Starting phenix.real_space_refine on Mon Jun 23 11:27:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vjh_8697/06_2025/5vjh_8697.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vjh_8697/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5vjh_8697/06_2025/5vjh_8697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vjh_8697/06_2025/5vjh_8697.map" model { file = "/net/cci-nas-00/data/ceres_data/5vjh_8697/06_2025/5vjh_8697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vjh_8697/06_2025/5vjh_8697.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.29, per 1000 atoms: 0.59 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: 8.27 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 3.86 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: 10.32 Time building geometry restraints manager: 9.31 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 884 or resid 1001 thr \ ough 1002)) selection = (chain 'B' and (resid 165 through 656 or resid 672 through 884 or resid 1001 thr \ ough 1002)) selection = (chain 'C' and (resid 165 through 656 or resid 672 through 884 or resid 1001 thr \ ough 1002)) selection = (chain 'D' and (resid 165 through 656 or resid 672 through 884 or resid 1001 thr \ ough 1002)) selection = (chain 'E' and (resid 165 through 656 or resid 672 through 884 or resid 1001 thr \ ough 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 63.490 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.630 ------------------------------------------------------------------------------- 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 : 11.18 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (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 HIS 0.014 0.003 HIS E 363 PHE 0.040 0.007 PHE A 685 TYR 0.073 0.009 TYR F 680 ARG 0.012 0.001 ARG D 595 Details of bonding type rmsd hydrogen bonds : bond 0.17155 ( 1432) hydrogen bonds : angle 8.21674 ( 4035) SS BOND : bond 0.18680 ( 1) SS BOND : angle 4.46398 ( 2) covalent geometry : bond 0.02369 (27932) covalent geometry : angle 1.94035 (37680) 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 : 3.406 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: 0.8772 (p) REVERT: A 216 ILE cc_start: 0.8662 (pt) cc_final: 0.8454 (mt) REVERT: A 352 LEU cc_start: 0.8439 (mt) cc_final: 0.8150 (mp) REVERT: B 238 LEU cc_start: 0.8348 (mt) cc_final: 0.8110 (mt) REVERT: B 320 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7137 (mt-10) REVERT: B 580 VAL cc_start: 0.8397 (t) cc_final: 0.7952 (p) REVERT: B 791 ILE cc_start: 0.7953 (mm) cc_final: 0.7645 (mm) REVERT: C 271 GLU cc_start: 0.6042 (tt0) cc_final: 0.5756 (tm-30) REVERT: C 280 VAL cc_start: 0.8614 (t) cc_final: 0.8267 (m) REVERT: C 310 LEU cc_start: 0.7109 (mt) cc_final: 0.6632 (mt) REVERT: C 349 VAL cc_start: 0.9105 (t) cc_final: 0.8877 (t) REVERT: C 547 SER cc_start: 0.8828 (m) cc_final: 0.8620 (t) REVERT: C 680 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.7091 (p90) REVERT: C 765 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7746 (mtt-85) REVERT: D 183 LEU cc_start: 0.7379 (mt) cc_final: 0.6636 (mt) REVERT: D 269 LEU cc_start: 0.8373 (mt) cc_final: 0.8011 (tp) REVERT: D 271 GLU cc_start: 0.6471 (tt0) cc_final: 0.6042 (tp30) REVERT: D 310 LEU cc_start: 0.8552 (mt) cc_final: 0.8031 (mt) REVERT: D 333 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6961 (ttp-110) REVERT: D 626 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8102 (mmmt) REVERT: D 686 ASP cc_start: 0.7380 (m-30) cc_final: 0.7175 (m-30) REVERT: D 727 SER cc_start: 0.8332 (t) cc_final: 0.7772 (t) REVERT: D 746 THR cc_start: 0.8202 (m) cc_final: 0.7893 (m) REVERT: D 783 ILE cc_start: 0.8749 (mt) cc_final: 0.8521 (mt) REVERT: E 238 LEU cc_start: 0.6015 (pt) cc_final: 0.5683 (tp) REVERT: E 348 THR cc_start: 0.7797 (m) cc_final: 0.7544 (m) REVERT: E 359 TYR cc_start: 0.8072 (m-80) cc_final: 0.7608 (m-10) REVERT: E 578 SER cc_start: 0.8169 (p) cc_final: 0.7761 (t) REVERT: E 587 ILE cc_start: 0.8554 (mt) cc_final: 0.7882 (mt) REVERT: E 708 ILE cc_start: 0.7631 (mm) cc_final: 0.7115 (tt) REVERT: E 826 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8247 (mmt180) REVERT: F 174 MET cc_start: 0.6244 (mmm) cc_final: 0.5769 (tpp) REVERT: F 216 ILE cc_start: 0.5154 (tt) cc_final: 0.4424 (tt) REVERT: F 310 LEU cc_start: 0.7852 (tp) cc_final: 0.7522 (tt) REVERT: F 361 ILE cc_start: 0.7177 (mt) cc_final: 0.6935 (mt) REVERT: F 615 LEU cc_start: 0.7599 (mt) cc_final: 0.7361 (mt) outliers start: 28 outliers final: 18 residues processed: 1178 average time/residue: 0.4751 time to fit residues: 828.5528 Evaluate side-chains 630 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 608 time to evaluate : 3.423 ------------------------------------------------------------------------------- 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 289 optimal weight: 7.9990 chunk 259 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 311 optimal weight: 5.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 ** A 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** C 781 HIS D 673 ASN ** D 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 781 HIS ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3953 r_free = 0.3953 target = 0.153984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131653 restraints weight = 51404.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133187 restraints weight = 34213.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.134419 restraints weight = 23374.544| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27943 Z= 0.235 Angle : 0.896 15.955 37682 Z= 0.474 Chirality : 0.050 0.272 4368 Planarity : 0.006 0.102 4817 Dihedral : 11.227 141.106 4068 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.82 % Favored : 94.74 % Rotamer: Outliers : 3.73 % Allowed : 12.01 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3421 helix: 0.03 (0.11), residues: 1793 sheet: -0.25 (0.25), residues: 386 loop : -0.57 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.003 HIS A 781 PHE 0.035 0.003 PHE A 630 TYR 0.034 0.003 TYR C 677 ARG 0.016 0.001 ARG E 202 Details of bonding type rmsd hydrogen bonds : bond 0.06257 ( 1432) hydrogen bonds : angle 6.61689 ( 4035) SS BOND : bond 0.02178 ( 1) SS BOND : angle 2.32372 ( 2) covalent geometry : bond 0.00517 (27932) covalent geometry : angle 0.89621 (37680) Misc. bond : bond 0.00281 ( 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 873 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 762 time to evaluate : 3.388 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: A 173 ASP cc_start: 0.7865 (t0) cc_final: 0.7627 (t70) REVERT: A 237 ILE cc_start: 0.9026 (pt) cc_final: 0.8813 (tt) REVERT: A 287 HIS cc_start: 0.7249 (p-80) cc_final: 0.4762 (p-80) REVERT: A 290 MET cc_start: 0.4520 (mtp) cc_final: 0.4216 (mtp) REVERT: A 397 ASP cc_start: 0.7806 (t70) cc_final: 0.7261 (t70) REVERT: A 588 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7705 (ptpt) REVERT: A 635 GLU cc_start: 0.7080 (mp0) cc_final: 0.6833 (mt-10) REVERT: A 638 MET cc_start: 0.8219 (tpp) cc_final: 0.7114 (ttp) REVERT: A 781 HIS cc_start: 0.6004 (m-70) cc_final: 0.5742 (m-70) REVERT: A 783 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8423 (tp) REVERT: B 192 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8270 (mm-30) REVERT: B 236 THR cc_start: 0.7749 (m) cc_final: 0.7264 (p) REVERT: B 355 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8842 (tp) REVERT: B 580 VAL cc_start: 0.8876 (t) cc_final: 0.8504 (p) REVERT: B 584 MET cc_start: 0.8352 (mmm) cc_final: 0.7767 (mmm) REVERT: B 605 ARG cc_start: 0.7087 (mtp180) cc_final: 0.6849 (mtp180) REVERT: B 616 SER cc_start: 0.8022 (m) cc_final: 0.7498 (p) REVERT: B 692 HIS cc_start: 0.7623 (t-90) cc_final: 0.7378 (t-90) REVERT: C 174 MET cc_start: 0.8331 (mmm) cc_final: 0.7857 (ttt) REVERT: C 200 LEU cc_start: 0.9453 (mt) cc_final: 0.9133 (mt) REVERT: C 280 VAL cc_start: 0.9170 (t) cc_final: 0.8631 (m) REVERT: C 328 ASP cc_start: 0.7041 (t70) cc_final: 0.6606 (m-30) REVERT: C 363 HIS cc_start: 0.7286 (m170) cc_final: 0.7051 (m170) REVERT: C 636 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7358 (t0) REVERT: C 680 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.7120 (p90) REVERT: C 819 TYR cc_start: 0.7853 (t80) cc_final: 0.7575 (t80) REVERT: C 848 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7243 (mm-30) REVERT: D 183 LEU cc_start: 0.8410 (mt) cc_final: 0.8100 (mt) REVERT: D 192 GLU cc_start: 0.7765 (mp0) cc_final: 0.6982 (mp0) REVERT: D 269 LEU cc_start: 0.8687 (mt) cc_final: 0.8419 (tp) REVERT: D 310 LEU cc_start: 0.8801 (mt) cc_final: 0.8240 (mt) REVERT: D 626 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8752 (mmmt) REVERT: D 720 ASN cc_start: 0.8184 (t0) cc_final: 0.7797 (t0) REVERT: D 795 PHE cc_start: 0.6967 (m-10) cc_final: 0.6565 (m-10) REVERT: E 170 TYR cc_start: 0.8664 (m-80) cc_final: 0.8327 (m-80) REVERT: E 183 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.6804 (mm) REVERT: E 238 LEU cc_start: 0.8326 (pt) cc_final: 0.7813 (tp) REVERT: E 284 ASP cc_start: 0.5972 (t70) cc_final: 0.5681 (t70) REVERT: E 578 SER cc_start: 0.8437 (p) cc_final: 0.7884 (t) REVERT: E 587 ILE cc_start: 0.8709 (mt) cc_final: 0.8150 (mt) REVERT: E 763 LEU cc_start: 0.8047 (mt) cc_final: 0.7255 (tp) REVERT: E 806 LEU cc_start: 0.6516 (mp) cc_final: 0.6255 (mt) REVERT: E 838 ASN cc_start: 0.8038 (m-40) cc_final: 0.7004 (p0) REVERT: F 166 TYR cc_start: 0.6064 (m-80) cc_final: 0.5819 (m-80) REVERT: F 218 LYS cc_start: 0.7618 (tppp) cc_final: 0.7374 (tppt) REVERT: F 219 THR cc_start: 0.8346 (m) cc_final: 0.8140 (p) REVERT: F 290 MET cc_start: 0.6058 (mmt) cc_final: 0.4858 (tmm) REVERT: F 338 ILE cc_start: 0.8527 (mt) cc_final: 0.8327 (mt) REVERT: F 544 ASP cc_start: 0.7387 (m-30) cc_final: 0.6963 (p0) REVERT: F 585 ASP cc_start: 0.6565 (m-30) cc_final: 0.5622 (t0) REVERT: F 737 GLN cc_start: 0.6349 (mm-40) cc_final: 0.5955 (mp10) REVERT: F 747 LYS cc_start: 0.7055 (pttt) cc_final: 0.6221 (tptt) REVERT: F 801 HIS cc_start: 0.8023 (OUTLIER) cc_final: 0.7262 (m-70) REVERT: F 831 LEU cc_start: 0.9035 (tp) cc_final: 0.8684 (tp) outliers start: 111 outliers final: 64 residues processed: 832 average time/residue: 0.4356 time to fit residues: 561.3623 Evaluate side-chains 651 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 579 time to evaluate : 3.146 ------------------------------------------------------------------------------- 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 275 SER 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 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 769 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 390 ASP Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 665 TYR 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 560 LYS 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 D residue 751 MET 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 663 VAL Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain E residue 703 LEU 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 694 ASP 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 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 100 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 251 optimal weight: 0.9980 chunk 331 optimal weight: 8.9990 chunk 211 optimal weight: 3.9990 chunk 202 optimal weight: 0.0060 chunk 194 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 287 optimal weight: 8.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS C 363 HIS ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS D 743 GLN E 347 GLN F 177 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.153522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.128978 restraints weight = 51090.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132039 restraints weight = 30001.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134023 restraints weight = 19788.261| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27943 Z= 0.177 Angle : 0.791 17.031 37682 Z= 0.409 Chirality : 0.048 0.282 4368 Planarity : 0.006 0.100 4817 Dihedral : 10.590 144.783 4033 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.91 % Favored : 94.65 % Rotamer: Outliers : 4.41 % Allowed : 15.17 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3421 helix: 0.15 (0.12), residues: 1807 sheet: -0.57 (0.24), residues: 402 loop : -0.90 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS A 781 PHE 0.036 0.002 PHE E 685 TYR 0.041 0.002 TYR C 170 ARG 0.007 0.001 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.05071 ( 1432) hydrogen bonds : angle 6.30364 ( 4035) SS BOND : bond 0.01676 ( 1) SS BOND : angle 2.75046 ( 2) covalent geometry : bond 0.00391 (27932) covalent geometry : angle 0.79117 (37680) Misc. bond : bond 0.00588 ( 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 811 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 680 time to evaluate : 3.323 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: A 167 LEU cc_start: 0.8826 (mm) cc_final: 0.8419 (mm) REVERT: A 319 ASN cc_start: 0.7087 (m110) cc_final: 0.6509 (t0) REVERT: A 397 ASP cc_start: 0.7831 (t70) cc_final: 0.7264 (t70) REVERT: A 613 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6060 (mm) REVERT: A 645 GLU cc_start: 0.7156 (pp20) cc_final: 0.6822 (mp0) REVERT: A 781 HIS cc_start: 0.6060 (m-70) cc_final: 0.5765 (m-70) REVERT: B 278 LEU cc_start: 0.8415 (tp) cc_final: 0.7918 (mt) REVERT: B 324 ILE cc_start: 0.8234 (mt) cc_final: 0.7970 (tt) REVERT: B 352 LEU cc_start: 0.9428 (mp) cc_final: 0.8990 (tp) REVERT: B 605 ARG cc_start: 0.7217 (mtp180) cc_final: 0.7017 (mtp180) REVERT: B 616 SER cc_start: 0.7619 (m) cc_final: 0.7295 (p) REVERT: B 670 PHE cc_start: 0.7843 (m-80) cc_final: 0.7637 (m-10) REVERT: B 883 HIS cc_start: 0.2782 (OUTLIER) cc_final: 0.0003 (m90) REVERT: C 170 TYR cc_start: 0.7727 (m-10) cc_final: 0.7429 (m-10) REVERT: C 174 MET cc_start: 0.8228 (mmm) cc_final: 0.7819 (ttt) REVERT: C 280 VAL cc_start: 0.9140 (t) cc_final: 0.8684 (m) REVERT: C 328 ASP cc_start: 0.7396 (t70) cc_final: 0.6732 (m-30) REVERT: C 333 ARG cc_start: 0.8360 (tmm160) cc_final: 0.7767 (tpt90) REVERT: C 579 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7268 (mm-30) REVERT: C 605 ARG cc_start: 0.7683 (mmm-85) cc_final: 0.7374 (mmt-90) REVERT: C 649 LYS cc_start: 0.6627 (tttt) cc_final: 0.6385 (tttt) REVERT: C 785 ASP cc_start: 0.7770 (t0) cc_final: 0.7236 (t0) REVERT: C 819 TYR cc_start: 0.7826 (t80) cc_final: 0.7475 (t80) REVERT: C 848 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7050 (tp30) REVERT: D 183 LEU cc_start: 0.8495 (mt) cc_final: 0.8235 (mt) REVERT: D 192 GLU cc_start: 0.7826 (mp0) cc_final: 0.6954 (mp0) REVERT: D 258 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8085 (ptmm) REVERT: D 361 ILE cc_start: 0.8864 (mm) cc_final: 0.8592 (mm) REVERT: D 390 ASP cc_start: 0.7889 (t0) cc_final: 0.7618 (t70) REVERT: D 583 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7343 (mm-40) REVERT: D 626 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8735 (mmmt) REVERT: D 720 ASN cc_start: 0.8339 (t0) cc_final: 0.8133 (t0) REVERT: E 183 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7441 (mm) REVERT: E 189 ARG cc_start: 0.8664 (mmt180) cc_final: 0.8409 (mmt-90) REVERT: E 192 GLU cc_start: 0.7363 (mp0) cc_final: 0.6821 (mp0) REVERT: E 238 LEU cc_start: 0.8444 (pt) cc_final: 0.8019 (tp) REVERT: E 587 ILE cc_start: 0.9057 (mt) cc_final: 0.8800 (mt) REVERT: E 763 LEU cc_start: 0.8078 (mt) cc_final: 0.7248 (tp) REVERT: E 806 LEU cc_start: 0.6320 (mp) cc_final: 0.5894 (mt) REVERT: E 808 GLN cc_start: 0.7277 (mm-40) cc_final: 0.6810 (tm-30) REVERT: E 838 ASN cc_start: 0.7795 (m-40) cc_final: 0.6887 (p0) REVERT: F 170 TYR cc_start: 0.6547 (m-10) cc_final: 0.6269 (m-10) REVERT: F 218 LYS cc_start: 0.7488 (tppp) cc_final: 0.7063 (mttt) REVERT: F 219 THR cc_start: 0.8214 (m) cc_final: 0.7913 (p) REVERT: F 221 ILE cc_start: 0.7411 (mt) cc_final: 0.7144 (mt) REVERT: F 290 MET cc_start: 0.5936 (mmt) cc_final: 0.4775 (tmm) REVERT: F 324 ILE cc_start: 0.7176 (mt) cc_final: 0.6929 (mt) REVERT: F 544 ASP cc_start: 0.7381 (m-30) cc_final: 0.7068 (p0) REVERT: F 585 ASP cc_start: 0.6681 (m-30) cc_final: 0.5800 (t0) REVERT: F 747 LYS cc_start: 0.7068 (pttt) cc_final: 0.6193 (tptt) REVERT: F 761 GLU cc_start: 0.8265 (mp0) cc_final: 0.7911 (mp0) outliers start: 131 outliers final: 71 residues processed: 763 average time/residue: 0.4155 time to fit residues: 500.2267 Evaluate side-chains 630 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 554 time to evaluate : 3.339 ------------------------------------------------------------------------------- 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 275 SER Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 596 LEU 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 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 B residue 248 LEU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 665 TYR 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 700 LEU 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 305 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 638 MET 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 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 601 LEU Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 672 THR 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 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 288 MET Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 732 GLU 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 623 LEU Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET 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 302 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 235 optimal weight: 10.0000 chunk 267 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 315 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS E 764 ASN F 606 GLN F 756 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.151890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.127169 restraints weight = 51829.