) cc_final: 0.8476 (mm) REVERT: A 192 GLU cc_start: 0.6948 (mp0) cc_final: 0.6514 (mp0) REVERT: A 247 ASP cc_start: 0.7264 (p0) cc_final: 0.6929 (p0) REVERT: A 274 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6712 (pp20) REVERT: A 285 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6900 (tt0) REVERT: A 287 HIS cc_start: 0.7411 (p90) cc_final: 0.6216 (p90) REVERT: A 288 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7406 (mtp) REVERT: A 319 ASN cc_start: 0.6854 (m110) cc_final: 0.6477 (t0) REVERT: A 325 VAL cc_start: 0.8380 (p) cc_final: 0.7471 (p) REVERT: A 397 ASP cc_start: 0.7714 (t70) cc_final: 0.7202 (t70) REVERT: A 588 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7707 (ptpt) REVERT: A 601 LEU cc_start: 0.5905 (mt) cc_final: 0.5643 (tp) REVERT: A 781 HIS cc_start: 0.6240 (m-70) cc_final: 0.5607 (m90) REVERT: A 833 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: B 192 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8235 (mm-30) REVERT: B 243 LEU cc_start: 0.9452 (tp) cc_final: 0.9174 (tt) REVERT: B 278 LEU cc_start: 0.8343 (tp) cc_final: 0.8105 (mt) REVERT: B 643 CYS cc_start: 0.8355 (m) cc_final: 0.7968 (m) REVERT: B 694 ASP cc_start: 0.8414 (p0) cc_final: 0.8110 (p0) REVERT: B 702 MET cc_start: 0.8296 (tmm) cc_final: 0.8076 (tmm) REVERT: B 840 LEU cc_start: 0.8902 (tp) cc_final: 0.8450 (tt) REVERT: B 883 HIS cc_start: 0.2823 (OUTLIER) cc_final: 0.0166 (m90) REVERT: C 167 LEU cc_start: 0.8857 (tp) cc_final: 0.8430 (tp) REVERT: C 231 ASP cc_start: 0.7279 (p0) cc_final: 0.7033 (m-30) REVERT: C 271 GLU cc_start: 0.5995 (tt0) cc_final: 0.5656 (tm-30) REVERT: C 328 ASP cc_start: 0.8011 (t70) cc_final: 0.7294 (m-30) REVERT: C 363 HIS cc_start: 0.7394 (m170) cc_final: 0.7138 (m170) REVERT: C 579 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7222 (mm-30) REVERT: C 605 ARG cc_start: 0.7672 (mmm-85) cc_final: 0.7439 (mmt-90) REVERT: C 649 LYS cc_start: 0.6459 (tttt) cc_final: 0.5944 (mtpt) REVERT: C 680 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.6758 (p90) REVERT: C 848 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7152 (tp30) REVERT: C 853 GLU cc_start: 0.7058 (tp30) cc_final: 0.6707 (tp30) REVERT: D 183 LEU cc_start: 0.8730 (mt) cc_final: 0.8509 (mt) REVERT: D 361 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8516 (mm) REVERT: D 394 ASP cc_start: 0.7542 (m-30) cc_final: 0.7298 (m-30) REVERT: D 626 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8767 (mmmt) REVERT: D 720 ASN cc_start: 0.8399 (t0) cc_final: 0.8163 (t0) REVERT: D 767 SER cc_start: 0.8812 (m) cc_final: 0.8584 (m) REVERT: E 174 MET cc_start: 0.8669 (mmm) cc_final: 0.8126 (mmm) REVERT: E 183 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7262 (mm) REVERT: E 189 ARG cc_start: 0.8803 (mmt180) cc_final: 0.8491 (mmt-90) REVERT: E 238 LEU cc_start: 0.8477 (pt) cc_final: 0.7925 (tp) REVERT: E 302 LYS cc_start: 0.7376 (mmtt) cc_final: 0.7104 (mmtt) REVERT: E 334 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7179 (ptp-110) REVERT: E 763 LEU cc_start: 0.8081 (mt) cc_final: 0.7410 (tp) REVERT: E 806 LEU cc_start: 0.6097 (mp) cc_final: 0.5842 (mt) REVERT: E 808 GLN cc_start: 0.7379 (mm-40) cc_final: 0.6837 (tm-30) REVERT: E 838 ASN cc_start: 0.7705 (m-40) cc_final: 0.7076 (m-40) REVERT: F 176 GLU cc_start: 0.6862 (tp30) cc_final: 0.6651 (mt-10) REVERT: F 205 LYS cc_start: 0.7999 (mmtm) cc_final: 0.7676 (mmtm) REVERT: F 218 LYS cc_start: 0.7532 (tppp) cc_final: 0.7252 (mttt) REVERT: F 219 THR cc_start: 0.8345 (m) cc_final: 0.8061 (p) REVERT: F 221 ILE cc_start: 0.7428 (mt) cc_final: 0.7167 (mt) REVERT: F 290 MET cc_start: 0.5917 (mmt) cc_final: 0.5060 (tmm) REVERT: F 544 ASP cc_start: 0.7232 (m-30) cc_final: 0.6943 (p0) REVERT: F 585 ASP cc_start: 0.6513 (m-30) cc_final: 0.5714 (t0) REVERT: F 634 ASP cc_start: 0.7886 (t0) cc_final: 0.7571 (t0) REVERT: F 678 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.5954 (tppp) REVERT: F 737 GLN cc_start: 0.6302 (mm-40) cc_final: 0.5732 (mp10) REVERT: F 747 LYS cc_start: 0.6929 (pttt) cc_final: 0.6047 (tptt) REVERT: F 772 PHE cc_start: 0.7406 (m-80) cc_final: 0.6920 (m-10) REVERT: F 801 HIS cc_start: 0.7509 (OUTLIER) cc_final: 0.7250 (m-70) outliers start: 127 outliers final: 83 residues processed: 699 average time/residue: 0.1890 time to fit residues: 211.5589 Evaluate side-chains 638 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 542 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 673 ASN Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 719 SER Chi-restraints excluded: chain E residue 732 GLU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 801 HIS Chi-restraints excluded: chain F residue 857 VAL Chi-restraints excluded: chain F residue 877 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 76 optimal weight: 5.9990 chunk 26 optimal weight: 0.0570 chunk 307 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 286 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 289 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 GLN ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 571 HIS ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.144869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.119932 restraints weight = 52123.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122502 restraints weight = 31849.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124081 restraints weight = 21983.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125373 restraints weight = 16925.