Starting phenix.real_space_refine on Mon Sep 14 01:13:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5vjh_8697/09_2026/5vjh_8697.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vjh_8697/09_2026/5vjh_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/5vjh_8697/09_2026/5vjh_8697.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5vjh_8697/09_2026/5vjh_8697.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5vjh_8697/09_2026/5vjh_8697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vjh_8697/09_2026/5vjh_8697.map" model { file = "/net/cci-nas-00/data/ceres_data/5vjh_8697/09_2026/5vjh_8697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vjh_8697/09_2026/5vjh_8697.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 120 5.16 5 C 17230 2.51 5 N 4835 2.21 5 O 5356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27577 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4530 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain breaks: 2 Chain: "B" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4530 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain breaks: 2 Chain: "C" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4530 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain breaks: 2 Chain: "D" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4530 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain breaks: 2 Chain: "E" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4530 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain breaks: 2 Chain: "F" Number of atoms: 4424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4424 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 17, 'TRANS': 546} Chain breaks: 3 Chain: "P" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 131 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 25} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.63, per 1000 atoms: 0.20 Number of scatterers: 27577 At special positions: 0 Unit cell: (135, 143, 131, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 36 15.00 O 5356 8.00 N 4835 7.00 C 17230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 718 " - pdb=" SG CYS F 721 " distance=2.22 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 917.5 milliseconds 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: 0.82 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: 4.27 Time building geometry restraints manager: 2.73 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: 16875 30.06 - 60.11: 318 60.11 - 90.17: 46 90.17 - 120.22: 0 120.22 - 150.28: 1 Dihedral angle restraints: 17240 sinusoidal: 7163 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 17237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3159 0.108 - 0.215: 1013 0.215 - 0.323: 177 0.323 - 0.430: 16 0.430 - 0.538: 3 Chirality restraints: 4368 Sorted by residual: chirality pdb=" CG LEU C 700 " pdb=" CB LEU C 700 " pdb=" CD1 LEU C 700 " pdb=" CD2 LEU C 700 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.23e+00 chirality pdb=" CB ILE F 216 " pdb=" CA ILE F 216 " pdb=" CG1 ILE F 216 " pdb=" CG2 ILE F 216 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CB VAL D 695 " pdb=" CA VAL D 695 " pdb=" CG1 VAL D 695 " pdb=" CG2 VAL D 695 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.45 2.00e-01 2.50e+01 5.16e+00 ... (remaining 4365 not shown) Planarity restraints: 4817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 680 " -0.073 2.00e-02 2.50e+03 3.92e-02 3.08e+01 pdb=" CG TYR F 680 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR F 680 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR F 680 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR F 680 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR F 680 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR F 680 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 680 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 302 " -0.089 5.00e-02 4.00e+02 1.36e-01 2.94e+01 pdb=" N PRO A 303 " 0.234 5.00e-02 4.00e+02 pdb=" CA PRO A 303 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 303 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 650 " 0.066 2.00e-02 2.50e+03 3.36e-02 2.25e+01 pdb=" CG TYR E 650 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR E 650 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 650 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR E 650 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E 650 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR E 650 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 650 " 0.044 2.00e-02 2.50e+03 ... (remaining 4814 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 17 1.94 - 2.68: 2095 2.68 - 3.42: 41795 3.42 - 4.16: 71614 4.16 - 4.90: 125675 Nonbonded interactions: 241196 Sorted by model distance: nonbonded pdb=" OE2 GLU C 326 " pdb=" OE1 GLN D 712 " model vdw 1.198 3.040 nonbonded pdb=" NZ LYS C 205 " pdb=" NH1 ARG C 333 " model vdw 1.355 3.200 nonbonded pdb=" OE2 GLU C 326 " pdb=" CD GLN D 712 " model vdw 1.356 3.270 nonbonded pdb=" CE2 TYR E 662 " pdb=" OH TYR F 650 " model vdw 1.400 3.340 nonbonded pdb=" OE2 GLU C 326 " pdb=" NE2 GLN D 712 " model vdw 1.632 3.120 ... (remaining 241191 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 165 through 656 or resid 672 through 1002)) selection = (chain 'B' and (resid 165 through 656 or resid 672 through 1002)) selection = (chain 'C' and (resid 165 through 656 or resid 672 through 1002)) selection = (chain 'D' and (resid 165 through 656 or resid 672 through 1002)) selection = (chain 'E' and (resid 165 through 656 or resid 672 through 1002)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.480 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 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 : 11.768 150.281 10713 Min Nonbonded Distance : 1.198 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.96 % Allowed : 3.77 % Favored : 95.26 % Rotamer: Outliers : 0.94 % Allowed : 0.81 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.14), residues: 3421 helix: -0.60 (0.11), residues: 1760 sheet: 0.38 (0.25), residues: 358 loop : -0.20 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 595 TYR 0.073 0.009 TYR F 680 PHE 0.040 0.007 PHE A 685 HIS 0.014 0.003 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.02369 / 1.30 (27932) covalent geometry : angle 1.94035 / 1.31 (37680) SS BOND : bond 0.18680 / 9.83 ( 1) SS BOND : angle 4.46398 / 2.46 ( 2) hydrogen bonds : bond 0.17155 / 11.45 ( 1432) hydrogen bonds : angle 8.21674 / 5.79 ( 4035) Misc. bond : bond 0.35583 / 19.28 ( 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 : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 SER cc_start: 0.9386 (m) cc_final: 0.8774 (p) REVERT: A 216 ILE cc_start: 0.8662 (pt) cc_final: 0.8456 (mt) REVERT: A 352 LEU cc_start: 0.8439 (mt) cc_final: 0.8151 (mp) REVERT: B 238 LEU cc_start: 0.8348 (mt) cc_final: 0.8112 (mt) REVERT: B 320 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7139 (mt-10) REVERT: B 580 VAL cc_start: 0.8397 (t) cc_final: 0.7942 (p) REVERT: B 791 ILE cc_start: 0.7953 (mm) cc_final: 0.7660 (mm) REVERT: C 271 GLU cc_start: 0.6042 (tt0) cc_final: 0.5757 (tm-30) REVERT: C 280 VAL cc_start: 0.8614 (t) cc_final: 0.8296 (m) REVERT: C 310 LEU cc_start: 0.7109 (mt) cc_final: 0.6626 (mt) REVERT: C 349 VAL cc_start: 0.9105 (t) cc_final: 0.8873 (t) REVERT: C 680 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.7103 (p90) REVERT: C 765 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7750 (mtt-85) REVERT: D 183 LEU cc_start: 0.7379 (mt) cc_final: 0.6630 (mt) REVERT: D 269 LEU cc_start: 0.8373 (mt) cc_final: 0.8016 (tp) REVERT: D 271 GLU cc_start: 0.6471 (tt0) cc_final: 0.6034 (tp30) REVERT: D 310 LEU cc_start: 0.8552 (mt) cc_final: 0.8026 (mt) REVERT: D 333 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6972 (ttp-110) REVERT: D 626 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8104 (mmmt) REVERT: D 686 ASP cc_start: 0.7380 (m-30) cc_final: 0.7179 (m-30) REVERT: D 727 SER cc_start: 0.8332 (t) cc_final: 0.7771 (t) REVERT: D 746 THR cc_start: 0.8202 (m) cc_final: 0.7886 (m) REVERT: D 783 ILE cc_start: 0.8749 (mt) cc_final: 0.8523 (mt) REVERT: E 238 LEU cc_start: 0.6015 (pt) cc_final: 0.5682 (tp) REVERT: E 348 THR cc_start: 0.7798 (m) cc_final: 0.7554 (m) REVERT: E 359 TYR cc_start: 0.8071 (m-80) cc_final: 0.7612 (m-10) REVERT: E 578 SER cc_start: 0.8169 (p) cc_final: 0.7771 (t) REVERT: E 587 ILE cc_start: 0.8554 (mt) cc_final: 0.7886 (mt) REVERT: E 708 ILE cc_start: 0.7631 (mm) cc_final: 0.7113 (tt) REVERT: E 826 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8244 (mmt180) REVERT: F 174 MET cc_start: 0.6244 (mmm) cc_final: 0.5761 (tpp) REVERT: F 216 ILE cc_start: 0.5154 (tt) cc_final: 0.4425 (tt) REVERT: F 310 LEU cc_start: 0.7853 (tp) cc_final: 0.7521 (tt) REVERT: F 361 ILE cc_start: 0.7177 (mt) cc_final: 0.6943 (mt) REVERT: F 615 LEU cc_start: 0.7599 (mt) cc_final: 0.7359 (mt) outliers start: 28 outliers final: 18 residues processed: 1178 average time/residue: 0.2039 time to fit residues: 359.9886 Evaluate side-chains 637 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 615 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 643 CYS Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 680 TYR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 826 ARG Chi-restraints excluded: chain F residue 334 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN A 347 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN B 239 GLN B 299 ASN B 377 GLN B 743 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 HIS ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS D 673 ASN ** D 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 781 HIS E 363 HIS E 764 ASN F 177 GLN ** F 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.154756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.131980 restraints weight = 51744.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.133983 restraints weight = 33512.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135180 restraints weight = 22558.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135918 restraints weight = 17097.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.136383 restraints weight = 14319.681| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4107 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= 0.227 Angle : 0.901 13.591 37682 Z= 0.475 Chirality : 0.051 0.262 4368 Planarity : 0.006 0.102 4817 Dihedral : 9.746 137.329 3936 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.79 % Favored : 94.77 % Rotamer: Outliers : 3.80 % Allowed : 12.14 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.14), residues: 3421 helix: -0.03 (0.11), residues: 1791 sheet: -0.30 (0.25), residues: 386 loop : -0.61 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 202 TYR 0.033 0.003 TYR C 677 PHE 0.035 0.003 PHE A 630 HIS 0.016 0.003 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 (27932) covalent geometry : angle 0.90137 / 0.48 (37680) SS BOND : bond 0.00970 / 0.51 ( 1) SS BOND : angle 1.77621 / 1.04 ( 2) hydrogen bonds : bond 0.06133 / 4.11 ( 1432) hydrogen bonds : angle 6.60407 / 4.70 ( 4035) Misc. bond : bond 0.00353 / 0.19 ( 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 889 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 776 time to evaluate : 1.038 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: A 167 LEU cc_start: 0.8831 (mm) cc_final: 0.8470 (mm) REVERT: A 173 ASP cc_start: 0.7874 (t0) cc_final: 0.7602 (t70) REVERT: A 287 HIS cc_start: 0.7257 (p-80) cc_final: 0.4777 (p-80) REVERT: A 332 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8043 (pp20) REVERT: A 397 ASP cc_start: 0.7858 (t70) cc_final: 0.7307 (t70) REVERT: A 588 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7694 (ptpt) REVERT: A 613 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.5937 (mm) REVERT: A 622 GLU cc_start: 0.7493 (tp30) cc_final: 0.7125 (tp30) REVERT: A 635 GLU cc_start: 0.7172 (mp0) cc_final: 0.6804 (mt-10) REVERT: A 638 MET cc_start: 0.8223 (tpp) cc_final: 0.7117 (ttp) REVERT: A 743 GLN cc_start: 0.6848 (OUTLIER) cc_final: 0.6529 (mp10) REVERT: A 781 HIS cc_start: 0.6056 (m-70) cc_final: 0.5800 (m-70) REVERT: B 183 LEU cc_start: 0.7657 (pt) cc_final: 0.6492 (pp) REVERT: B 192 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8330 (mm-30) REVERT: B 236 THR cc_start: 0.7823 (m) cc_final: 0.7390 (p) REVERT: B 333 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7981 (ttp80) REVERT: B 355 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8906 (tp) REVERT: B 580 VAL cc_start: 0.8901 (t) cc_final: 0.8524 (p) REVERT: B 605 ARG cc_start: 0.7150 (mtp180) cc_final: 0.6931 (mtp180) REVERT: B 616 SER cc_start: 0.8064 (m) cc_final: 0.7491 (p) REVERT: B 702 MET cc_start: 0.8354 (tmm) cc_final: 0.8130 (tmm) REVERT: C 174 MET cc_start: 0.8322 (mmm) cc_final: 0.7831 (ttt) REVERT: C 200 LEU cc_start: 0.9452 (mt) cc_final: 0.9194 (mt) REVERT: C 231 ASP cc_start: 0.7163 (p0) cc_final: 0.6803 (m-30) REVERT: C 328 ASP cc_start: 0.7067 (t70) cc_final: 0.6666 (m-30) REVERT: C 636 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7418 (t0) REVERT: C 705 ASP cc_start: 0.7563 (t0) cc_final: 0.7345 (t0) REVERT: C 819 TYR cc_start: 0.7843 (t80) cc_final: 0.7517 (t80) REVERT: C 848 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7179 (tp30) REVERT: D 183 LEU cc_start: 0.8421 (mt) cc_final: 