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.130146 restraints weight = 30787.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.132114 restraints weight = 20464.899| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 27943 Z= 0.183 Angle : 0.756 15.803 37682 Z= 0.387 Chirality : 0.047 0.254 4368 Planarity : 0.005 0.089 4817 Dihedral : 10.309 146.720 4027 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.97 % Favored : 94.59 % Rotamer: Outliers : 4.41 % Allowed : 17.02 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3421 helix: 0.23 (0.12), residues: 1808 sheet: -0.63 (0.25), residues: 389 loop : -0.87 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS C 287 PHE 0.028 0.002 PHE A 630 TYR 0.080 0.002 TYR E 665 ARG 0.012 0.001 ARG F 765 Details of bonding type rmsd hydrogen bonds : bond 0.04555 ( 1432) hydrogen bonds : angle 6.05828 ( 4035) SS BOND : bond 0.00798 ( 1) SS BOND : angle 1.86399 ( 2) covalent geometry : bond 0.00409 (27932) covalent geometry : angle 0.75544 (37680) Misc. bond : bond 0.00622 ( 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 764 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 633 time to evaluate : 3.769 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: A 167 LEU cc_start: 0.8819 (mm) cc_final: 0.8484 (mm) REVERT: A 173 ASP cc_start: 0.8324 (t70) cc_final: 0.8081 (t0) REVERT: A 192 GLU cc_start: 0.7077 (mp0) cc_final: 0.6578 (mp0) REVERT: A 247 ASP cc_start: 0.7262 (p0) cc_final: 0.6964 (p0) REVERT: A 288 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7731 (mpp) REVERT: A 319 ASN cc_start: 0.6808 (m110) cc_final: 0.6426 (t0) REVERT: A 397 ASP cc_start: 0.7725 (t70) cc_final: 0.7245 (t70) REVERT: A 613 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.5855 (mt) REVERT: A 638 MET cc_start: 0.8125 (tpp) cc_final: 0.6993 (ttp) REVERT: A 781 HIS cc_start: 0.6176 (m-70) cc_final: 0.5864 (m-70) REVERT: B 192 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8059 (mm-30) REVERT: B 243 LEU cc_start: 0.9431 (tp) cc_final: 0.9146 (tt) REVERT: B 352 LEU cc_start: 0.9441 (mp) cc_final: 0.9041 (tp) REVERT: B 616 SER cc_start: 0.7771 (m) cc_final: 0.7562 (p) REVERT: B 694 ASP cc_start: 0.8448 (p0) cc_final: 0.8163 (p0) REVERT: B 883 HIS cc_start: 0.2807 (OUTLIER) cc_final: 0.0137 (m90) REVERT: C 280 VAL cc_start: 0.9257 (t) cc_final: 0.8789 (m) REVERT: C 328 ASP cc_start: 0.7912 (t70) cc_final: 0.7099 (m-30) REVERT: C 333 ARG cc_start: 0.8370 (tmm160) cc_final: 0.7638 (tpt90) REVERT: C 579 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7231 (mm-30) REVERT: C 605 ARG cc_start: 0.7756 (mmm-85) cc_final: 0.7440 (mmt-90) REVERT: C 819 TYR cc_start: 0.7846 (t80) cc_final: 0.7546 (t80) REVERT: C 822 ASP cc_start: 0.7035 (p0) cc_final: 0.6770 (p0) REVERT: C 848 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7078 (tp30) REVERT: D 183 LEU cc_start: 0.8610 (mt) cc_final: 0.8381 (mt) REVERT: D 192 GLU cc_start: 0.7787 (mp0) cc_final: 0.6889 (mp0) REVERT: D 269 LEU cc_start: 0.8645 (mt) cc_final: 0.8309 (tp) REVERT: D 310 LEU cc_start: 0.8782 (mt) cc_final: 0.8514 (mt) REVERT: D 361 ILE cc_start: 0.8892 (mm) cc_final: 0.8580 (mm) REVERT: D 626 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8752 (mmmt) REVERT: D 720 ASN cc_start: 0.8431 (t0) cc_final: 0.8174 (t0) REVERT: D 767 SER cc_start: 0.8929 (m) cc_final: 0.8678 (m) REVERT: E 174 MET cc_start: 0.8753 (mmm) cc_final: 0.8404 (mmm) REVERT: E 183 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7244 (mm) REVERT: E 189 ARG cc_start: 0.8718 (mmt180) cc_final: 0.8453 (mmt-90) REVERT: E 238 LEU cc_start: 0.8580 (pt) cc_final: 0.8102 (tp) REVERT: E 262 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6776 (tp30) REVERT: E 334 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7250 (ptp-110) REVERT: E 572 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8236 (ppp) REVERT: E 587 ILE cc_start: 0.8957 (mt) cc_final: 0.8755 (mt) REVERT: E 591 SER cc_start: 0.8666 (m) cc_final: 0.8419 (p) REVERT: E 758 PHE cc_start: 0.8068 (m-80) cc_final: 0.7848 (m-10) REVERT: E 763 LEU cc_start: 0.8088 (mt) cc_final: 0.7426 (tp) REVERT: E 806 LEU cc_start: 0.6151 (mp) cc_final: 0.5714 (mt) REVERT: E 808 GLN cc_start: 0.7417 (mm-40) cc_final: 0.6873 (tm-30) REVERT: E 838 ASN cc_start: 0.7767 (m-40) cc_final: 0.7207 (m-40) REVERT: F 205 LYS cc_start: 0.8010 (mmtm) cc_final: 0.7714 (mmtm) REVERT: F 218 LYS cc_start: 0.7516 (tppp) cc_final: 0.7214 (mttt) REVERT: F 219 THR cc_start: 0.8328 (m) cc_final: 0.8023 (p) REVERT: F 221 ILE cc_start: 0.7438 (mt) cc_final: 0.7179 (mt) REVERT: F 282 PHE cc_start: 0.8481 (t80) cc_final: 0.8266 (t80) REVERT: F 290 MET cc_start: 0.6004 (mmt) cc_final: 0.4925 (tmm) REVERT: F 544 ASP cc_start: 0.7354 (m-30) cc_final: 0.7125 (p0) REVERT: F 585 ASP cc_start: 0.6563 (m-30) cc_final: 0.5805 (t0) REVERT: F 737 GLN cc_start: 0.6285 (mm-40) cc_final: 0.5702 (mp10) REVERT: F 747 LYS cc_start: 0.7149 (pttt) cc_final: 0.6308 (tptt) outliers start: 131 outliers final: 84 residues processed: 713 average time/residue: 0.5668 time to fit residues: 649.6640 Evaluate side-chains 641 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 549 time to evaluate : 3.389 ------------------------------------------------------------------------------- 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 288 MET Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 596 LEU 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 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 804 LEU Chi-restraints excluded: chain A residue 855 VAL 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 665 TYR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 686 ASP 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 802 TYR Chi-restraints excluded: chain B residue 832 ILE 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 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 546 ILE Chi-restraints excluded: chain C residue 549 THR 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 C residue 853 GLU 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 305 LEU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 395 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 680 TYR Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 746 THR 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 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 572 MET Chi-restraints excluded: chain E residue 573 GLU 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 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 623 LEU Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET 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 227 optimal weight: 0.9990 chunk 282 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 ASN ** B 720 ASN ** 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 363 HIS C 764 ASN C 781 HIS ** 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 = 0.3912 r_free = 0.3912 target = 0.150310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.125868 restraints weight = 51389.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.128729 restraints weight = 30188.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130597 restraints weight = 20190.141| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27943 Z= 0.187 Angle : 0.743 14.873 37682 Z= 0.380 Chirality : 0.047 0.260 4368 Planarity : 0.005 0.088 4817 Dihedral : 10.082 147.154 4027 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.17 % Favored : 94.42 % Rotamer: Outliers : 4.10 % Allowed : 19.11 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3421 helix: 0.28 (0.12), residues: 1808 sheet: -0.60 (0.25), residues: 401 loop : -0.90 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS C 287 PHE 0.026 0.002 PHE A 630 TYR 0.074 0.002 TYR E 665 ARG 0.008 0.001 ARG D 843 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 1432) hydrogen bonds : angle 5.96630 ( 4035) SS BOND : bond 0.00735 ( 1) SS BOND : angle 1.28377 ( 2) covalent geometry : bond 0.00426 (27932) covalent geometry : angle 0.74308 (37680) Misc. bond : bond 0.00692 ( 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 716 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 594 time to evaluate : 3.043 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: A 167 LEU cc_start: 0.8811 (mm) cc_final: 0.8489 (mm) REVERT: A 173 ASP cc_start: 0.8264 (t70) cc_final: 0.8046 (t0) REVERT: A 192 GLU cc_start: 0.6982 (mp0) cc_final: 0.6541 (mp0) REVERT: A 247 ASP cc_start: 0.7311 (p0) cc_final: 0.7068 (p0) REVERT: A 319 ASN cc_start: 0.6596 (m110) cc_final: 0.6160 (t0) REVERT: A 397 ASP cc_start: 0.7691 (t70) cc_final: 0.7229 (t70) REVERT: A 588 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7696 (ptpt) REVERT: A 635 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6269 (mt-10) REVERT: A 725 MET cc_start: 0.7248 (mtm) cc_final: 0.7027 (mtm) REVERT: A 781 HIS cc_start: 0.6247 (m-70) cc_final: 0.5952 (m-70) REVERT: B 352 LEU cc_start: 0.9482 (mp) cc_final: 0.9201 (mt) REVERT: B 616 SER cc_start: 0.7986 (m) cc_final: 0.7735 (p) REVERT: B 643 CYS cc_start: 0.8250 (m) cc_final: 0.7939 (m) REVERT: B 687 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5523 (mt-10) REVERT: B 694 ASP cc_start: 0.8461 (p0) cc_final: 0.8183 (p0) REVERT: B 883 HIS cc_start: 0.2712 (OUTLIER) cc_final: 0.0113 (m90) REVERT: C 280 VAL cc_start: 0.9180 (t) cc_final: 0.8802 (m) REVERT: C 328 ASP cc_start: 0.8093 (t70) cc_final: 0.7227 (m-30) REVERT: C 680 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.6691 (p90) REVERT: C 712 GLN cc_start: 0.6678 (OUTLIER) cc_final: 0.6435 (pt0) REVERT: C 848 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7171 (tp30) REVERT: D 183 LEU cc_start: 0.8661 (mt) cc_final: 0.8374 (mt) REVERT: D 192 GLU cc_start: 0.7734 (mp0) cc_final: 0.6885 (mp0) REVERT: D 300 ILE cc_start: 0.4993 (OUTLIER) cc_final: 0.4453 (mt) REVERT: D 361 ILE cc_start: 0.8863 (mm) cc_final: 0.8561 (mm) REVERT: D 626 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8734 (mmmt) REVERT: D 720 ASN cc_start: 0.8413 (t0) cc_final: 0.8114 (t0) REVERT: D 732 GLU cc_start: 0.7640 (pm20) cc_final: 0.7270 (tt0) REVERT: E 170 TYR cc_start: 0.8735 (m-80) cc_final: 0.8284 (m-10) REVERT: E 183 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7368 (mm) REVERT: E 203 ARG cc_start: 0.6765 (tpp-160) cc_final: 0.6073 (tpp80) REVERT: E 238 LEU cc_start: 0.8577 (pt) cc_final: 0.8136 (tp) REVERT: E 262 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6795 (tp30) REVERT: E 302 LYS cc_start: 0.7170 (mmtt) cc_final: 0.6697 (mmtt) REVERT: E 334 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7137 (ptp-110) REVERT: E 572 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8338 (ppp) REVERT: E 591 SER cc_start: 0.8632 (m) cc_final: 0.8350 (p) REVERT: E 763 LEU cc_start: 0.8088 (mt) cc_final: 0.7428 (tp) REVERT: E 806 LEU cc_start: 0.6178 (mp) cc_final: 0.5768 (mt) REVERT: E 808 GLN cc_start: 0.7513 (mm-40) cc_final: 0.6898 (tm-30) REVERT: E 838 ASN cc_start: 0.7567 (m-40) cc_final: 0.7018 (m-40) REVERT: F 218 LYS cc_start: 0.7306 (tppp) cc_final: 0.7056 (mttt) REVERT: F 219 THR cc_start: 0.8210 (m) cc_final: 0.7985 (p) REVERT: F 221 ILE cc_start: 0.7280 (mt) cc_final: 0.7041 (mt) REVERT: F 290 MET cc_start: 0.5928 (mmt) cc_final: 0.5057 (tmm) REVERT: F 544 ASP cc_start: 0.7325 (m-30) cc_final: 0.7039 (p0) REVERT: F 585 ASP cc_start: 0.6501 (m-30) cc_final: 0.5763 (t0) REVERT: F 737 GLN cc_start: 0.6341 (mm-40) cc_final: 0.5947 (mp10) REVERT: F 747 LYS cc_start: 0.6855 (pttt) cc_final: 0.6085 (tptt) outliers start: 122 outliers final: 83 residues processed: 665 average time/residue: 0.3919 time to fit residues: 415.7376 Evaluate side-chains 642 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 548 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 596 LEU 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 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 791 ILE Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 645 GLU 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 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 883 HIS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 257 TYR 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 345 VAL Chi-restraints excluded: chain C residue 546 ILE 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 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 712 GLN 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 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 305 LEU Chi-restraints excluded: chain D residue 324 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 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 875 GLU 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 334 ARG Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 573 GLU Chi-restraints excluded: chain E residue 659 THR 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 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 284 ASP Chi-restraints excluded: chain F residue 539 ASN 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 745 SER 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 197 optimal weight: 0.8980 chunk 253 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 308 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 278 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN C 363 HIS ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS D 798 ASN ** D 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 HIS ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.150872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.126659 restraints weight = 51386.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.129510 restraints weight = 29992.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131371 restraints weight = 19931.493| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 27943 Z= 0.171 Angle : 0.735 15.697 37682 Z= 0.374 Chirality : 0.047 0.305 4368 Planarity : 0.005 0.085 4817 Dihedral : 9.848 146.168 4025 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.32 % Favored : 94.27 % Rotamer: Outliers : 4.37 % Allowed : 19.44 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3421 helix: 0.33 (0.12), residues: 1803 sheet: -0.62 (0.25), residues: 398 loop : -0.98 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 287 PHE 0.035 0.002 PHE C 813 TYR 0.025 0.002 TYR E 665 ARG 0.007 0.000 ARG A 765 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 1432) hydrogen bonds : angle 5.88473 ( 4035) SS BOND : bond 0.00637 ( 1) SS BOND : angle 1.11450 ( 2) covalent geometry : bond 0.00393 (27932) covalent geometry : angle 0.73501 (37680) Misc. bond : bond 0.00249 ( 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 726 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 596 time to evaluate : 3.672 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: 0.8821 (mm) cc_final: 0.8494 (mm) REVERT: A 173 ASP cc_start: 0.8267 (t70) cc_final: 0.7999 (t0) REVERT: A 192 GLU cc_start: 0.6780 (mp0) cc_final: 0.6372 (mp0) REVERT: A 236 THR cc_start: 0.8032 (p) cc_final: 0.7664 (t) REVERT: A 247 ASP cc_start: 0.7412 (p0) cc_final: 0.7178 (p0) REVERT: A 262 GLU cc_start: 0.7908 (mp0) cc_final: 0.7632 (mt-10) REVERT: A 287 HIS cc_start: 0.7210 (OUTLIER) cc_final: 0.6756 (t70) REVERT: A 319 ASN cc_start: 0.6752 (m110) cc_final: 0.6337 (t0) REVERT: A 397 ASP cc_start: 0.7767 (t70) cc_final: 0.7343 (t70) REVERT: A 635 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6180 (mt-10) REVERT: A 638 MET cc_start: 0.8090 (tpp) cc_final: 0.6965 (ttp) REVERT: A 763 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8261 (mm) REVERT: A 781 HIS cc_start: 0.6381 (m-70) cc_final: 0.6009 (m-70) REVERT: A 783 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8538 (tt) REVERT: A 812 ASP cc_start: 0.3071 (m-30) cc_final: 0.2609 (t0) REVERT: B 616 SER cc_start: 0.7965 (m) cc_final: 0.7736 (p) REVERT: B 643 CYS cc_start: 0.8325 (m) cc_final: 0.8033 (m) REVERT: B 686 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6417 (m-30) REVERT: B 687 GLU cc_start: 0.5920 (OUTLIER) cc_final: 0.5607 (mt-10) REVERT: B 692 HIS cc_start: 0.7797 (t-90) cc_final: 0.7010 (t-90) REVERT: B 694 ASP cc_start: 0.8442 (p0) cc_final: 0.7858 (p0) REVERT: B 883 HIS cc_start: 0.2692 (OUTLIER) cc_final: 0.0119 (m90) REVERT: C 280 VAL cc_start: 0.9210 (t) cc_final: 0.8843 (m) REVERT: C 328 ASP cc_start: 0.8029 (t70) cc_final: 0.7396 (m-30) REVERT: C 649 LYS cc_start: 0.6436 (tttt) cc_final: 0.6131 (tttt) REVERT: C 680 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6508 (p90) REVERT: C 712 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.6516 (pt0) REVERT: C 848 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7129 (tp30) REVERT: D 183 LEU cc_start: 0.8689 (mt) cc_final: 0.8398 (mt) REVERT: D 192 GLU cc_start: 0.7700 (mp0) cc_final: 0.6879 (mp0) REVERT: D 269 LEU cc_start: 0.8682 (mt) cc_final: 0.8378 (tp) REVERT: D 300 ILE cc_start: 0.5173 (OUTLIER) cc_final: 0.4436 (mt) REVERT: D 361 ILE cc_start: 0.8797 (mm) cc_final: 0.8497 (mm) REVERT: D 572 MET cc_start: 0.8643 (ttt) cc_final: 0.8405 (ttp) REVERT: D 626 LYS cc_start: 0.9061 (mmtt) cc_final: 0.8787 (mmmt) REVERT: D 720 ASN cc_start: 0.8461 (t0) cc_final: 0.8197 (t0) REVERT: D 729 LEU cc_start: 0.9211 (mt) cc_final: 0.8978 (mp) REVERT: D 732 GLU cc_start: 0.7678 (pm20) cc_final: 0.7235 (tt0) REVERT: E 170 TYR cc_start: 0.8772 (m-80) cc_final: 0.8498 (m-10) REVERT: E 174 MET cc_start: 0.8591 (mmm) cc_final: 0.8363 (mmt) REVERT: E 183 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7450 (mm) REVERT: E 189 ARG cc_start: 0.8832 (mmt-90) cc_final: 0.8594 (mmp-170) REVERT: E 203 ARG cc_start: 0.6921 (tpp-160) cc_final: 0.6390 (tpp80) REVERT: E 238 LEU cc_start: 0.8629 (pt) cc_final: 0.8234 (tp) REVERT: E 262 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6731 (tp30) REVERT: E 302 LYS cc_start: 0.7268 (mmtt) cc_final: 0.6814 (mmtt) REVERT: E 328 ASP cc_start: 0.5990 (t70) cc_final: 0.5682 (m-30) REVERT: E 334 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7186 (ptp-110) REVERT: E 591 SER cc_start: 0.8739 (m) cc_final: 0.7850 (m) REVERT: E 637 MET cc_start: 0.7318 (tpt) cc_final: 0.6832 (tpt) REVERT: E 763 LEU cc_start: 0.8041 (mt) cc_final: 0.7400 (tp) REVERT: E 780 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8910 (tp) REVERT: E 806 LEU cc_start: 0.6085 (mp) cc_final: 0.5753 (mt) REVERT: E 808 GLN cc_start: 0.7507 (mm-40) cc_final: 0.6812 (tm-30) REVERT: E 838 ASN cc_start: 0.7617 (m-40) cc_final: 0.7012 (m-40) REVERT: F 218 LYS cc_start: 0.7283 (tppp) cc_final: 0.7018 (mttt) REVERT: F 219 THR cc_start: 0.8276 (m) cc_final: 0.8075 (p) REVERT: F 221 ILE cc_start: 0.6907 (mt) cc_final: 0.6655 (mt) REVERT: F 290 MET cc_start: 0.5912 (mmt) cc_final: 0.5058 (tmm) REVERT: F 544 ASP cc_start: 0.7190 (m-30) cc_final: 0.6906 (p0) REVERT: F 585 ASP cc_start: 0.6532 (m-30) cc_final: 0.5797 (t0) REVERT: F 747 LYS cc_start: 0.6946 (pttt) cc_final: 0.6122 (tptt) outliers start: 130 outliers final: 88 residues processed: 670 average time/residue: 0.4420 time to fit residues: 476.4255 Evaluate side-chains 648 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 546 time to evaluate : 3.270 ------------------------------------------------------------------------------- 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 287 HIS Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 596 LEU 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 659 THR 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 763 LEU Chi-restraints excluded: chain A residue 783 ILE Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 337 LYS 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 246 LEU Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 325 VAL 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 554 THR Chi-restraints excluded: chain C residue 569 LEU 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 688 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 712 GLN 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 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 301 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 642 ASP 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 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 773 ASN 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 D residue 875 GLU 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 708 ILE Chi-restraints excluded: chain E residue 719 SER Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 780 ILE 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 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 623 LEU 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 802 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 182 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 307 optimal weight: 20.0000 chunk 292 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 GLN ** B 701 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 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 GLN E 177 GLN E 773 ASN E 883 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.143556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.118893 restraints weight = 52822.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121341 restraints weight = 32980.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122938 restraints weight = 23038.907| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.6515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 27943 Z= 0.309 Angle : 0.889 17.240 37682 Z= 0.452 Chirality : 0.052 0.292 4368 Planarity : 0.006 0.090 4817 Dihedral : 10.135 142.787 4025 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.40 % Favored : 93.25 % Rotamer: Outliers : 4.81 % Allowed : 20.52 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3421 helix: 0.16 (0.12), residues: 1790 sheet: -1.00 (0.25), residues: 394 loop : -1.05 (0.18), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.002 HIS C 287 PHE 0.029 0.003 PHE D 612 TYR 0.025 0.003 TYR E 665 ARG 0.014 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 1432) hydrogen bonds : angle 6.05328 ( 4035) SS BOND : bond 0.00595 ( 1) SS BOND : angle 0.67620 ( 2) covalent geometry : bond 0.00702 (27932) covalent geometry : angle 0.88860 (37680) Misc. bond : bond 0.00622 ( 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 727 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 584 time to evaluate : 3.426 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: 0.8840 (mm) cc_final: 0.8491 (mm) REVERT: A 173 ASP cc_start: 0.8224 (t0) cc_final: 0.7860 (t0) REVERT: A 192 GLU cc_start: 0.6509 (mp0) cc_final: 0.6250 (mp0) REVERT: A 206 SER cc_start: 0.8262 (m) cc_final: 0.8060 (p) REVERT: A 216 ILE cc_start: 0.9281 (pt) cc_final: 0.9053 (mt) REVERT: A 236 THR cc_start: 0.8187 (p) cc_final: 0.7849 (t) REVERT: A 285 GLU cc_start: 0.7662 (tt0) cc_final: 0.7281 (tt0) REVERT: A 287 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.6574 (t70) REVERT: A 319 ASN cc_start: 0.6985 (m110) cc_final: 0.6558 (t0) REVERT: A 638 MET cc_start: 0.8084 (tpp) cc_final: 0.7283 (ttp) REVERT: A 662 TYR cc_start: 0.8222 (m-10) cc_final: 0.7764 (m-80) REVERT: A 781 HIS cc_start: 0.6478 (m-70) cc_final: 0.6041 (m-70) REVERT: A 783 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8663 (tp) REVERT: A 812 ASP cc_start: 0.2795 (m-30) cc_final: 0.2176 (t0) REVERT: B 243 LEU cc_start: 0.9449 (tp) cc_final: 0.9091 (tt) REVERT: B 252 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7826 (p) REVERT: B 288 MET cc_start: 0.6002 (ptt) cc_final: 0.5644 (ptm) REVERT: B 325 VAL cc_start: 0.8930 (t) cc_final: 0.8702 (p) REVERT: B 670 PHE cc_start: 0.7976 (m-80) cc_final: 0.7355 (m-10) REVERT: B 686 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6629 (m-30) REVERT: B 692 HIS cc_start: 0.7970 (t-90) cc_final: 0.7498 (t-90) REVERT: B 694 ASP cc_start: 0.8488 (p0) cc_final: 0.7899 (p0) REVERT: B 883 HIS cc_start: 0.2991 (OUTLIER) cc_final: 0.0333 (m90) REVERT: C 223 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: C 280 VAL cc_start: 0.9249 (t) cc_final: 0.8961 (m) REVERT: C 328 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7945 (t0) REVERT: C 385 TYR cc_start: 0.7835 (m-10) cc_final: 0.7227 (m-80) REVERT: C 579 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7260 (mm-30) REVERT: C 712 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7048 (pt0) REVERT: C 765 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6580 (mtt180) REVERT: C 848 GLU cc_start: 0.8168 (mt-10) cc_final: 0.6321 (tp30) REVERT: D 183 LEU cc_start: 0.8743 (mt) cc_final: 0.8525 (mt) REVERT: D 192 GLU cc_start: 0.7752 (mp0) cc_final: 0.6880 (mp0) REVERT: D 269 LEU cc_start: 0.8801 (mt) cc_final: 0.8566 (mt) REVERT: D 307 ARG cc_start: 0.7565 (mmp80) cc_final: 0.7028 (mmp80) REVERT: D 361 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8472 (mm) REVERT: D 626 LYS cc_start: 0.9122 (mmtt) cc_final: 0.8893 (mmtt) REVERT: D 670 PHE cc_start: 0.8085 (m-80) cc_final: 0.7779 (m-80) REVERT: E 170 TYR cc_start: 0.8854 (m-80) cc_final: 0.8638 (m-10) REVERT: E 174 MET cc_start: 0.8612 (mmm) cc_final: 0.8288 (mmt) REVERT: E 177 GLN cc_start: 0.8311 (tt0) cc_final: 0.7952 (tt0) REVERT: E 203 ARG cc_start: 0.7280 (tpp-160) cc_final: 0.6819 (tpp80) REVERT: E 238 LEU cc_start: 0.8664 (pt) cc_final: 0.8144 (tp) REVERT: E 302 LYS cc_start: 0.7394 (mmtt) cc_final: 0.6666 (mmtt) REVERT: E 328 ASP cc_start: 0.6389 (t70) cc_final: 0.6135 (m-30) REVERT: E 334 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7282 (ptp-110) REVERT: E 572 MET cc_start: 0.8443 (tmm) cc_final: 0.8195 (ppp) REVERT: E 689 GLU cc_start: 0.7824 (pm20) cc_final: 0.7590 (pm20) REVERT: E 707 ARG cc_start: 0.8119 (mpt180) cc_final: 0.7907 (mpt180) REVERT: E 763 LEU cc_start: 0.8149 (mt) cc_final: 0.7524 (tp) REVERT: E 806 LEU cc_start: 0.6670 (mp) cc_final: 0.6266 (mt) REVERT: E 808 GLN cc_start: 0.7800 (mm-40) cc_final: 0.6887 (tm-30) REVERT: E 838 ASN cc_start: 0.7928 (m-40) cc_final: 0.7422 (m110) REVERT: F 218 LYS cc_start: 0.7389 (tppp) cc_final: 0.7015 (mttt) REVERT: F 219 THR cc_start: 0.8260 (m) cc_final: 0.8052 (p) REVERT: F 221 ILE cc_start: 0.6930 (mt) cc_final: 0.6661 (mt) REVERT: F 290 MET cc_start: 0.5787 (mmt) cc_final: 0.5294 (tmm) REVERT: F 544 ASP cc_start: 0.7361 (m-30) cc_final: 0.6842 (p0) REVERT: F 585 