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126185 restraints weight = 13973.963| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.6022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 27943 Z= 0.269 Angle : 0.814 14.226 37682 Z= 0.419 Chirality : 0.050 0.291 4368 Planarity : 0.006 0.092 4817 Dihedral : 10.190 145.216 4023 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.99 % Favored : 93.60 % Rotamer: Outliers : 5.62 % Allowed : 18.30 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.14), residues: 3421 helix: 0.19 (0.12), residues: 1774 sheet: -1.03 (0.24), residues: 400 loop : -0.94 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 307 TYR 0.038 0.002 TYR E 665 PHE 0.025 0.003 PHE A 630 HIS 0.015 0.002 HIS C 287 Details of bonding type rmsd covalent geometry : bond 0.00609 (27932) covalent geometry : angle 0.81348 (37680) SS BOND : bond 0.04082 ( 1) SS BOND : angle 2.66883 ( 2) hydrogen bonds : bond 0.04815 ( 1432) hydrogen bonds : angle 6.08850 ( 4035) Misc. bond : bond 0.00435 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 584 time to evaluate : 1.105 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8832 (mm) cc_final: 0.8488 (mm) REVERT: A 192 GLU cc_start: 0.6745 (mp0) cc_final: 0.6363 (mp0) REVERT: A 247 ASP cc_start: 0.7505 (p0) cc_final: 0.7225 (p0) REVERT: A 274 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6495 (pp20) REVERT: A 285 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6920 (tt0) REVERT: A 287 HIS cc_start: 0.7549 (p90) cc_final: 0.6426 (p90) REVERT: A 288 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7430 (mtp) REVERT: A 319 ASN cc_start: 0.6855 (m110) cc_final: 0.6432 (t0) REVERT: A 397 ASP cc_start: 0.7793 (t70) cc_final: 0.7381 (t70) REVERT: A 588 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7474 (ptpp) REVERT: A 601 LEU cc_start: 0.6052 (mt) cc_final: 0.5782 (tp) REVERT: A 635 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6113 (mt-10) REVERT: A 662 TYR cc_start: 0.8133 (m-80) cc_final: 0.7763 (m-80) REVERT: A 763 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8310 (mm) REVERT: A 781 HIS cc_start: 0.6250 (m-70) cc_final: 0.5881 (m-70) REVERT: A 833 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7142 (mp10) REVERT: B 192 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8210 (mm-30) REVERT: B 243 LEU cc_start: 0.9479 (tp) cc_final: 0.9117 (tt) REVERT: B 307 ARG cc_start: 0.8416 (mmp-170) cc_final: 0.7958 (mmp-170) REVERT: B 687 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.5944 (tp30) REVERT: B 694 ASP cc_start: 0.8431 (p0) cc_final: 0.8097 (p0) REVERT: B 840 LEU cc_start: 0.8873 (tp) cc_final: 0.8552 (tt) REVERT: B 883 HIS cc_start: 0.2821 (OUTLIER) cc_final: 0.0134 (m90) REVERT: C 167 LEU cc_start: 0.8927 (tp) cc_final: 0.8397 (tp) REVERT: C 328 ASP cc_start: 0.8078 (t70) cc_final: 0.7175 (m-30) REVERT: C 363 HIS cc_start: 0.7433 (m170) cc_final: 0.7204 (m170) REVERT: C 385 TYR cc_start: 0.7777 (m-10) cc_final: 0.7354 (m-80) REVERT: C 579 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7289 (mm-30) REVERT: C 680 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.6751 (p90) REVERT: C 822 ASP cc_start: 0.6983 (p0) cc_final: 0.6739 (p0) REVERT: C 848 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.6430 (tp30) REVERT: D 183 LEU cc_start: 0.8785 (mt) cc_final: 0.8569 (mt) REVERT: D 192 GLU cc_start: 0.7714 (mt-10) cc_final: 0.6983 (mp0) REVERT: D 230 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8510 (tt) REVERT: D 307 ARG cc_start: 0.7371 (mmp80) cc_final: 0.7033 (mmp80) REVERT: D 361 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8459 (mm) REVERT: D 626 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8852 (mmmt) REVERT: D 702 MET cc_start: 0.8272 (tmm) cc_final: 0.7993 (tmm) REVERT: D 725 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7563 (mtp) REVERT: D 767 SER cc_start: 0.8879 (m) cc_final: 0.8279 (p) REVERT: E 203 ARG cc_start: 0.7168 (tpp-160) cc_final: 0.6328 (tpp80) REVERT: E 238 LEU cc_start: 0.8510 (pt) cc_final: 0.7993 (tp) REVERT: E 290 MET cc_start: 0.7810 (mmp) cc_final: 0.7393 (mmp) REVERT: E 328 ASP cc_start: 0.6147 (t70) cc_final: 0.5712 (m-30) REVERT: E 334 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7275 (ptp-110) REVERT: E 572 MET cc_start: 0.8355 (tmm) cc_final: 0.7910 (ppp) REVERT: E 763 LEU cc_start: 0.8143 (mt) cc_final: 0.7477 (tp) REVERT: E 806 LEU cc_start: 0.6411 (mp) cc_final: 0.6103 (mt) REVERT: E 808 GLN cc_start: 0.7709 (mm-40) cc_final: 0.6965 (tm-30) REVERT: E 838 ASN cc_start: 0.7813 (m-40) cc_final: 0.7331 (m110) REVERT: F 170 TYR cc_start: 0.6529 (m-10) cc_final: 0.6309 (m-10) REVERT: F 176 GLU cc_start: 0.7006 (tp30) cc_final: 0.6755 (mt-10) REVERT: F 218 LYS cc_start: 0.7564 (tppp) cc_final: 0.7265 (mttt) REVERT: F 221 ILE cc_start: 0.7361 (mt) cc_final: 0.7076 (mt) REVERT: F 290 MET cc_start: 0.6180 (mmt) cc_final: 0.5343 (tmm) REVERT: F 544 ASP cc_start: 0.7190 (m-30) cc_final: 0.6718 (p0) REVERT: F 585 ASP cc_start: 0.6370 (m-30) cc_final: 0.5625 (t0) REVERT: F 737 GLN cc_start: 0.6357 (mm-40) cc_final: 0.5869 (mp10) REVERT: F 747 LYS cc_start: 0.7191 (pttt) cc_final: 0.6162 (tptt) REVERT: F 801 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.7314 (m-70) outliers start: 167 outliers final: 102 residues processed: 696 average time/residue: 0.1835 time to fit residues: 205.4215 Evaluate side-chains 646 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 529 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 802 TYR Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 781 HIS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 673 ASN Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 573 GLU Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 719 SER Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 830 ARG Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 801 HIS Chi-restraints excluded: chain F residue 857 VAL Chi-restraints excluded: chain F residue 877 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 55 optimal weight: 10.0000 chunk 154 optimal weight: 0.9980 chunk 317 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 299 optimal weight: 7.9990 chunk 72 optimal weight: 0.5980 chunk 309 optimal weight: 0.0270 chunk 67 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 362 HIS ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN B 720 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 HIS ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 798 ASN D 801 HIS E 362 HIS F 287 HIS ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.149605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125517 restraints weight = 51295.