0.8137 (mt) REVERT: D 192 GLU cc_start: 0.7755 (mp0) cc_final: 0.7003 (mp0) REVERT: D 269 LEU cc_start: 0.8679 (mt) cc_final: 0.8396 (tp) REVERT: D 310 LEU cc_start: 0.8776 (mt) cc_final: 0.8255 (mt) REVERT: D 626 LYS cc_start: 0.9038 (mmtt) cc_final: 0.8770 (mmmt) REVERT: D 720 ASN cc_start: 0.8245 (t0) cc_final: 0.7861 (t0) REVERT: D 766 ILE cc_start: 0.8951 (mm) cc_final: 0.8363 (tp) REVERT: D 795 PHE cc_start: 0.6897 (m-10) cc_final: 0.6484 (m-10) REVERT: E 170 TYR cc_start: 0.8628 (m-80) cc_final: 0.8239 (m-80) REVERT: E 183 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.6733 (mm) REVERT: E 238 LEU cc_start: 0.8354 (pt) cc_final: 0.7841 (tp) REVERT: E 284 ASP cc_start: 0.5846 (t70) cc_final: 0.5541 (t70) REVERT: E 578 SER cc_start: 0.8455 (p) cc_final: 0.7911 (t) REVERT: E 587 ILE cc_start: 0.8741 (mt) cc_final: 0.8184 (mt) REVERT: E 603 ASN cc_start: 0.8525 (t0) cc_final: 0.8111 (t0) REVERT: E 763 LEU cc_start: 0.8030 (mt) cc_final: 0.7208 (tp) REVERT: E 806 LEU cc_start: 0.6445 (mp) cc_final: 0.6200 (mt) REVERT: E 838 ASN cc_start: 0.8089 (m-40) cc_final: 0.7019 (p0) REVERT: F 166 TYR cc_start: 0.6178 (m-80) cc_final: 0.5870 (m-80) REVERT: F 218 LYS cc_start: 0.7607 (tppp) cc_final: 0.7345 (tppt) REVERT: F 290 MET cc_start: 0.6057 (mmt) cc_final: 0.4869 (tmm) REVERT: F 338 ILE cc_start: 0.8514 (mt) cc_final: 0.8305 (mt) REVERT: F 544 ASP cc_start: 0.7541 (m-30) cc_final: 0.7130 (p0) REVERT: F 585 ASP cc_start: 0.6520 (m-30) cc_final: 0.5554 (t0) REVERT: F 678 LYS cc_start: 0.6038 (ttmt) cc_final: 0.5822 (tppp) REVERT: F 747 LYS cc_start: 0.7071 (pttt) cc_final: 0.6256 (tptt) REVERT: F 801 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7313 (m-70) REVERT: F 831 LEU cc_start: 0.9091 (tp) cc_final: 0.8781 (tp) outliers start: 113 outliers final: 60 residues processed: 850 average time/residue: 0.1811 time to fit residues: 240.7358 Evaluate side-chains 653 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 583 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 743 GLN Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 643 CYS Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 710 SER Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 777 ARG Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 680 TYR Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 762 PHE Chi-restraints excluded: chain F residue 801 HIS Chi-restraints excluded: chain F residue 816 LYS Chi-restraints excluded: chain F residue 857 VAL Chi-restraints excluded: chain F residue 877 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 121 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 217 optimal weight: 0.0020 chunk 270 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 HIS A 336 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN B 673 ASN ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS C 363 HIS C 781 HIS D 743 GLN F 606 GLN F 756 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.151997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.127245 restraints weight = 51721.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.130186 restraints weight = 30605.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132125 restraints weight = 20400.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.133493 restraints weight = 15135.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134120 restraints weight = 12252.333| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 27943 Z= 0.200 Angle : 0.792 16.406 37682 Z= 0.411 Chirality : 0.048 0.286 4368 Planarity : 0.005 0.093 4817 Dihedral : 9.135 139.384 3899 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.88 % Favored : 94.68 % Rotamer: Outliers : 4.71 % Allowed : 15.14 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3421 helix: 0.17 (0.12), residues: 1789 sheet: -0.54 (0.24), residues: 404 loop : -0.82 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 179 TYR 0.041 0.002 TYR E 665 PHE 0.032 0.002 PHE E 685 HIS 0.016 0.002 HIS C 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (27932) covalent geometry : angle 0.79190 / 0.41 (37680) SS BOND : bond 0.00964 / 0.51 ( 1) SS BOND : angle 2.53963 / 1.42 ( 2) hydrogen bonds : bond 0.05063 / 3.38 ( 1432) hydrogen bonds : angle 6.26553 / 4.46 ( 4035) Misc. bond : bond 0.00934 / 0.51 ( 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 795 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 655 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8842 (mm) cc_final: 0.8470 (mm) REVERT: A 274 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6734 (pp20) REVERT: A 319 ASN cc_start: 0.6848 (m110) cc_final: 0.6375 (t0) REVERT: A 397 ASP cc_start: 0.7849 (t70) cc_final: 0.7283 (t70) REVERT: A 645 GLU cc_start: 0.7285 (pp20) cc_final: 0.6944 (mp0) REVERT: A 781 HIS cc_start: 0.6308 (m-70) cc_final: 0.5557 (m90) REVERT: B 243 LEU cc_start: 0.9428 (tp) cc_final: 0.9079 (tt) REVERT: B 278 LEU cc_start: 0.8478 (tp) cc_final: 0.8085 (mt) REVERT: B 288 MET cc_start: 0.7845 (tpp) cc_final: 0.7615 (ptm) REVERT: B 584 MET cc_start: 0.8651 (mmm) cc_final: 0.8111 (mmm) REVERT: B 616 SER cc_start: 0.7783 (m) cc_final: 0.7511 (p) REVERT: B 883 HIS cc_start: 0.2653 (OUTLIER) cc_final: -0.0081 (m90) REVERT: C 174 MET cc_start: 0.8180 (mmm) cc_final: 0.7925 (ttt) REVERT: C 231 ASP cc_start: 0.7206 (p0) cc_final: 0.6889 (m-30) REVERT: C 233 ASP cc_start: 0.7143 (t0) cc_final: 0.6869 (t70) REVERT: C 307 ARG cc_start: 0.8172 (mmp-170) cc_final: 0.7376 (mmp-170) REVERT: C 328 ASP cc_start: 0.7458 (t70) cc_final: 0.6755 (m-30) REVERT: C 333 ARG cc_start: 0.8378 (tmm160) cc_final: 0.7777 (tpt90) REVERT: C 579 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7273 (mm-30) REVERT: C 605 ARG cc_start: 0.7716 (mmm-85) cc_final: 0.7478 (mmt-90) REVERT: C 636 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7616 (t0) REVERT: C 649 LYS cc_start: 0.6494 (tttt) cc_final: 0.6266 (tttt) REVERT: C 819 TYR cc_start: 0.7826 (t80) cc_final: 0.7529 (t80) REVERT: C 848 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7161 (tp30) REVERT: D 183 LEU cc_start: 0.8550 (mt) cc_final: 0.8296 (mt) REVERT: D 192 GLU cc_start: 0.7865 (mp0) cc_final: 0.7028 (mp0) REVERT: D 361 ILE cc_start: 0.8858 (mm) cc_final: 0.8591 (mm) REVERT: D 390 ASP cc_start: 0.7900 (t0) cc_final: 0.7685 (t70) REVERT: D 626 LYS cc_start: 0.9032 (mmtt) cc_final: 0.8725 (mmmt) REVERT: D 720 ASN cc_start: 0.8379 (t0) cc_final: 0.8139 (t0) REVERT: E 238 LEU cc_start: 0.8452 (pt) cc_final: 0.7945 (tp) REVERT: E 282 PHE cc_start: 0.8672 (t80) cc_final: 0.8441 (t80) REVERT: E 302 LYS cc_start: 0.7032 (mmtt) cc_final: 0.6755 (mmtt) REVERT: E 587 ILE cc_start: 0.9063 (mt) cc_final: 0.8814 (mt) REVERT: E 637 MET cc_start: 