ASP cc_start: 0.6731 (m-30) cc_final: 0.5874 (t0) REVERT: F 638 MET cc_start: 0.7020 (pp-130) cc_final: 0.6162 (pp-130) REVERT: F 737 GLN cc_start: 0.6515 (mm-40) cc_final: 0.6024 (mp10) outliers start: 143 outliers final: 105 residues processed: 667 average time/residue: 0.4415 time to fit residues: 475.9296 Evaluate side-chains 646 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 530 time to evaluate : 4.650 ------------------------------------------------------------------------------- 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 287 HIS Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 399 SER 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 665 TYR 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 783 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 601 LEU 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 688 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 742 ILE 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 223 GLU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 246 LEU 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 317 THR 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 351 ILE 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 627 VAL 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 712 GLN 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 773 ASN Chi-restraints excluded: chain C residue 828 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 305 LEU 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 717 ASP 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 848 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 875 GLU Chi-restraints excluded: chain E residue 183 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 541 VAL 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 623 LEU Chi-restraints excluded: chain F residue 652 VAL 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 762 PHE Chi-restraints excluded: chain F residue 801 HIS Chi-restraints excluded: chain F residue 802 TYR Chi-restraints excluded: chain F residue 877 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 279 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 327 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 328 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN A 336 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 HIS C 781 HIS D 798 ASN D 805 ASN E 748 ASN F 571 HIS ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.148324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124226 restraints weight = 52102.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126717 restraints weight = 32256.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.128523 restraints weight = 22418.583| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.6737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 27943 Z= 0.177 Angle : 0.766 13.698 37682 Z= 0.389 Chirality : 0.048 0.386 4368 Planarity : 0.005 0.090 4817 Dihedral : 9.787 140.011 4025 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.73 % Favored : 93.89 % Rotamer: Outliers : 3.94 % Allowed : 22.57 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3421 helix: 0.24 (0.12), residues: 1787 sheet: -0.92 (0.25), residues: 393 loop : -0.94 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS C 287 PHE 0.019 0.002 PHE A 630 TYR 0.029 0.002 TYR E 677 ARG 0.015 0.001 ARG A 765 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 1432) hydrogen bonds : angle 5.93785 ( 4035) SS BOND : bond 0.00536 ( 1) SS BOND : angle 0.93384 ( 2) covalent geometry : bond 0.00408 (27932) covalent geometry : angle 0.76566 (37680) Misc. bond : bond 0.00515 ( 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 714 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 597 time to evaluate : 3.573 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: 0.8625 (mm) cc_final: 0.8295 (mm) REVERT: A 173 ASP cc_start: 0.8172 (t0) cc_final: 0.7803 (t0) REVERT: A 192 GLU cc_start: 0.6530 (mp0) cc_final: 0.6295 (mp0) REVERT: A 216 ILE cc_start: 0.9241 (pt) cc_final: 0.8992 (mt) REVERT: A 236 THR cc_start: 0.8145 (p) cc_final: 0.7817 (t) REVERT: A 285 GLU cc_start: 0.7523 (tt0) cc_final: 0.6977 (tt0) REVERT: A 287 HIS cc_start: 0.7357 (OUTLIER) cc_final: 0.6894 (t70) REVERT: A 288 MET cc_start: 0.8211 (mpp) cc_final: 0.7651 (mpp) REVERT: A 319 ASN cc_start: 0.6866 (m110) cc_final: 0.6546 (t0) REVERT: A 397 ASP cc_start: 0.7856 (t70) cc_final: 0.7647 (t70) REVERT: A 662 TYR cc_start: 0.8125 (m-10) cc_final: 0.7776 (m-80) REVERT: A 763 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8212 (mm) REVERT: A 781 HIS cc_start: 0.6351 (m-70) cc_final: 0.5945 (m-70) REVERT: A 812 ASP cc_start: 0.2588 (m-30) cc_final: 0.2081 (t0) REVERT: A 833 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: A 875 GLU cc_start: 0.4921 (tt0) cc_final: 0.4673 (tt0) REVERT: B 252 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7697 (p) REVERT: B 288 MET cc_start: 0.5880 (ptt) cc_final: 0.5671 (ptm) REVERT: B 639 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7740 (mt) REVERT: B 692 HIS cc_start: 0.7852 (t-90) cc_final: 0.7552 (t-90) REVERT: B 883 HIS cc_start: 0.2673 (OUTLIER) cc_final: 0.0102 (m90) REVERT: C 280 VAL cc_start: 0.9179 (t) cc_final: 0.8877 (m) REVERT: C 328 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7141 (m-30) REVERT: C 712 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6897 (pt0) REVERT: C 848 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7319 (tp30) REVERT: D 183 LEU cc_start: 0.8665 (mt) cc_final: 0.8421 (mt) REVERT: D 192 GLU cc_start: 0.7666 (mp0) cc_final: 0.6835 (mp0) REVERT: D 198 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8505 (ttm170) REVERT: D 269 LEU cc_start: 0.8651 (mt) cc_final: 0.8425 (mm) REVERT: D 282 PHE cc_start: 0.9039 (t80) cc_final: 0.8629 (t80) REVERT: D 307 ARG cc_start: 0.7472 (mmp80) cc_final: 0.7242 (mmp80) REVERT: D 361 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8457 (mm) REVERT: D 626 LYS cc_start: 0.9058 (mmtt) cc_final: 0.8781 (mmtt) REVERT: D 645 GLU cc_start: 0.7642 (pp20) cc_final: 0.7072 (pp20) REVERT: D 673 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.7227 (t0) REVERT: D 877 LEU cc_start: 0.8814 (mt) cc_final: 0.8261 (mt) REVERT: E 174 MET cc_start: 0.8562 (mmm) cc_final: 0.8170 (mmm) REVERT: E 177 GLN cc_start: 0.8185 (tt0) cc_final: 0.7515 (tt0) REVERT: E 203 ARG cc_start: 0.7381 (tpp-160) cc_final: 0.6958 (tpp80) REVERT: E 238 LEU cc_start: 0.8636 (pt) cc_final: 0.8228 (tp) REVERT: E 302 LYS cc_start: 0.7226 (mmtt) cc_final: 0.6673 (mmtt) REVERT: E 328 ASP cc_start: 0.6342 (t70) cc_final: 0.6084 (m-30) REVERT: E 334 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7201 (ptp-110) REVERT: E 572 MET cc_start: 0.8442 (tmm) cc_final: 0.8052 (ppp) REVERT: E 588 LYS cc_start: 0.8819 (mtmm) cc_final: 0.8452 (mtmm) REVERT: E 605 ARG cc_start: 0.7617 (mmm160) cc_final: 0.7413 (mmt180) REVERT: E 717 ASP cc_start: 0.7733 (t70) cc_final: 0.7513 (t0) REVERT: E 763 LEU cc_start: 0.8009 (mt) cc_final: 0.7379 (tp) REVERT: E 780 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8873 (tp) REVERT: E 806 LEU cc_start: 0.6216 (mp) cc_final: 0.5907 (mt) REVERT: E 808 GLN cc_start: 0.7873 (mm-40) cc_final: 0.6966 (tm-30) REVERT: F 218 LYS cc_start: 0.7352 (tppp) cc_final: 0.7112 (mttt) REVERT: F 221 ILE cc_start: 0.6957 (mt) cc_final: 0.6709 (mt) REVERT: F 290 MET cc_start: 0.5907 (mmt) cc_final: 0.5328 (tmm) REVERT: F 544 ASP cc_start: 0.7333 (m-30) cc_final: 0.6977 (p0) REVERT: F 572 MET cc_start: 0.5482 (tpt) cc_final: 0.5191 (tpt) REVERT: F 585 ASP cc_start: 0.6564 (m-30) cc_final: 0.5675 (t0) REVERT: F 638 MET cc_start: 0.6915 (pp-130) cc_final: 0.6048 (pp-130) REVERT: F 737 GLN cc_start: 0.6200 (mm110) cc_final: 0.5826 (mp10) outliers start: 117 outliers final: 80 residues processed: 676 average time/residue: 0.3926 time to fit residues: 425.1753 Evaluate side-chains 632 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 539 time to evaluate : 3.102 ------------------------------------------------------------------------------- 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 287 HIS Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 700 LEU 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 257 TYR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 317 THR 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 546 ILE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 560 LYS Chi-restraints excluded: chain C residue 569 LEU 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 712 GLN 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 828 LEU Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 198 ARG 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 305 LEU 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 591 SER 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 848 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 875 GLU 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 395 LEU Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 564 SER 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 780 ILE 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 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 623 LEU 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 802 TYR 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 296 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 159 optimal weight: 7.9990 chunk 161 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 274 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 329 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN A 336 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 GLN ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS ** F 606 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 = 0.3904 r_free = 0.3904 target = 0.150100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.126130 restraints weight = 51403.