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.128362 restraints weight = 29850.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130247 restraints weight = 19764.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.131555 restraints weight = 14620.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.132272 restraints weight = 11787.174| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 27943 Z= 0.154 Angle : 0.745 17.075 37682 Z= 0.378 Chirality : 0.047 0.403 4368 Planarity : 0.005 0.088 4817 Dihedral : 9.750 142.397 4023 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.47 % Favored : 94.12 % Rotamer: Outliers : 4.07 % Allowed : 21.33 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.09 % 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: -0.48 (0.14), residues: 3421 helix: 0.33 (0.12), residues: 1784 sheet: -0.92 (0.25), residues: 393 loop : -0.90 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 322 TYR 0.025 0.002 TYR F 382 PHE 0.041 0.002 PHE B 261 HIS 0.039 0.002 HIS C 781 Details of bonding type rmsd covalent geometry : bond 0.00347 (27932) covalent geometry : angle 0.74506 (37680) SS BOND : bond 0.00598 ( 1) SS BOND : angle 2.23929 ( 2) hydrogen bonds : bond 0.04235 ( 1432) hydrogen bonds : angle 5.92677 ( 4035) Misc. bond : bond 0.00315 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 619 time to evaluate : 1.153 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8736 (mm) cc_final: 0.8352 (mm) REVERT: A 173 ASP cc_start: 0.7769 (t0) cc_final: 0.7489 (t70) REVERT: A 192 GLU cc_start: 0.6535 (mp0) cc_final: 0.6200 (mp0) REVERT: A 206 SER cc_start: 0.8034 (m) cc_final: 0.7740 (p) REVERT: A 236 THR cc_start: 0.8046 (p) cc_final: 0.7645 (t) REVERT: A 247 ASP cc_start: 0.7354 (p0) cc_final: 0.7105 (p0) REVERT: A 274 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6538 (pp20) REVERT: A 288 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7630 (mtp) REVERT: A 319 ASN cc_start: 0.7063 (m110) cc_final: 0.6567 (t0) REVERT: A 336 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8355 (mt0) REVERT: A 397 ASP cc_start: 0.7824 (t70) cc_final: 0.7424 (t70) REVERT: A 622 GLU cc_start: 0.6740 (tm-30) cc_final: 0.6280 (tm-30) REVERT: A 635 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6015 (mt-10) REVERT: A 662 TYR cc_start: 0.8036 (m-80) cc_final: 0.7759 (m-80) REVERT: A 705 ASP cc_start: 0.7420 (t0) cc_final: 0.6924 (p0) REVERT: A 781 HIS cc_start: 0.6217 (m-70) cc_final: 0.5749 (m-70) REVERT: A 812 ASP cc_start: 0.3019 (m-30) cc_final: 0.2574 (t0) REVERT: A 833 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: A 875 GLU cc_start: 0.5210 (tt0) cc_final: 0.4848 (tt0) REVERT: B 192 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8186 (mm-30) REVERT: B 307 ARG cc_start: 0.8242 (mmp-170) cc_final: 0.8030 (mmp-170) REVERT: B 670 PHE cc_start: 0.7870 (m-10) cc_final: 0.7607 (m-10) REVERT: B 687 GLU cc_start: 0.5823 (OUTLIER) cc_final: 0.5598 (mt-10) REVERT: B 699 MET cc_start: 0.7474 (tpp) cc_final: 0.7043 (tpp) REVERT: B 725 MET cc_start: 0.7976 (mmt) cc_final: 0.7503 (mmt) REVERT: B 751 MET cc_start: 0.7748 (mmm) cc_final: 0.7504 (mmt) REVERT: B 840 LEU cc_start: 0.8835 (tp) cc_final: 0.8584 (tp) REVERT: B 883 HIS cc_start: 0.2587 (OUTLIER) cc_final: 0.0020 (m90) REVERT: C 192 GLU cc_start: 0.5939 (mt-10) cc_final: 0.5411 (mt-10) REVERT: C 231 ASP cc_start: 0.7374 (p0) cc_final: 0.7158 (m-30) REVERT: C 328 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7381 (m-30) REVERT: C 765 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6547 (mtt180) REVERT: C 848 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6360 (tp30) REVERT: D 192 GLU cc_start: 0.7565 (mt-10) cc_final: 0.6914 (mp0) REVERT: D 230 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8454 (tt) REVERT: D 307 ARG cc_start: 0.7295 (mmp80) cc_final: 0.7091 (mmp80) REVERT: D 361 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8250 (mt) REVERT: D 363 HIS cc_start: 0.7903 (m170) cc_final: 0.7583 (m170) REVERT: D 372 LEU cc_start: 0.8989 (mm) cc_final: 0.8696 (mm) REVERT: D 626 LYS cc_start: 0.9076 (mmtt) cc_final: 0.8811 (mmmt) REVERT: D 673 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7483 (t0) REVERT: D 725 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7683 (mtp) REVERT: D 767 SER cc_start: 0.8899 (m) cc_final: 0.8328 (p) REVERT: D 877 LEU cc_start: 0.8695 (mt) cc_final: 0.8477 (mt) REVERT: E 174 MET cc_start: 0.7813 (mmt) cc_final: 0.7588 (mmt) REVERT: E 203 ARG cc_start: 0.7260 (tpp-160) cc_final: 0.6418 (tpp80) REVERT: E 238 LEU cc_start: 0.8572 (pt) cc_final: 0.8185 (tp) REVERT: E 290 MET cc_start: 0.7817 (mmp) cc_final: 0.7491 (mmp) REVERT: E 328 ASP cc_start: 0.6317 (t70) cc_final: 0.5895 (m-30) REVERT: E 572 MET cc_start: 0.8305 (tmm) cc_final: 0.7965 (ppp) REVERT: E 637 MET cc_start: 0.6890 (tpt) cc_final: 0.6337 (tpt) REVERT: E 738 GLN cc_start: 0.7770 (pp30) cc_final: 0.7499 (pm20) REVERT: E 763 LEU cc_start: 0.8015 (mt) cc_final: 0.7393 (tp) REVERT: E 806 LEU cc_start: 0.5958 (mp) cc_final: 0.5751 (mt) REVERT: E 808 GLN cc_start: 0.7634 (mm-40) cc_final: 