0.7004 (tpt) cc_final: 0.6515 (tpt) REVERT: E 678 LYS cc_start: 0.8411 (mtmt) cc_final: 0.8192 (ttmt) REVERT: E 763 LEU cc_start: 0.8091 (mt) cc_final: 0.7230 (tp) REVERT: E 806 LEU cc_start: 0.6290 (mp) cc_final: 0.6030 (mp) REVERT: E 808 GLN cc_start: 0.7290 (mm-40) cc_final: 0.6794 (tm-30) REVERT: E 838 ASN cc_start: 0.7812 (m-40) cc_final: 0.7458 (m110) REVERT: F 170 TYR cc_start: 0.6562 (m-10) cc_final: 0.6293 (m-10) REVERT: F 218 LYS cc_start: 0.7496 (tppp) cc_final: 0.7032 (mttt) REVERT: F 219 THR cc_start: 0.8300 (m) cc_final: 0.8035 (p) REVERT: F 221 ILE cc_start: 0.7423 (mt) cc_final: 0.7136 (mt) REVERT: F 290 MET cc_start: 0.5751 (mmt) cc_final: 0.4841 (tmm) REVERT: F 358 LYS cc_start: 0.6671 (mtpt) cc_final: 0.6339 (mttt) REVERT: F 544 ASP cc_start: 0.7364 (m-30) cc_final: 0.7062 (p0) REVERT: F 572 MET cc_start: 0.5151 (tpt) cc_final: 0.4899 (tpt) REVERT: F 585 ASP cc_start: 0.6672 (m-30) cc_final: 0.5806 (t0) REVERT: F 678 LYS cc_start: 0.6093 (ttmt) cc_final: 0.5744 (tppp) REVERT: F 737 GLN cc_start: 0.6247 (mm-40) cc_final: 0.5766 (mp10) REVERT: F 747 LYS cc_start: 0.7142 (pttt) cc_final: 0.6292 (tptt) REVERT: F 801 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.7132 (m-70) outliers start: 140 outliers final: 83 residues processed: 744 average time/residue: 0.1852 time to fit residues: 221.8919 Evaluate side-chains 639 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 551 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 336 GLN 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 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 285 GLU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 636 ASP 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 804 LEU 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 540 VAL 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 725 MET Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 719 SER Chi-restraints excluded: chain E residue 732 GLU Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 801 HIS Chi-restraints excluded: chain F residue 816 LYS Chi-restraints excluded: chain F residue 857 VAL Chi-restraints excluded: chain F residue 877 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 175 optimal weight: 1.9990 chunk 255 optimal weight: 0.4980 chunk 129 optimal weight: 0.7980 chunk 277 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 338 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 264 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS E 764 ASN ** F 362 HIS ** 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 = 0.3948 r_free = 0.3948 target = 0.153230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130650 restraints weight = 51504.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.131845 restraints weight = 34362.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.132995 restraints weight = 25036.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.133817 restraints weight = 18881.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.134407 restraints weight = 15603.582| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 27943 Z= 0.164 Angle : 0.748 15.497 37682 Z= 0.384 Chirality : 0.048 0.399 4368 Planarity : 0.005 0.089 4817 Dihedral : 8.935 139.029 3893 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.82 % Favored : 94.74 % Rotamer: Outliers : 4.31 % Allowed : 17.09 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3421 helix: 0.26 (0.12), residues: 1776 sheet: -0.67 (0.24), residues: 402 loop : -0.86 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 598 TYR 0.046 0.002 TYR E 665 PHE 0.029 0.002 PHE A 630 HIS 0.012 0.002 HIS C 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (27932) covalent geometry : angle 0.74776 / 0.38 (37680) SS BOND : bond 0.00761 / 0.40 ( 1) SS BOND : angle 1.97487 / 1.13 ( 2) hydrogen bonds : bond 0.04557 / 3.05 ( 1432) hydrogen bonds : angle 6.07429 / 4.35 ( 4035) Misc. bond : bond 0.01063 / 0.70 ( 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 781 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 653 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8814 (mm) cc_final: 0.8448 (mm) REVERT: A 247 ASP cc_start: 0.7214 (p0) cc_final: 0.6936 (p0) REVERT: A 274 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6719 (pp20) REVERT: A 288 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7758 (mtm) REVERT: A 319 ASN cc_start: 0.6670 (m110) cc_final: 0.6280 (t0) REVERT: A 397 ASP cc_start: 0.7683 (t70) cc_final: 0.7209 (t70) REVERT: A 638 MET cc_start: 0.8131 (tpp) cc_final: 0.6923 (ttp) REVERT: A 645 GLU cc_start: 0.7321 (pp20) cc_final: 0.6798 (mp0) REVERT: A 781 HIS cc_start: 0.6085 (m-70) cc_final: 0.5541 (m90) REVERT: A 875 GLU cc_start: 0.5456 (tt0) cc_final: 0.4808 (tt0) REVERT: B 192 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8023 (mm-30) REVERT: B 243 LEU cc_start: 0.9388 (tp) cc_final: 0.9121 (tt) REVERT: B 278 LEU cc_start: 0.8411 (tp) cc_final: 0.8121 (mt) REVERT: B 288 MET cc_start: 0.7917 (tpp) cc_final: 0.7715 (ptm) REVERT: B 352 LEU cc_start: 0.9372 (mp) cc_final: 0.9102 (mt) REVERT: B 556 ILE cc_start: 0.7782 (mm) cc_final: 0.7516 (mm) REVERT: B 616 SER cc_start: 0.7536 (m) cc_final: 0.7285 (p) REVERT: B 694 ASP cc_start: 0.8350 (p0) cc_final: 0.8025 (p0) REVERT: B 883 HIS cc_start: 0.2890 (OUTLIER) cc_final: 0.0204 (m90) REVERT: C 174 MET cc_start: 0.8063 (mmm) cc_final: 0.7851 (ttm) REVERT: C 231 ASP cc_start: 0.7210 (p0) cc_final: 0.6957 (m-30) REVERT: C 307 ARG cc_start: 0.8085 (mmp-170) cc_final: 0.7854 (mmm160) REVERT: C 328 ASP cc_start: 0.7898 (t70) cc_final: 0.7084 (m-30) REVERT: C 333 ARG cc_start: 0.8285 (tmm160) cc_final: 0.7390 (tpt90) REVERT: C 372 LEU cc_start: 0.8847 (mt) cc_final: 0.8485 (mt) REVERT: C 833 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8795 (tp40) REVERT: C 836 ILE cc_start: 0.8801 (mp) cc_final: 0.8583 (mt) REVERT: C 848 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6785 (tp30) REVERT: D 183 LEU cc_start: 0.8619 (mt) cc_final: 0.8360 (mt) REVERT: D 192 GLU cc_start: 0.7668 (mp0) cc_final: 0.6787 (mp0) REVERT: D 258 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8138 (ptmm) REVERT: D 269 LEU cc_start: 0.8637 (mt) cc_final: 0.8313 (tp) REVERT: D 300 ILE cc_start: 0.5350 (tt) cc_final: 0.4653 (mt) REVERT: D 310 LEU cc_start: 0.8745 (mt) cc_final: 0.8466 (mt) REVERT: D 361 ILE cc_start: 0.8851 (mm) cc_final: 0.8558 (mm) REVERT: D 390 ASP cc_start: 0.7780 (t0) cc_final: 0.7291 (t0) REVERT: D 553 LEU cc_start: 0.8783 (mt) cc_final: 0.8401 (mp) REVERT: D 583 GLN cc_start: 0.7343 (mm-40) cc_final: 0.7137 (mm-40) REVERT: D 626 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8693 (mmmt) REVERT: E 174 MET cc_start: 