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128820 restraints weight = 30926.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130710 restraints weight = 20962.296| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.6948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27943 Z= 0.162 Angle : 0.781 14.059 37682 Z= 0.395 Chirality : 0.049 0.493 4368 Planarity : 0.005 0.098 4817 Dihedral : 9.654 137.343 4025 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.82 % Favored : 93.89 % Rotamer: Outliers : 3.83 % Allowed : 23.75 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3421 helix: 0.23 (0.12), residues: 1794 sheet: -0.88 (0.26), residues: 390 loop : -0.93 (0.18), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS C 287 PHE 0.021 0.002 PHE A 630 TYR 0.037 0.002 TYR E 170 ARG 0.010 0.001 ARG D 826 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 1432) hydrogen bonds : angle 5.91846 ( 4035) SS BOND : bond 0.00105 ( 1) SS BOND : angle 2.93802 ( 2) covalent geometry : bond 0.00372 (27932) covalent geometry : angle 0.78028 (37680) Misc. bond : bond 0.00449 ( 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 704 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 590 time to evaluate : 3.724 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: 0.8604 (mm) cc_final: 0.8194 (mm) REVERT: A 173 ASP cc_start: 0.8204 (t0) cc_final: 0.7850 (t0) REVERT: A 192 GLU cc_start: 0.6479 (mp0) cc_final: 0.6202 (mp0) REVERT: A 216 ILE cc_start: 0.9300 (pt) cc_final: 0.9000 (mt) REVERT: A 236 THR cc_start: 0.8033 (p) cc_final: 0.7715 (t) REVERT: A 270 LYS cc_start: 0.8477 (mmtt) cc_final: 0.8062 (mtmm) REVERT: A 287 HIS cc_start: 0.7217 (OUTLIER) cc_final: 0.6836 (t70) REVERT: A 319 ASN cc_start: 0.6905 (m110) cc_final: 0.6534 (t0) REVERT: A 635 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6013 (mt-10) REVERT: A 662 TYR cc_start: 0.8052 (m-10) cc_final: 0.7772 (m-80) REVERT: A 693 PRO cc_start: 0.8316 (Cg_exo) cc_final: 0.7957 (Cg_endo) REVERT: A 728 ASN cc_start: 0.7172 (m-40) cc_final: 0.6727 (t0) REVERT: A 763 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8204 (mm) REVERT: A 781 HIS cc_start: 0.6361 (m-70) cc_final: 0.5936 (m-70) REVERT: A 812 ASP cc_start: 0.2835 (m-30) cc_final: 0.2329 (t0) REVERT: A 833 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7375 (mp10) REVERT: B 192 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8128 (mm-30) REVERT: B 252 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7720 (p) REVERT: B 377 GLN cc_start: 0.7145 (tt0) cc_final: 0.6917 (tt0) REVERT: B 639 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7757 (mt) REVERT: B 692 HIS cc_start: 0.7911 (t-90) cc_final: 0.7586 (t-90) REVERT: B 883 HIS cc_start: 0.2574 (OUTLIER) cc_final: 0.0055 (m90) REVERT: C 192 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7502 (mm-30) REVERT: C 280 VAL cc_start: 0.9181 (t) cc_final: 0.8857 (m) REVERT: C 542 ASP cc_start: 0.8078 (p0) cc_final: 0.7743 (p0) REVERT: C 638 MET cc_start: 0.8604 (ppp) cc_final: 0.8400 (ppp) REVERT: C 649 LYS cc_start: 0.6231 (tttt) cc_final: 0.5844 (ttpt) REVERT: C 712 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6835 (pt0) REVERT: C 804 LEU cc_start: 0.7607 (tt) cc_final: 0.7257 (tp) REVERT: C 848 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7214 (tp30) REVERT: D 183 LEU cc_start: 0.8717 (mt) cc_final: 0.8466 (mt) REVERT: D 192 GLU cc_start: 0.7683 (mp0) cc_final: 0.6861 (mp0) REVERT: D 198 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8472 (ttm170) REVERT: D 282 PHE cc_start: 0.9031 (t80) cc_final: 0.8598 (t80) REVERT: D 361 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8391 (mm) REVERT: D 626 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8762 (mmmt) REVERT: D 645 GLU cc_start: 0.7717 (pp20) cc_final: 0.7103 (pp20) REVERT: D 673 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7239 (t0) REVERT: D 877 LEU cc_start: 0.8818 (mt) cc_final: 0.8024 (mt) REVERT: E 170 TYR cc_start: 0.8850 (m-10) cc_final: 0.8620 (m-80) REVERT: E 174 MET cc_start: 0.8582 (mmm) cc_final: 0.8200 (mmt) REVERT: E 203 ARG cc_start: 0.7251 (tpp-160) cc_final: 0.6593 (tpp80) REVERT: E 238 LEU cc_start: 0.8592 (pt) cc_final: 0.8256 (tp) REVERT: E 302 LYS cc_start: 0.7195 (mmtt) cc_final: 0.6722 (mmtt) REVERT: E 328 ASP cc_start: 0.6417 (t70) cc_final: 0.6179 (m-30) REVERT: E 338 ILE cc_start: 0.8806 (mp) cc_final: 0.8560 (tp) REVERT: E 572 MET cc_start: 0.8600 (tmm) cc_final: 0.8080 (ppp) REVERT: E 637 MET cc_start: 0.7320 (tpt) cc_final: 0.7108 (tpt) REVERT: E 717 ASP cc_start: 0.7773 (t70) cc_final: 0.7547 (t0) REVERT: E 763 LEU cc_start: 0.7951 (mt) cc_final: 0.7298 (tp) REVERT: E 806 LEU cc_start: 0.5920 (mp) cc_final: 0.5583 (mt) REVERT: E 808 GLN cc_start: 0.7879 (mm-40) cc_final: 0.6952 (tm-30) REVERT: E 838 ASN cc_start: 0.7534 (m-40) cc_final: 0.7067 (m110) REVERT: F 179 ARG cc_start: 0.6677 (tpm170) cc_final: 0.6274 (ptm-80) REVERT: F 218 LYS cc_start: 0.7461 (tppp) cc_final: 0.7227 (mttt) REVERT: F 221 ILE cc_start: 0.6970 (mt) cc_final: 0.6720 (mt) REVERT: F 290 MET cc_start: 0.5470 (mmt) cc_final: 0.5093 (tmm) REVERT: F 544 ASP cc_start: 0.7339 (m-30) cc_final: 0.7030 (p0) REVERT: F 572 MET cc_start: 0.5462 (tpt) cc_final: 0.5100 (tpt) REVERT: F 585 ASP cc_start: 0.6502 (m-30) cc_final: 0.5761 (t0) REVERT: F 747 LYS cc_start: 0.7266 (pttt) cc_final: 0.6196 (tptt) REVERT: F 794 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.8242 (ttm-80) outliers start: 114 outliers final: 82 residues processed: 654 average time/residue: 0.5759 time to fit residues: 599.5791 Evaluate side-chains 631 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 539 time to evaluate : 4.335 ------------------------------------------------------------------------------- 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 275 SER Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU 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 833 GLN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 700 LEU 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 257 TYR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 325 VAL 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 554 THR Chi-restraints excluded: chain C residue 560 LYS Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 642 ASP 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 712 GLN 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 802 TYR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 198 ARG 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 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 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 D residue 875 GLU Chi-restraints excluded: chain E residue 225 VAL 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 541 VAL Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 719 SER 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 209 CYS Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 539 ASN 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 745 SER Chi-restraints excluded: chain F residue 762 PHE Chi-restraints excluded: chain F residue 802 TYR 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 7 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 333 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 108 optimal weight: 0.0030 chunk 147 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 chunk 303 optimal weight: 5.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 336 GLN ** B 712 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS D 720 ASN E 177 GLN ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 757 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.150981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.127006 restraints weight = 51859.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.129706 restraints weight = 31277.