0.6882 (tm-30) REVERT: E 838 ASN cc_start: 0.7629 (m-40) cc_final: 0.7069 (m-40) REVERT: F 219 THR cc_start: 0.8317 (m) cc_final: 0.8103 (p) REVERT: F 221 ILE cc_start: 0.6979 (mt) cc_final: 0.6699 (mt) REVERT: F 290 MET cc_start: 0.5997 (mmt) cc_final: 0.5107 (tmm) REVERT: F 338 ILE cc_start: 0.8536 (mt) cc_final: 0.8327 (mt) REVERT: F 544 ASP cc_start: 0.7247 (m-30) cc_final: 0.6857 (p0) REVERT: F 585 ASP cc_start: 0.6650 (m-30) cc_final: 0.5830 (t0) REVERT: F 634 ASP cc_start: 0.7514 (t0) cc_final: 0.7277 (t0) REVERT: F 638 MET cc_start: 0.6949 (pp-130) cc_final: 0.6175 (pp-130) REVERT: F 673 ASN cc_start: 0.3706 (p0) cc_final: 0.3413 (p0) REVERT: F 747 LYS cc_start: 0.7169 (pttt) cc_final: 0.6174 (tptt) outliers start: 121 outliers final: 79 residues processed: 691 average time/residue: 0.1829 time to fit residues: 203.9598 Evaluate side-chains 640 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 548 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 802 TYR Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 673 ASN Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 719 SER Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 830 ARG Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 762 PHE Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 857 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 34 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 chunk 285 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 chunk 169 optimal weight: 0.0970 chunk 142 optimal weight: 0.7980 chunk 241 optimal weight: 3.9990 chunk 319 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 HIS ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS D 798 ASN D 805 ASN E 177 GLN ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.144568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120099 restraints weight = 52679.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122636 restraints weight = 32542.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124401 restraints weight = 22524.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125590 restraints weight = 17109.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126137 restraints weight = 14079.433| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.6596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 27943 Z= 0.263 Angle : 0.817 21.311 37682 Z= 0.415 Chirality : 0.050 0.390 4368 Planarity : 0.006 0.094 4817 Dihedral : 9.884 141.386 4019 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.17 % Favored : 93.42 % Rotamer: Outliers : 4.54 % Allowed : 22.13 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.15 % 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: -0.58 (0.14), residues: 3421 helix: 0.29 (0.12), residues: 1785 sheet: -1.14 (0.24), residues: 408 loop : -0.96 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 307 TYR 0.022 0.002 TYR F 382 PHE 0.033 0.003 PHE B 261 HIS 0.013 0.002 HIS C 287 Details of bonding type rmsd covalent geometry : bond 0.00606 (27932) covalent geometry : angle 0.81666 (37680) SS BOND : bond 0.00554 ( 1) SS BOND : angle 1.63620 ( 2) hydrogen bonds : bond 0.04550 ( 1432) hydrogen bonds : angle 5.92672 ( 4035) Misc. bond : bond 0.00283 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 562 time to evaluate : 1.125 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8680 (mm) cc_final: 0.8304 (mm) REVERT: A 173 ASP cc_start: 0.7785 (t0) cc_final: 0.7525 (t70) REVERT: A 192 GLU cc_start: 0.6531 (mp0) cc_final: 0.6260 (mp0) REVERT: A 207 ASN cc_start: 0.8633 (m110) cc_final: 0.8407 (m110) REVERT: A 236 THR cc_start: 0.8140 (p) cc_final: 0.7778 (t) REVERT: A 247 ASP cc_start: 0.7562 (p0) cc_final: 0.7353 (p0) REVERT: A 288 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7578 (mtp) REVERT: A 319 ASN cc_start: 0.7043 (m110) cc_final: 0.6550 (t0) REVERT: A 397 ASP cc_start: 0.7784 (t70) cc_final: 0.7366 (t70) REVERT: A 662 TYR cc_start: 0.8240 (m-80) cc_final: 0.7733 (m-80) REVERT: A 781 HIS cc_start: 0.6363 (m-70) cc_final: 0.5686 (m90) REVERT: A 812 ASP cc_start: 0.3015 (m-30) cc_final: 0.2323 (t0) REVERT: A 833 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7279 (mp10) REVERT: A 875 GLU cc_start: 0.5185 (tt0) cc_final: 0.4885 (tt0) REVERT: B 243 LEU cc_start: 0.9465 (tp) cc_final: 0.9079 (tt) REVERT: B 694 ASP cc_start: 0.8423 (p0) cc_final: 0.7982 (p0) REVERT: B 725 MET cc_start: 0.8177 (mmt) cc_final: 0.7604 (mmt) REVERT: B 751 MET cc_start: 0.7732 (mmm) cc_final: 0.7483 (mmm) REVERT: B 883 HIS cc_start: 0.2708 (OUTLIER) cc_final: 0.0106 (m90) REVERT: C 192 GLU cc_start: 0.6212 (mt-10) cc_final: 0.5654 (mt-10) REVERT: C 328 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7328 (m-30) REVERT: C 765 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6745 (mtt180) REVERT: C 848 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.6553 (tp30) REVERT: D 183 LEU cc_start: 0.8786 (mt) cc_final: 0.8347 (mt) REVERT: D 192 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7006 (mp0) REVERT: D 361 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8375 (mm) REVERT: D 372 LEU cc_start: 0.8981 (mm) cc_final: 0.8706 (mm) REVERT: D 670 PHE cc_start: 0.8035 (m-80) cc_final: 0.7810 (m-80) REVERT: D 673 ASN cc_start: 0.7987 (OUTLIER) cc_final: 0.7265 (t0) REVERT: D 767 SER cc_start: 0.8871 (m) cc_final: 0.8343 (p) REVERT: D 877 LEU cc_start: 0.8886 (mt) cc_final: 0.8597 (mt) REVERT: E 183 LEU cc_start: 0.7740 (mm) cc_final: 0.7474 (pt) REVERT: E 203 ARG cc_start: 0.7325 (tpp-160) cc_final: 0.6545 (tpp80) REVERT: E 238 LEU cc_start: 0.8630 (pt) cc_final: 0.8139 (tp) REVERT: E 290 MET cc_start: 0.7510 (mmp) cc_final: 0.6976 (mmp) REVERT: E 328 ASP cc_start: 0.6511 (t70) cc_final: 0.6100 (m-30) REVERT: E 334 