0.8664 (mmm) cc_final: 0.8002 (mmm) REVERT: E 177 GLN cc_start: 0.8203 (tt0) cc_final: 0.7177 (tt0) REVERT: E 202 ARG cc_start: 0.5683 (ptm160) cc_final: 0.5467 (ptm160) REVERT: E 238 LEU cc_start: 0.8592 (pt) cc_final: 0.8075 (tp) REVERT: E 302 LYS cc_start: 0.7354 (mmtt) cc_final: 0.7095 (mmtt) REVERT: E 334 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7239 (ptp-110) REVERT: E 572 MET cc_start: 0.8591 (tmm) cc_final: 0.8086 (ppp) REVERT: E 591 SER cc_start: 0.8677 (m) cc_final: 0.8404 (p) REVERT: E 637 MET cc_start: 0.7153 (tpt) cc_final: 0.6292 (tpt) REVERT: E 763 LEU cc_start: 0.8053 (mt) cc_final: 0.7222 (tp) REVERT: E 806 LEU cc_start: 0.6065 (mp) cc_final: 0.5655 (mt) REVERT: E 808 GLN cc_start: 0.7365 (mm-40) cc_final: 0.6851 (tm-30) REVERT: E 838 ASN cc_start: 0.7620 (m-40) cc_final: 0.7105 (m-40) REVERT: F 205 LYS cc_start: 0.7949 (mmtm) cc_final: 0.7692 (mmtm) REVERT: F 219 THR cc_start: 0.8192 (m) cc_final: 0.7915 (p) REVERT: F 221 ILE cc_start: 0.7239 (mt) cc_final: 0.6964 (mt) REVERT: F 290 MET cc_start: 0.6113 (mmt) cc_final: 0.4898 (tmm) REVERT: F 572 MET cc_start: 0.4971 (tpt) cc_final: 0.4544 (tpt) REVERT: F 585 ASP cc_start: 0.6574 (m-30) cc_final: 0.5817 (t0) REVERT: F 634 ASP cc_start: 0.7828 (t0) cc_final: 0.7525 (t0) REVERT: F 678 LYS cc_start: 0.6309 (ttmt) cc_final: 0.5910 (tppp) REVERT: F 737 GLN cc_start: 0.6050 (mm-40) cc_final: 0.5661 (mp10) REVERT: F 747 LYS cc_start: 0.7111 (pttt) cc_final: 0.6325 (tptt) REVERT: F 772 PHE cc_start: 0.7225 (m-80) cc_final: 0.6796 (m-10) REVERT: F 801 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.7352 (m-70) outliers start: 128 outliers final: 82 residues processed: 730 average time/residue: 0.1811 time to fit residues: 213.4872 Evaluate side-chains 638 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 548 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 261 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 288 MET 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 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 804 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 802 TYR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 833 GLN 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 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 680 TYR Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 573 GLU Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 732 GLU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 801 HIS Chi-restraints excluded: chain F residue 857 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 76 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 307 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 286 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 289 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN B 377 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN C 363 HIS C 781 HIS D 673 ASN D 720 ASN D 798 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.152213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.127399 restraints weight = 50790.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.130479 restraints weight = 29200.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.132517 restraints weight = 19080.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.133689 restraints weight = 14005.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134734 restraints weight = 11429.117| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27943 Z= 0.166 Angle : 0.736 17.547 37682 Z= 0.376 Chirality : 0.047 0.323 4368 Planarity : 0.005 0.087 4817 Dihedral : 8.771 139.220 3889 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.14 % Favored : 94.48 % Rotamer: Outliers : 4.41 % Allowed : 18.77 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3421 helix: 0.31 (0.12), residues: 1797 sheet: -0.80 (0.24), residues: 401 loop : -0.81 (0.18), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 777 TYR 0.051 0.002 TYR E 665 PHE 0.026 0.002 PHE A 630 HIS 0.013 0.001 HIS C 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (27932) covalent geometry : angle 0.73560 / 0.38 (37680) SS BOND : bond 0.00657 / 0.35 ( 1) SS BOND : angle 1.47280 / 0.84 ( 2) hydrogen bonds : bond 0.04334 / 2.91 ( 1432) hydrogen bonds : angle 5.93622 / 4.25 ( 4035) Misc. bond : bond 0.00527 / 0.39 ( 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 728 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 597 time to evaluate : 1.115 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: A 167 LEU cc_start: 0.8781 (mm) cc_final: 0.8431 (mm) REVERT: A 247 ASP cc_start: 0.7229 (p0) cc_final: 0.6951 (p0) REVERT: A 274 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6430 (pp20) REVERT: A 287 HIS cc_start: 0.7556 (p90) cc_final: 0.7196 (p90) REVERT: A 288 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7126 (mtm) REVERT: A 319 ASN cc_start: 0.6687 (m110) cc_final: 0.6278 (t0) REVERT: A 397 ASP cc_start: 0.7781 (t70) cc_final: 0.7260 (t70) REVERT: A 588 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7948 (ptpt) REVERT: A 635 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6169 (mt-10) REVERT: A 645 GLU cc_start: 0.7236 (pp20) cc_final: 0.6790 (mp0) REVERT: A 781 HIS cc_start: 0.6060 (m-70) cc_final: 0.5616 (m90) REVERT: A 875 GLU cc_start: 0.5364 (tt0) cc_final: 0.4869 (tt0) REVERT: B 243 LEU cc_start: 0.9411 (tp) cc_final: 0.9151 (tt) REVERT: B 278 LEU cc_start: 0.8397 (tp) cc_final: 0.8077 (mt) REVERT: B 377 GLN cc_start: 0.7199 (tt0) cc_final: 0.6964 (tt0) REVERT: B 556 ILE cc_start: 0.7626 (mm) cc_final: 0.7346 (mm) REVERT: B 616 SER cc_start: 0.7764 (m) cc_final: 0.7525 (p) REVERT: B 694 ASP cc_start: 0.8343 (p0) cc_final: 0.8013 (p0) REVERT: B 751 MET cc_start: 0.7482 (mmm) cc_final: 0.7224 (tpt) REVERT: B 883 HIS cc_start: 0.2530 (OUTLIER) cc_final: -0.0036 (m90) REVERT: C 192 GLU cc_start: 0.5933 (mt-10) cc_final: 0.5644 (mt-10) REVERT: C 231 ASP cc_start: 0.7246 (p0) cc_final: 0.7033 (m-30) REVERT: C 328 ASP cc_start: 0.8059 (t70) cc_final: 0.7223 (m-30) REVERT: C 333 ARG cc_start: 0.8310 (tmm160) cc_final: 0.7539 (tpt90) REVERT: C 649 LYS cc_start: 0.6346 (tttt) cc_final: 0.5971 (mtpt) REVERT: C 680 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.6742 (p90) REVERT: C 848 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7125 (tp30) REVERT: D 183 LEU cc_start: 0.8724 (mt) cc_final: 0.8479 (mt) REVERT: D 192 GLU cc_start: 0.7676 (mp0) cc_final: 0.6842 (mp0) REVERT: D 258 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8164 (ptmm) REVERT: D 300 ILE cc_start: 0.5121 (OUTLIER) cc_final: 0.4429 (mt) REVERT: D 361 ILE cc_start: 0.8793 (mm) cc_final: 0.8508 (mm) REVERT: D 363 HIS cc_start: 0.7224 (m-70) cc_final: 