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.131464 restraints weight = 21362.740| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.7159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 27943 Z= 0.167 Angle : 0.803 15.372 37682 Z= 0.402 Chirality : 0.049 0.429 4368 Planarity : 0.005 0.103 4817 Dihedral : 9.545 135.039 4019 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.76 % Favored : 93.95 % Rotamer: Outliers : 3.26 % Allowed : 24.42 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3421 helix: 0.21 (0.12), residues: 1806 sheet: -0.89 (0.25), residues: 398 loop : -0.92 (0.19), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS C 287 PHE 0.032 0.002 PHE B 265 TYR 0.030 0.002 TYR E 170 ARG 0.014 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 1432) hydrogen bonds : angle 5.87283 ( 4035) SS BOND : bond 0.00730 ( 1) SS BOND : angle 2.85613 ( 2) covalent geometry : bond 0.00387 (27932) covalent geometry : angle 0.80305 (37680) Misc. bond : bond 0.00505 ( 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 675 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 578 time to evaluate : 3.511 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: 0.8643 (mm) cc_final: 0.8311 (mm) REVERT: A 173 ASP cc_start: 0.8238 (t0) cc_final: 0.7919 (t0) REVERT: A 192 GLU cc_start: 0.6465 (mp0) cc_final: 0.6129 (mp0) REVERT: A 216 ILE cc_start: 0.9343 (pt) cc_final: 0.9059 (mt) REVERT: A 236 THR cc_start: 0.8050 (p) cc_final: 0.7733 (t) REVERT: A 237 ILE cc_start: 0.9055 (pt) cc_final: 0.8617 (mt) REVERT: A 270 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8048 (mtmm) REVERT: A 287 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6996 (t70) REVERT: A 319 ASN cc_start: 0.6939 (m110) cc_final: 0.6621 (t0) REVERT: A 635 GLU cc_start: 0.7290 (mm-30) cc_final: 0.5863 (mt-10) REVERT: A 662 TYR cc_start: 0.8014 (m-10) cc_final: 0.7755 (m-80) REVERT: A 728 ASN cc_start: 0.7220 (m-40) cc_final: 0.6726 (t0) REVERT: A 763 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8236 (mm) REVERT: A 781 HIS cc_start: 0.6306 (m-70) cc_final: 0.5869 (m-70) REVERT: A 812 ASP cc_start: 0.2731 (m-30) cc_final: 0.2272 (t0) REVERT: A 833 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7346 (mp10) REVERT: B 192 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8207 (mm-30) REVERT: B 252 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7683 (p) REVERT: B 377 GLN cc_start: 0.7325 (tt0) cc_final: 0.7087 (tt0) REVERT: B 639 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7581 (mt) REVERT: B 692 HIS cc_start: 0.7853 (t-90) cc_final: 0.7569 (t-90) REVERT: B 883 HIS cc_start: 0.2746 (OUTLIER) cc_final: 0.0230 (m90) REVERT: C 192 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7518 (mm-30) REVERT: C 223 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6915 (mp0) REVERT: C 307 ARG cc_start: 0.8400 (mmp-170) cc_final: 0.8178 (mmp-170) REVERT: C 336 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7909 (tm-30) REVERT: C 394 ASP cc_start: 0.8038 (t0) cc_final: 0.7806 (t0) REVERT: C 638 MET cc_start: 0.8646 (ppp) cc_final: 0.8384 (ppp) REVERT: C 712 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6698 (pt0) REVERT: C 804 LEU cc_start: 0.7629 (tt) cc_final: 0.7368 (tp) REVERT: C 848 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7135 (tp30) REVERT: D 183 LEU cc_start: 0.8688 (mt) cc_final: 0.8477 (mt) REVERT: D 192 GLU cc_start: 0.7662 (mp0) cc_final: 0.6895 (mp0) REVERT: D 198 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8475 (ttm170) REVERT: D 282 PHE cc_start: 0.9004 (t80) cc_final: 0.8703 (t80) REVERT: D 361 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8425 (mm) REVERT: D 626 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8731 (mmmt) REVERT: D 673 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7216 (t0) REVERT: D 877 LEU cc_start: 0.8788 (mt) cc_final: 0.7999 (mt) REVERT: E 170 TYR cc_start: 0.8876 (m-10) cc_final: 0.8525 (m-10) REVERT: E 174 MET cc_start: 0.8608 (mmm) cc_final: 0.8221 (mmt) REVERT: E 177 GLN cc_start: 0.8287 (tt0) cc_final: 0.7952 (tt0) REVERT: E 189 ARG cc_start: 0.8758 (mmt180) cc_final: 0.8533 (mmt-90) REVERT: E 203 ARG cc_start: 0.7300 (tpp-160) cc_final: 0.6632 (tpp80) REVERT: E 238 LEU cc_start: 0.8626 (pt) cc_final: 0.8319 (tp) REVERT: E 302 LYS cc_start: 0.7219 (mmtt) cc_final: 0.6819 (mmtt) REVERT: E 310 LEU cc_start: 0.8392 (tt) cc_final: 0.8077 (tp) REVERT: E 328 ASP cc_start: 0.6573 (t70) cc_final: 0.6355 (m-30) REVERT: E 338 ILE cc_start: 0.8799 (mp) cc_final: 0.8528 (tp) REVERT: E 572 MET cc_start: 0.8501 (tmm) cc_final: 0.8005 (ppp) REVERT: E 637 MET cc_start: 0.7342 (tpt) cc_final: 0.7075 (tpt) REVERT: E 717 ASP cc_start: 0.7764 (t70) cc_final: 0.7477 (t0) REVERT: E 763 LEU cc_start: 0.7958 (mt) cc_final: 0.7318 (tp) REVERT: E 806 LEU cc_start: 0.5833 (mp) cc_final: 0.5513 (mt) REVERT: E 808 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7014 (tm-30) REVERT: E 838 ASN cc_start: 0.7602 (m-40) cc_final: 0.7133 (m110) REVERT: F 179 ARG cc_start: 0.6768 (tpm170) cc_final: 0.6420 (ptm-80) REVERT: F 218 LYS cc_start: 0.7385 (tppp) cc_final: 0.7185 (mttt) REVERT: F 221 ILE cc_start: 0.6821 (mt) cc_final: 0.6586 (mt) REVERT: F 290 MET cc_start: 0.5366 (mmt) cc_final: 0.5013 (tmm) REVERT: F 544 ASP cc_start: 0.7345 (m-30) cc_final: 0.7037 (p0) REVERT: F 572 MET cc_start: 0.5418 (tpt) cc_final: 0.5044 (tpt) REVERT: F 585 ASP cc_start: 0.6453 (m-30) cc_final: 0.5691 (t0) REVERT: F 747 LYS cc_start: 0.7237 (pttt) cc_final: 0.6049 (tptt) REVERT: F 835 GLU cc_start: 0.6250 (tp30) cc_final: 0.5887 (tp30) outliers start: 97 outliers final: 75 residues processed: 631 average time/residue: 0.3931 time to fit residues: 394.1777 Evaluate side-chains 618 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 533 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU 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 833 GLN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 639 ILE 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 688 VAL 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 257 TYR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 325 VAL 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 554 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 712 GLN 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 802 TYR Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 TYR 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 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 848 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 875 GLU Chi-restraints excluded: chain E residue 225 VAL 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 541 VAL Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 708 ILE 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 296 ASP Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 539 ASN 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 745 SER Chi-restraints excluded: chain F residue 762 PHE Chi-restraints excluded: chain F residue 802 TYR 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 305 optimal weight: 6.9990 chunk 314 optimal weight: 5.9990 chunk 299 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 304 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 227 optimal weight: 0.1980 chunk 288 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 712 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS ** E 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 757 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.150727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128874 restraints weight = 51865.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.129418 restraints weight = 38350.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130128 restraints weight = 27799.475| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.7272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27943 Z= 0.170 Angle : 0.806 16.127 37682 Z= 0.401 Chirality : 0.049 0.425 4368 Planarity : 0.005 0.098 4817 Dihedral : 9.482 133.425 4015 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.96 % Favored : 93.74 % Rotamer: Outliers : 3.16 % Allowed : 24.86 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3421 helix: 0.24 (0.12), residues: 1815 sheet: -0.97 (0.25), residues: 400 loop : -0.95 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS C 287 PHE 0.076 0.002 PHE B 265 TYR 0.029 0.002 TYR F 382 ARG 0.011 0.001 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 1432) hydrogen bonds : angle 5.86421 ( 4035) SS BOND : bond 0.00682 ( 1) SS BOND : angle 2.43670 ( 2) covalent geometry : bond 0.00398 (27932) covalent geometry : angle 0.80569 (37680) Misc. bond : bond 0.00509 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11423.51 seconds wall clock time: 205 minutes 9.40 seconds (12309.40 seconds total)