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7414 (ptp-110) REVERT: E 689 GLU cc_start: 0.7798 (pm20) cc_final: 0.7535 (pm20) REVERT: E 738 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7774 (pm20) REVERT: E 763 LEU cc_start: 0.8113 (mt) cc_final: 0.7484 (tp) REVERT: E 806 LEU cc_start: 0.6311 (mp) cc_final: 0.5986 (mt) REVERT: E 808 GLN cc_start: 0.7869 (mm-40) cc_final: 0.6998 (tm-30) REVERT: E 838 ASN cc_start: 0.7742 (m-40) cc_final: 0.7075 (m-40) REVERT: F 221 ILE cc_start: 0.7210 (mt) cc_final: 0.6914 (mt) REVERT: F 283 ILE cc_start: 0.9313 (tp) cc_final: 0.8646 (pt) REVERT: F 290 MET cc_start: 0.6127 (mmt) cc_final: 0.5538 (tmm) REVERT: F 544 ASP cc_start: 0.7297 (m-30) cc_final: 0.6830 (p0) REVERT: F 634 ASP cc_start: 0.7495 (t0) cc_final: 0.7249 (t0) REVERT: F 673 ASN cc_start: 0.3877 (p0) cc_final: 0.3649 (p0) REVERT: F 737 GLN cc_start: 0.6403 (mm-40) cc_final: 0.5957 (mp10) REVERT: F 808 GLN cc_start: 0.6501 (mm-40) cc_final: 0.5135 (mm-40) outliers start: 135 outliers final: 103 residues processed: 648 average time/residue: 0.1854 time to fit residues: 192.2509 Evaluate side-chains 632 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 519 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 802 TYR Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 673 ASN Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 734 ILE Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 798 ASN Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 719 SER Chi-restraints excluded: chain E residue 738 GLN Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 830 ARG Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 652 VAL Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain F residue 762 PHE Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 857 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 153 optimal weight: 0.6980 chunk 205 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 163 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 176 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 119 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN C 363 HIS ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 798 ASN E 177 GLN E 748 ASN F 606 GLN F 737 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.149971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126098 restraints weight = 52097.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.128740 restraints weight = 31257.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.130437 restraints weight = 21371.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131756 restraints weight = 16210.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.132314 restraints weight = 13253.398| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.6832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27943 Z= 0.154 Angle : 0.755 12.285 37682 Z= 0.384 Chirality : 0.047 0.369 4368 Planarity : 0.005 0.089 4817 Dihedral : 9.555 137.144 4019 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.61 % Favored : 94.01 % Rotamer: Outliers : 3.77 % Allowed : 23.14 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.14), residues: 3421 helix: 0.33 (0.12), residues: 1789 sheet: -1.00 (0.25), residues: 400 loop : -0.91 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 605 TYR 0.027 0.002 TYR F 382 PHE 0.036 0.002 PHE D 282 HIS 0.011 0.001 HIS C 287 Details of bonding type rmsd covalent geometry : bond 0.00346 (27932) covalent geometry : angle 0.75516 (37680) SS BOND : bond 0.00521 ( 1) SS BOND : angle 2.08054 ( 2) hydrogen bonds : bond 0.04125 ( 1432) hydrogen bonds : angle 5.87097 ( 4035) Misc. bond : bond 0.00456 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 608 time to evaluate : 1.151 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8592 (mm) cc_final: 0.8255 (mm) REVERT: A 173 ASP cc_start: 0.7740 (t0) cc_final: 0.7486 (t70) REVERT: A 192 GLU cc_start: 0.6535 (mp0) cc_final: 0.6174 (mp0) REVERT: A 216 ILE cc_start: 0.9215 (pt) cc_final: 0.8894 (mt) REVERT: A 236 THR cc_start: 0.8045 (p) cc_final: 0.7713 (t) REVERT: A 288 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7582 (mtp) REVERT: A 319 ASN cc_start: 0.6866 (m110) cc_final: 0.6416 (t0) REVERT: A 397 ASP cc_start: 0.7747 (t70) cc_final: 0.7340 (t70) REVERT: A 662 TYR cc_start: 0.8049 (m-80) cc_final: 0.7662 (m-80) REVERT: A 693 PRO cc_start: 0.8294 (Cg_exo) cc_final: 0.7943 (Cg_endo) REVERT: A 705 ASP cc_start: 0.7249 (t0) cc_final: 0.6910 (p0) REVERT: A 781 HIS cc_start: 0.6284 (m-70) cc_final: 0.5854 (m-70) REVERT: A 812 ASP cc_start: 0.2789 (m-30) cc_final: 0.2354 (t0) REVERT: A 875 GLU cc_start: 0.5110 (tt0) cc_final: 0.4898 (tt0) REVERT: B 192 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8074 (mm-30) REVERT: B 202 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.8051 (mtm-85) REVERT: B 325 VAL cc_start: 0.8850 (t) cc_final: 0.8609 (p) REVERT: B 377 GLN cc_start: 0.7241 (tt0) cc_final: 0.6938 (tt0) REVERT: B 385 TYR cc_start: 0.8333 (m-10) cc_final: 0.7876 (m-10) REVERT: B 692 HIS cc_start: 0.7768 (t-90) cc_final: 0.7360 (t-90) REVERT: B 751 MET cc_start: 0.7645 (mmm) cc_final: 0.7373 (mmm) REVERT: B 883 HIS cc_start: 0.2387 (OUTLIER) cc_final: -0.0177 (m90) REVERT: C 192 GLU cc_start: 0.5821 (mt-10) cc_final: 0.5331 (mt-10) REVERT: C 328 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: C 398 ILE cc_start: 0.9405 (mm) cc_final: 0.9194 (mm) REVERT: C 765 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6406 (mtt180) REVERT: C 848 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.6556 (tp30) REVERT: D 192 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6869 (mp0) REVERT: D 198 ARG cc_start: 0.8808 (ttm-80) cc_final: 0.8480 (ttm170) REVERT: D 361 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8371 (mm) REVERT: D 372 LEU cc_start: 0.8891 (mm) cc_final: 0.8643 (mm) REVERT: D 572 MET cc_start: 0.8441 (ttp) cc_final: 0.8011 (tmm) REVERT: D 673 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7444 (t0) REVERT: D 702 MET cc_start: 0.8217 (tmm) cc_final: 0.7929 (tmm) REVERT: D 767 SER cc_start: 0.8807 (m) cc_final: 0.8359 (p) REVERT: D 877 LEU cc_start: 0.8767 (mt) cc_final: 0.8259 (mt) REVERT: E 203 ARG cc_start: 0.7231 (tpp-160) cc_final: 0.6511 (tpp80) REVERT: E 238 LEU cc_start: 0.8550 (pt) cc_final: 0.8225 (tp) REVERT: E 328 ASP cc_start: 0.6531 (t70) cc_final: 0.6195 (m-30) REVERT: E 334 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7264 (ptp-110) REVERT: E 572 MET cc_start: 0.8106 (tmm) cc_final: 0.7819 (ppp) REVERT: E 738 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: E 763 LEU cc_start: 0.7980 (mt) cc_final: 0.7380 (tp) REVERT: E 806 LEU cc_start: 0.5866 (mp) cc_final: 0.5634 (mt) REVERT: E 808 GLN cc_start: 0.7801 (mm-40) cc_final: 0.6932 (tm-30) REVERT: F 213 GLU cc_start: 0.5680 (mp0) cc_final: 0.5151 (pt0) REVERT: F 221 ILE cc_start: 0.7203 (mt) cc_final: 0.6918 (mt) REVERT: F 290 MET cc_start: 0.5364 (mmt) cc_final: 0.5080 (tmm) REVERT: F 338 ILE cc_start: 0.8550 (mt) cc_final: 0.8279 (mt) REVERT: F 544 ASP cc_start: 0.7189 (m-30) cc_final: 0.6960 (p0) REVERT: F 585 ASP cc_start: 0.6603 (m-30) cc_final: 0.5696 (t0) REVERT: F 634 ASP cc_start: 0.7491 (t0) cc_final: 0.7212 (t0) REVERT: F 808 GLN cc_start: 0.6363 (mm-40) cc_final: 0.5048 (mm-40) outliers start: 112 outliers final: 81 residues processed: 676 average time/residue: 0.1958 time to fit residues: 208.3065 Evaluate side-chains 637 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 547 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 673 ASN Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 765 ARG Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 719 SER Chi-restraints excluded: chain E residue 738 GLN Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 830 ARG Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 762 PHE Chi-restraints excluded: chain F residue 770 VAL Chi-restraints excluded: chain F residue 857 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 25 optimal weight: 0.2980 chunk 49 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 342 optimal weight: 9.9990 chunk 235 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 chunk 331 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 798 ASN E 177 GLN F 838 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.149929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.126277 restraints weight = 52395.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.128906 restraints weight = 31872.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.130644 restraints weight = 21551.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131831 restraints weight = 16263.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132638 restraints weight = 13307.221| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.7020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27943 Z= 0.162 Angle : 0.763 12.149 37682 Z= 0.388 Chirality : 0.048 0.357 4368 Planarity : 0.005 0.092 4817 Dihedral : 9.433 136.098 4015 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.76 % Favored : 93.95 % Rotamer: Outliers : 4.20 % Allowed : 23.28 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.15 % 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: -0.46 (0.15), residues: 3421 helix: 0.34 (0.12), residues: 1795 sheet: -0.98 (0.25), residues: 398 loop : -0.87 (0.19), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 826 TYR 0.032 0.002 TYR E 677 PHE 0.040 0.002 PHE D 282 HIS 0.012 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00375 (27932) covalent geometry : angle 0.76338 (37680) SS BOND : bond 0.00480 ( 1) SS BOND : angle 1.80989 ( 2) hydrogen bonds : bond 0.04101 ( 1432) hydrogen bonds : angle 5.81989 ( 4035) Misc. bond : bond 0.00416 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 588 time to evaluate : 1.260 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8558 (mm) cc_final: 0.8233 (mm) REVERT: A 173 ASP cc_start: 0.7775 (t0) cc_final: 0.7533 (t70) REVERT: A 192 GLU cc_start: 0.6470 (mp0) cc_final: 0.6187 (mp0) REVERT: A 216 ILE cc_start: 0.9277 (pt) cc_final: 0.9025 (mt) REVERT: A 236 THR cc_start: 0.7996 (p) cc_final: 0.7694 (t) REVERT: A 274 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6410 (pp20) REVERT: A 288 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7503 (mtp) REVERT: A 319 ASN cc_start: 0.6793 (m110) cc_final: 0.6448 (t0) REVERT: A 397 ASP cc_start: 0.7730 (t70) cc_final: 0.7311 (t70) REVERT: A 622 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6613 (tm-30) REVERT: A 662 TYR cc_start: 0.8025 (m-80) cc_final: 0.7665 (m-80) REVERT: A 693 PRO cc_start: 0.8323 (Cg_exo) cc_final: 0.7988 (Cg_endo) REVERT: A 705 ASP cc_start: 0.7275 (t0) cc_final: 0.6944 (p0) REVERT: A 781 HIS cc_start: 0.6286 (m-70) cc_final: 0.5871 (m-70) REVERT: A 812 ASP cc_start: 0.2630 (m-30) cc_final: 0.2273 (t0) REVERT: B 377 GLN cc_start: 0.7218 (tt0) cc_final: 0.6998 (tt0) REVERT: B 692 HIS cc_start: 0.7778 (t-90) cc_final: 0.7467 (t-90) REVERT: B 751 MET cc_start: 0.7538 (mmm) cc_final: 0.7267 (mmm) REVERT: B 883 HIS cc_start: 0.2285 (OUTLIER) cc_final: -0.0122 (m90) REVERT: C 192 GLU cc_start: 0.5818 (mt-10) cc_final: 0.5292 (mt-10) REVERT: C 256 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8069 (mttp) REVERT: C 285 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6685 (mm-30) REVERT: C 328 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7224 (m-30) REVERT: C 398 ILE cc_start: 0.9394 (mm) cc_final: 0.9188 (mm) REVERT: C 542 ASP cc_start: 0.7916 (p0) cc_final: 0.7596 (p0) REVERT: C 765 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6459 (mtt180) REVERT: C 804 LEU cc_start: 0.7370 (tt) cc_final: 0.7134 (tp) REVERT: C 848 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.6596 (tp30) REVERT: D 192 GLU cc_start: 0.7609 (mt-10) cc_final: 0.6919 (mp0) REVERT: D 198 ARG cc_start: 0.8838 (ttm-80) cc_final: 0.8526 (ttm170) REVERT: D 372 LEU cc_start: 0.8918 (mm) cc_final: 0.8615 (mm) REVERT: D 572 MET cc_start: 0.8279 (ttp) cc_final: 0.7806 (tmm) REVERT: D 598 ARG cc_start: 0.7015 (tmt170) cc_final: 0.6627 (tpt-90) REVERT: D 645 GLU cc_start: 0.7545 (pp20) cc_final: 0.6956 (pp20) REVERT: D 673 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7301 (t0) REVERT: D 702 MET cc_start: 0.8226 (tmm) cc_final: 0.7870 (tmm) REVERT: D 767 SER cc_start: 0.8866 (m) cc_final: 0.8377 (p) REVERT: D 801 HIS cc_start: 0.6753 (p-80) cc_final: 0.5768 (p-80) REVERT: D 877 LEU cc_start: 0.8701 (mt) cc_final: 0.8056 (mt) REVERT: E 203 ARG cc_start: 0.7207 (tpp-160) cc_final: 0.6535 (tpp80) REVERT: E 238 LEU cc_start: 0.8513 (pt) cc_final: 0.8205 (tp) REVERT: E 328 ASP cc_start: 0.6566 (t70) cc_final: 0.6265 (m-30) REVERT: E 572 MET cc_start: 0.8014 (tmm) cc_final: 0.7740 (ppp) REVERT: E 573 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7332 (mm-30) REVERT: E 689 GLU cc_start: 0.7755 (pm20) cc_final: 0.7449 (pm20) REVERT: E 738 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: E 763 LEU cc_start: 0.8003 (mt) cc_final: 0.7372 (tp) REVERT: E 806 LEU cc_start: 0.5712 (mp) cc_final: 0.5464 (mt) REVERT: E 808 GLN cc_start: 0.7806 (mm-40) cc_final: 0.6937 (tm-30) REVERT: E 838 ASN cc_start: 0.7613 (m-40) cc_final: 0.7006 (m110) REVERT: F 179 ARG cc_start: 0.6675 (tpm170) cc_final: 0.6238 (ptm-80) REVERT: F 221 ILE cc_start: 0.7244 (mt) cc_final: 0.6965 (mt) REVERT: F 283 ILE cc_start: 0.9247 (tp) cc_final: 0.8437 (pt) REVERT: F 337 LYS cc_start: 0.8330 (mtmm) cc_final: 0.7789 (mttm) REVERT: F 549 THR cc_start: 0.5794 (OUTLIER) cc_final: 0.5580 (m) REVERT: F 585 ASP cc_start: 0.6477 (m-30) cc_final: 0.5692 (t0) REVERT: F 634 ASP cc_start: 0.7287 (t0) cc_final: 0.7059 (t0) REVERT: F 678 LYS cc_start: 0.6513 (OUTLIER) cc_final: 0.6148 (mmtm) REVERT: F 747 LYS cc_start: 0.7211 (pttt) cc_final: 0.6142 (tptt) outliers start: 125 outliers final: 88 residues processed: 656 average time/residue: 0.1894 time to fit residues: 198.4496 Evaluate side-chains 640 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 540 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 673 ASN Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 798 ASN Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 573 GLU Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 719 SER Chi-restraints excluded: chain E residue 738 GLN Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 830 ARG Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 762 PHE Chi-restraints excluded: chain F residue 814 LEU Chi-restraints excluded: chain F residue 857 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 14 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 306 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 HIS ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 798 ASN ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 GLN F 834 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.149754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126376 restraints weight = 52440.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128945 restraints weight = 31949.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.130701 restraints weight = 21984.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131744 restraints weight = 16680.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132630 restraints weight = 13827.247| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.7050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.220 27943 Z= 0.259 Angle : 0.926 59.195 37682 Z= 0.492 Chirality : 0.053 0.687 4368 Planarity : 0.006 0.125 4817 Dihedral : 9.414 136.037 4013 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.88 % Favored : 93.80 % Rotamer: Outliers : 3.70 % Allowed : 24.35 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % 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: -0.47 (0.15), residues: 3421 helix: 0.34 (0.12), residues: 1794 sheet: -0.96 (0.25), residues: 398 loop : -0.88 (0.19), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG F 707 TYR 0.045 0.002 TYR E 677 PHE 0.068 0.002 PHE F 282 HIS 0.023 0.002 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00638 (27932) covalent geometry : angle 0.92638 (37680) SS BOND : bond 0.00481 ( 1) SS BOND : angle 1.78522 ( 2) hydrogen bonds : bond 0.04108 ( 1432) hydrogen bonds : angle 5.82501 ( 4035) Misc. bond : bond 0.01371 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6842 Ramachandran restraints generated. 3421 Oldfield, 0 Emsley, 3421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 543 time to evaluate : 1.131 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8547 (mm) cc_final: 0.8242 (mm) REVERT: A 173 ASP cc_start: 0.7750 (t0) cc_final: 0.7507 (t70) REVERT: A 192 GLU cc_start: 0.6475 (mp0) cc_final: 0.6200 (mp0) REVERT: A 216 ILE cc_start: 0.9265 (pt) cc_final: 0.9016 (mt) REVERT: A 236 THR cc_start: 0.7989 (p) cc_final: 0.7682 (t) REVERT: A 274 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6385 (pp20) REVERT: A 288 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7473 (mtp) REVERT: A 319 ASN cc_start: 0.6818 (m110) cc_final: 0.6432 (t0) REVERT: A 397 ASP cc_start: 0.7715 (t70) cc_final: 0.7308 (t70) REVERT: A 605 ARG cc_start: 0.7557 (mmm160) cc_final: 0.7185 (mmp80) REVERT: A 622 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6603 (tm-30) REVERT: A 635 GLU cc_start: 0.7137 (mm-30) cc_final: 0.5959 (mt-10) REVERT: A 662 TYR cc_start: 0.8028 (m-80) cc_final: 0.7658 (m-80) REVERT: A 693 PRO cc_start: 0.8329 (Cg_exo) cc_final: 0.7980 (Cg_endo) REVERT: A 705 ASP cc_start: 0.7240 (t0) cc_final: 0.6889 (p0) REVERT: A 781 HIS cc_start: 0.6267 (m-70) cc_final: 0.5862 (m-70) REVERT: A 812 ASP cc_start: 0.2611 (m-30) cc_final: 0.2276 (t0) REVERT: B 377 GLN cc_start: 0.7226 (tt0) cc_final: 0.6980 (tt0) REVERT: B 692 HIS cc_start: 0.7746 (t-90) cc_final: 0.7397 (t-90) REVERT: B 751 MET cc_start: 0.7501 (mmm) cc_final: 0.7246 (mmm) REVERT: B 883 HIS cc_start: 0.2274 (OUTLIER) cc_final: -0.0130 (m90) REVERT: C 192 GLU cc_start: 0.5808 (mt-10) cc_final: 0.5287 (mt-10) REVERT: C 285 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6673 (mm-30) REVERT: C 328 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7186 (m-30) REVERT: C 765 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6455 (mtt180) REVERT: C 804 LEU cc_start: 0.7401 (tt) cc_final: 0.7141 (tp) REVERT: D 192 GLU cc_start: 0.7604 (mt-10) cc_final: 0.6899 (mp0) REVERT: D 198 ARG cc_start: 0.8823 (ttm-80) cc_final: 0.8518 (ttm170) REVERT: D 334 ARG cc_start: 0.6960 (mtm-85) cc_final: 0.6673 (mtm-85) REVERT: D 363 HIS cc_start: 0.8139 (m170) cc_final: 0.7874 (m170) REVERT: D 372 LEU cc_start: 0.8895 (mm) cc_final: 0.8617 (mm) REVERT: D 572 MET cc_start: 0.8255 (ttp) cc_final: 0.7807 (tmm) REVERT: D 598 ARG cc_start: 0.7003 (tmt170) cc_final: 0.6626 (tpt-90) REVERT: D 645 GLU cc_start: 0.7535 (pp20) cc_final: 0.6961 (pp20) REVERT: D 673 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7270 (t0) REVERT: D 702 MET cc_start: 0.8217 (tmm) cc_final: 0.7867 (tmm) REVERT: D 767 SER cc_start: 0.8848 (m) cc_final: 0.8370 (p) REVERT: D 801 HIS cc_start: 0.6714 (p-80) cc_final: 0.5771 (p-80) REVERT: D 877 LEU cc_start: 0.8665 (mt) cc_final: 0.8065 (mt) REVERT: E 203 ARG cc_start: 0.7256 (tpp-160) cc_final: 0.6561 (tpp80) REVERT: E 238 LEU cc_start: 0.8470 (pt) cc_final: 0.8158 (tp) REVERT: E 328 ASP cc_start: 0.6578 (t70) cc_final: 0.6259 (m-30) REVERT: E 334 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7361 (ptp-110) REVERT: E 689 GLU cc_start: 0.7722 (pm20) cc_final: 0.7409 (pm20) REVERT: E 738 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: E 763 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7370 (tp) REVERT: E 806 LEU cc_start: 0.5700 (mp) cc_final: 0.5433 (mt) REVERT: E 808 GLN cc_start: 0.7764 (mm-40) cc_final: 0.6908 (tm-30) REVERT: E 838 ASN cc_start: 0.7588 (m-40) cc_final: 0.6963 (m110) REVERT: F 179 ARG cc_start: 0.6646 (tpm170) cc_final: 0.6229 (ptm-80) REVERT: F 221 ILE cc_start: 0.7346 (mt) cc_final: 0.7049 (mt) REVERT: F 283 ILE cc_start: 0.9161 (tp) cc_final: 0.8454 (pt) REVERT: F 337 LYS cc_start: 0.8322 (mtmm) cc_final: 0.7770 (mttm) REVERT: F 549 THR cc_start: 0.5813 (OUTLIER) cc_final: 0.5609 (m) REVERT: F 585 ASP cc_start: 0.6474 (m-30) cc_final: 0.5694 (t0) REVERT: F 634 ASP cc_start: 0.7281 (t0) cc_final: 0.7049 (t0) REVERT: F 678 LYS cc_start: 0.6545 (OUTLIER) cc_final: 0.6138 (mmtm) REVERT: F 747 LYS cc_start: 0.7216 (pttt) cc_final: 0.6154 (tptt) outliers start: 110 outliers final: 93 residues processed: 608 average time/residue: 0.1863 time to fit residues: 181.6274 Evaluate side-chains 641 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 537 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 673 ASN Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 712 GLN Chi-restraints excluded: chain E residue 719 SER Chi-restraints excluded: chain E residue 738 GLN Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 830 ARG Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 762 PHE Chi-restraints excluded: chain F residue 814 LEU Chi-restraints excluded: chain F residue 857 VAL Chi-restraints excluded: chain F residue 876 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 218 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 306 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 180 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 HIS ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.149921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126417 restraints weight = 52333.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.128993 restraints weight = 32499.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.130768 restraints weight = 22413.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.131895 restraints weight = 17026.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132505 restraints weight = 14037.907| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.7058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.220 27943 Z= 0.259 Angle : 0.926 59.195 37682 Z= 0.492 Chirality : 0.053 0.687 4368 Planarity : 0.006 0.125 4817 Dihedral : 9.414 136.037 4013 Min Nonbonded Distance : 0.781 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.88 % Favored : 93.80 % Rotamer: Outliers : 3.50 % Allowed : 24.55 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % 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: -0.47 (0.15), residues: 3421 helix: 0.34 (0.12), residues: 1794 sheet: -0.96 (0.25), residues: 398 loop : -0.88 (0.19), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG F 707 TYR 0.045 0.002 TYR E 677 PHE 0.068 0.002 PHE F 282 HIS 0.023 0.002 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00638 (27932) covalent geometry : angle 0.92636 (37680) SS BOND : bond 0.00481 ( 1) SS BOND : angle 1.78522 ( 2) hydrogen bonds : bond 0.04108 ( 1432) hydrogen bonds : angle 5.82501 ( 4035) Misc. bond : bond 0.01371 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5491.07 seconds wall clock time: 96 minutes 10.40 seconds (5770.40 seconds total)