0.7007 (m170) REVERT: D 372 LEU cc_start: 0.9040 (mm) cc_final: 0.8788 (mm) REVERT: D 626 LYS cc_start: 0.9068 (mmtt) cc_final: 0.8770 (mmmt) REVERT: D 702 MET cc_start: 0.8330 (tmm) cc_final: 0.7979 (tmm) REVERT: E 170 TYR cc_start: 0.8738 (m-80) cc_final: 0.8243 (m-10) REVERT: E 174 MET cc_start: 0.8610 (mmm) cc_final: 0.8331 (mmt) REVERT: E 177 GLN cc_start: 0.8434 (tt0) cc_final: 0.8217 (tt0) REVERT: E 203 ARG cc_start: 0.7039 (tpp-160) cc_final: 0.6492 (tpp80) REVERT: E 238 LEU cc_start: 0.8536 (pt) cc_final: 0.8090 (tp) REVERT: E 262 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6405 (tp30) REVERT: E 334 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7214 (ptp-110) REVERT: E 572 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8197 (ppp) REVERT: E 587 ILE cc_start: 0.8771 (mt) cc_final: 0.8271 (mm) REVERT: E 591 SER cc_start: 0.8724 (m) cc_final: 0.7748 (m) REVERT: E 763 LEU cc_start: 0.8053 (mt) cc_final: 0.7434 (tp) REVERT: E 806 LEU cc_start: 0.6002 (mp) cc_final: 0.5640 (mt) REVERT: E 808 GLN cc_start: 0.7362 (mm-40) cc_final: 0.6844 (tm-30) REVERT: E 838 ASN cc_start: 0.7618 (m-40) cc_final: 0.7106 (m-40) REVERT: F 221 ILE cc_start: 0.6932 (mt) cc_final: 0.6655 (mt) REVERT: F 290 MET cc_start: 0.5868 (mmt) cc_final: 0.5019 (tmm) REVERT: F 585 ASP cc_start: 0.6551 (m-30) cc_final: 0.5827 (t0) REVERT: F 678 LYS cc_start: 0.6284 (ttmt) cc_final: 0.5970 (tppp) REVERT: F 747 LYS cc_start: 0.6994 (pttt) cc_final: 0.6250 (tptt) outliers start: 131 outliers final: 81 residues processed: 679 average time/residue: 0.1785 time to fit residues: 197.3825 Evaluate side-chains 629 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 537 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 261 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 290 MET 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 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 210 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 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 547 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 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 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 848 GLU Chi-restraints excluded: chain D residue 197 ILE 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 540 VAL Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 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 708 ILE Chi-restraints excluded: chain E residue 719 SER Chi-restraints excluded: chain E residue 732 GLU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 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 762 PHE Chi-restraints excluded: chain F residue 857 VAL Chi-restraints excluded: chain F residue 877 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 55 optimal weight: 9.9990 chunk 154 optimal weight: 0.6980 chunk 317 optimal weight: 8.9990 chunk 306 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 299 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 309 optimal weight: 20.0000 chunk 67 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN A 362 HIS ** A 728 ASN ** 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 363 HIS C 781 HIS D 798 ASN D 805 ASN E 177 GLN E 362 HIS ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.150503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127331 restraints weight = 51621.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.128554 restraints weight = 34385.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.129747 restraints weight = 23723.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.130359 restraints weight = 18892.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130431 restraints weight = 17316.007| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.6164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 27943 Z= 0.188 Angle : 0.738 16.799 37682 Z= 0.378 Chirality : 0.048 0.427 4368 Planarity : 0.005 0.091 4817 Dihedral : 8.673 138.706 3887 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.41 % Favored : 94.21 % Rotamer: Outliers : 4.68 % Allowed : 19.51 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3421 helix: 0.35 (0.12), residues: 1793 sheet: -0.86 (0.25), residues: 405 loop : -0.83 (0.19), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 307 TYR 0.024 0.002 TYR C 677 PHE 0.023 0.002 PHE A 630 HIS 0.012 0.001 HIS C 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (27932) covalent geometry : angle 0.73779 / 0.38 (37680) SS BOND : bond 0.00572 / 0.30 ( 1) SS BOND : angle 1.20122 / 0.69 ( 2) hydrogen bonds : bond 0.04273 / 2.87 ( 1432) hydrogen bonds : angle 5.85972 / 4.20 ( 4035) Misc. bond : bond 0.00234 / 0.16 ( 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 704 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 565 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8800 (mm) cc_final: 0.8414 (mm) REVERT: A 236 THR cc_start: 0.7973 (p) cc_final: 0.7629 (t) REVERT: A 247 ASP cc_start: 0.7368 (p0) cc_final: 0.7126 (p0) REVERT: A 270 LYS cc_start: 0.8322 (mmtt) cc_final: 0.7924 (mttp) REVERT: A 274 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6564 (pp20) REVERT: A 288 MET cc_start: 0.7786 (mtm) cc_final: 0.7465 (mtm) REVERT: A 319 ASN cc_start: 0.6815 (m110) cc_final: 0.6413 (t0) REVERT: A 397 ASP cc_start: 0.7723 (t70) cc_final: 0.7290 (t70) REVERT: A 588 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7526 (ptpp) REVERT: A 635 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6049 (mt-10) REVERT: A 638 MET cc_start: 0.8070 (tpp) cc_final: 0.6889 (ttp) REVERT: A 781 HIS cc_start: 0.6116 (m-70) cc_final: 0.5525 (m90) REVERT: A 812 ASP cc_start: 0.3006 (m-30) cc_final: 0.2634 (t0) REVERT: A 875 GLU cc_start: 0.5328 (tt0) cc_final: 0.4875 (tt0) REVERT: B 243 LEU cc_start: 0.9393 (tp) cc_final: 0.9149 (tt) REVERT: B 278 LEU cc_start: 0.8385 (tp) cc_final: 0.8153 (mt) REVERT: B 325 VAL cc_start: 0.9050 (t) cc_final: 0.8847 (p) REVERT: B 643 CYS cc_start: 0.8250 (m) cc_final: 0.7990 (m) REVERT: B 687 GLU cc_start: 0.5849 (OUTLIER) cc_final: 0.5529 (mt-10) REVERT: B 694 ASP cc_start: 0.8354 (p0) cc_final: 0.7943 (p0) REVERT: B 699 MET cc_start: 0.7333 (tpp) cc_final: 0.6978 (tpp) REVERT: B 725 MET cc_start: 0.8010 (mmt) cc_final: 0.7807 (mmt) REVERT: B 883 HIS cc_start: 0.3014 (OUTLIER) cc_final: 0.0426 (m90) REVERT: C 170 TYR cc_start: 0.7607 (m-10) cc_final: 0.7389 (m-10) REVERT: C 192 GLU cc_start: 0.5992 (mt-10) cc_final: 0.5768 (mt-10) REVERT: C 328 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7299 (m-30) REVERT: C 687 GLU cc_start: 0.7420 (mp0) cc_final: 0.6906 (mp0) REVERT: C 765 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6811 (mtt180) REVERT: C 819 TYR cc_start: 0.7821 (t80) cc_final: 0.7555 (t80) REVERT: C 848 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.6298 (tp30) REVERT: D 183 LEU cc_start: 0.8793 (mt) cc_final: 0.8543 (mt) REVERT: D 192 GLU cc_start: 0.7604 (mp0) cc_final: 0.6762 (mp0) REVERT: D 230 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8498 (tt) REVERT: D 269 LEU cc_start: 0.8716 (mt) cc_final: 0.8410 (tp) REVERT: D 361 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8472 (mm) REVERT: D 372 LEU cc_start: 0.8976 (mm) cc_final: 0.8736 (mm) REVERT: D 626 LYS cc_start: 0.9066 (mmtt) cc_final: 0.8798 (mmmt) REVERT: D 702 MET cc_start: 0.8259 (tmm) cc_final: 0.7999 (tmm) REVERT: E 170 TYR cc_start: 0.8817 (m-80) cc_final: 0.8489 (m-10) REVERT: E 174 MET cc_start: 0.8646 (mmm) cc_final: 0.8433 (mmt) REVERT: E 177 GLN cc_start: 0.8470 (tt0) cc_final: 0.8186 (tt0) REVERT: E 203 ARG cc_start: 0.7097 (tpp-160) cc_final: 0.6320 (tpp80) REVERT: E 238 LEU cc_start: 0.8739 (pt) cc_final: 0.8329 (tp) REVERT: E 262 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6574 (tp30) REVERT: E 328 ASP cc_start: 0.6271 (t70) cc_final: 0.5777 (m-30) REVERT: E 334 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7257 (ptp-110) REVERT: E 572 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8338 (ppp) REVERT: E 573 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7593 (mm-30) REVERT: E 591 SER cc_start: 0.8803 (m) cc_final: 0.7336 (p) REVERT: E 678 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8264 (mtpp) REVERT: E 751 MET cc_start: 0.7455 (mmm) cc_final: 0.7019 (mmm) REVERT: E 763 LEU cc_start: 0.8051 (mt) cc_final: 0.7408 (tp) REVERT: E 806 LEU cc_start: 0.6124 (mp) cc_final: 0.5774 (mt) REVERT: E 808 GLN cc_start: 0.7670 (mm-40) cc_final: 0.6899 (tm-30) REVERT: E 838 ASN cc_start: 0.7569 (m-40) cc_final: 0.6996 (m-40) REVERT: F 221 ILE cc_start: 0.6992 (mt) cc_final: 0.6694 (mt) REVERT: F 290 MET cc_start: 0.5896 (mmt) cc_final: 0.4983 (tmm) REVERT: F 572 MET cc_start: 0.4796 (OUTLIER) cc_final: 0.3777 (mmm) REVERT: F 585 ASP cc_start: 0.6557 (m-30) cc_final: 0.5867 (t0) REVERT: F 634 ASP cc_start: 0.7618 (t0) cc_final: 0.7386 (t0) REVERT: F 678 LYS cc_start: 0.6433 (OUTLIER) cc_final: 0.6055 (tppp) REVERT: F 737 GLN cc_start: 0.6262 (mm-40) cc_final: 0.5837 (mp10) REVERT: F 747 LYS cc_start: 0.6963 (pttt) cc_final: 0.6109 (tptt) outliers start: 139 outliers final: 93 residues processed: 653 average time/residue: 0.1752 time to fit residues: 184.7624 Evaluate side-chains 647 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 539 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 274 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 683 LEU 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 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 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 687 GLU Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 802 TYR Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 210 LEU 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 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 547 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 301 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 395 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 798 ASN Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 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 564 SER Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 573 GLU Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 719 SER Chi-restraints excluded: chain E residue 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 219 THR Chi-restraints excluded: chain F residue 285 GLU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 572 MET Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 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 Chi-restraints excluded: chain F residue 877 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 34 optimal weight: 7.9990 chunk 286 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 319 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 GLN D 798 ASN E 773 ASN E 883 HIS F 571 HIS ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118311 restraints weight = 53163.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120273 restraints weight = 32769.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121702 restraints weight = 22045.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.121855 restraints weight = 17412.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.122061 restraints weight = 17327.360| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 27943 Z= 0.355 Angle : 0.916 20.570 37682 Z= 0.469 Chirality : 0.053 0.451 4368 Planarity : 0.007 0.084 4817 Dihedral : 9.048 136.874 3883 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.40 % Favored : 93.22 % Rotamer: Outliers : 4.88 % Allowed : 20.69 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3421 helix: 0.08 (0.12), residues: 1780 sheet: -1.32 (0.23), residues: 428 loop : -1.00 (0.19), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 307 TYR 0.029 0.003 TYR C 677 PHE 0.036 0.003 PHE B 265 HIS 0.019 0.002 HIS C 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00802 / 0.35 (27932) covalent geometry : angle 0.91585 / 0.47 (37680) SS BOND : bond 0.00586 / 0.31 ( 1) SS BOND : angle 0.85862 / 0.50 ( 2) hydrogen bonds : bond 0.05080 / 3.42 ( 1432) hydrogen bonds : angle 6.09705 / 4.36 ( 4035) Misc. bond : bond 0.00266 / 0.17 ( 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 715 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 570 time to evaluate : 1.093 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: A 173 ASP cc_start: 0.7870 (t0) cc_final: 0.7597 (t70) REVERT: A 206 SER cc_start: 0.8356 (m) cc_final: 0.8147 (p) REVERT: A 216 ILE cc_start: 0.9335 (pt) cc_final: 0.9085 (mt) REVERT: A 247 ASP cc_start: 0.7691 (p0) cc_final: 0.7461 (p0) REVERT: A 274 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6856 (pp20) REVERT: A 319 ASN cc_start: 0.7087 (m110) cc_final: 0.6612 (t0) REVERT: A 588 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7593 (ptpp) REVERT: A 771 ILE cc_start: 0.7879 (mm) cc_final: 0.7640 (mp) REVERT: A 781 HIS cc_start: 0.6394 (m-70) cc_final: 0.5664 (m90) REVERT: A 812 ASP cc_start: 0.3050 (m-30) cc_final: 0.2308 (t0) REVERT: A 875 GLU cc_start: 0.5260 (tt0) cc_final: 0.4877 (tt0) REVERT: B 243 LEU cc_start: 0.9469 (tp) cc_final: 0.9130 (tt) REVERT: B 265 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7997 (t80) REVERT: B 288 MET cc_start: 0.5960 (ptt) cc_final: 0.5540 (ptm) REVERT: B 643 CYS cc_start: 0.8484 (m) cc_final: 0.7962 (m) REVERT: B 687 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.6204 (tp30) REVERT: B 694 ASP cc_start: 0.8284 (p0) cc_final: 0.7870 (p0) REVERT: B 883 HIS cc_start: 0.3252 (OUTLIER) cc_final: 0.0516 (m90) REVERT: C 192 GLU cc_start: 0.6419 (mt-10) cc_final: 0.5509 (mt-10) REVERT: C 328 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7874 (t0) REVERT: C 385 TYR cc_start: 0.7819 (m-10) cc_final: 0.7276 (m-80) REVERT: C 579 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7296 (mm-30) REVERT: C 680 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.6739 (p90) REVERT: C 686 ASP cc_start: 0.8334 (m-30) cc_final: 0.8103 (m-30) REVERT: C 765 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6893 (mtt180) REVERT: C 822 ASP cc_start: 0.7320 (p0) cc_final: 0.6976 (p0) REVERT: C 848 GLU cc_start: 0.8256 (mt-10) cc_final: 0.6347 (tp30) REVERT: D 192 GLU cc_start: 0.7680 (mp0) cc_final: 0.6814 (mp0) REVERT: D 230 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8576 (tt) REVERT: D 269 LEU cc_start: 0.8787 (mt) cc_final: 0.8541 (mt) REVERT: D 307 ARG cc_start: 0.7691 (mmp80) cc_final: 0.7465 (mmp80) REVERT: D 361 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8495 (mm) REVERT: D 372 LEU cc_start: 0.9016 (mm) cc_final: 0.8740 (mm) REVERT: D 394 ASP cc_start: 0.7453 (m-30) cc_final: 0.7025 (m-30) REVERT: D 670 PHE cc_start: 0.8080 (m-80) cc_final: 0.7688 (m-80) REVERT: D 801 HIS cc_start: 0.6265 (p90) cc_final: 0.5781 (p-80) REVERT: E 170 TYR cc_start: 0.8908 (m-80) cc_final: 0.8622 (m-10) REVERT: E 174 MET cc_start: 0.8757 (mmm) cc_final: 0.8511 (mmt) REVERT: E 177 GLN cc_start: 0.8373 (tt0) cc_final: 0.8134 (tt0) REVERT: E 192 GLU cc_start: 0.7254 (mp0) cc_final: 0.6316 (mp0) REVERT: E 203 ARG cc_start: 0.7262 (tpp-160) cc_final: 0.6538 (tpp80) REVERT: E 238 LEU cc_start: 0.8711 (pt) cc_final: 0.8195 (tp) REVERT: E 328 ASP cc_start: 0.6612 (t70) cc_final: 0.6199 (m-30) REVERT: E 689 GLU cc_start: 0.7941 (pm20) cc_final: 0.7723 (pm20) REVERT: E 751 MET cc_start: 0.7268 (mmm) cc_final: 0.6879 (mmm) REVERT: E 763 LEU cc_start: 0.8187 (mt) cc_final: 0.7581 (tp) REVERT: E 806 LEU cc_start: 0.6791 (mp) cc_final: 0.6373 (mt) REVERT: E 838 ASN cc_start: 0.8010 (m-40) cc_final: 0.7003 (m-40) REVERT: F 221 ILE cc_start: 0.7305 (mt) cc_final: 0.7021 (mt) REVERT: F 290 MET cc_start: 0.5724 (mmt) cc_final: 0.5389 (tmm) REVERT: F 337 LYS cc_start: 0.8335 (mtmm) cc_final: 0.8130 (mmtt) REVERT: F 338 ILE cc_start: 0.8529 (mt) cc_final: 0.8145 (mt) REVERT: F 605 ARG cc_start: 0.6578 (ppt170) cc_final: 0.5507 (mtp85) REVERT: F 634 ASP cc_start: 0.7611 (t0) cc_final: 0.7340 (t0) REVERT: F 699 MET cc_start: 0.5277 (OUTLIER) cc_final: 0.4335 (tpp) REVERT: F 808 GLN cc_start: 0.6573 (mm-40) cc_final: 0.5280 (mm-40) outliers start: 145 outliers final: 97 residues processed: 663 average time/residue: 0.1777 time to fit residues: 191.5665 Evaluate side-chains 616 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 508 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 274 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 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 B residue 172 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 883 HIS 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 328 ASP Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 781 HIS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 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 395 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 317 THR 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 698 VAL Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 719 SER Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 830 ARG Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 544 ASP Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 652 VAL Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 762 PHE Chi-restraints excluded: chain F residue 801 HIS Chi-restraints excluded: chain F residue 802 TYR Chi-restraints excluded: chain F residue 857 VAL 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 153 optimal weight: 0.6980 chunk 205 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 805 ASN D 798 ASN E 748 ASN ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.149243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.125255 restraints weight = 51938.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.127879 restraints weight = 31693.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.129658 restraints weight = 21608.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130802 restraints weight = 16342.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131676 restraints weight = 13430.580| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.6847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27943 Z= 0.164 Angle : 0.781 14.352 37682 Z= 0.398 Chirality : 0.048 0.405 4368 Planarity : 0.005 0.092 4817 Dihedral : 8.648 130.130 3879 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.61 % Favored : 94.01 % Rotamer: Outliers : 3.53 % Allowed : 22.94 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.14), residues: 3421 helix: 0.19 (0.12), residues: 1801 sheet: -1.08 (0.25), residues: 398 loop : -0.99 (0.19), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 605 TYR 0.032 0.002 TYR F 321 PHE 0.057 0.002 PHE B 261 HIS 0.038 0.002 HIS C 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (27932) covalent geometry : angle 0.78047 / 0.40 (37680) SS BOND : bond 0.00012 / 0.01 ( 1) SS BOND : angle 2.48727 / 1.33 ( 2) hydrogen bonds : bond 0.04309 / 2.87 ( 1432) hydrogen bonds : angle 5.91542 / 4.25 ( 4035) Misc. bond : bond 0.00530 / 0.32 ( 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 699 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 594 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8571 (mm) cc_final: 0.8226 (mm) REVERT: A 173 ASP cc_start: 0.7791 (t0) cc_final: 0.7526 (t70) REVERT: A 216 ILE cc_start: 0.9254 (pt) cc_final: 0.8971 (mt) REVERT: A 236 THR cc_start: 0.8100 (p) cc_final: 0.7760 (t) REVERT: A 274 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6414 (pp20) REVERT: A 319 ASN cc_start: 0.6848 (m110) cc_final: 0.6474 (t0) REVERT: A 588 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7570 (ptpp) REVERT: A 596 LEU cc_start: 0.8468 (mt) cc_final: 0.8155 (mm) REVERT: A 640 ARG cc_start: 0.7190 (mtt90) cc_final: 0.6939 (mtm-85) REVERT: A 705 ASP cc_start: 0.7336 (t0) cc_final: 0.6778 (p0) REVERT: A 771 ILE cc_start: 0.7682 (mm) cc_final: 0.7469 (mp) REVERT: A 781 HIS cc_start: 0.6277 (m-70) cc_final: 0.5714 (m90) REVERT: A 812 ASP cc_start: 0.2564 (m-30) cc_final: 0.2101 (t0) REVERT: A 830 ARG cc_start: 0.7454 (mmp80) cc_final: 0.6992 (tpp-160) REVERT: A 875 GLU cc_start: 0.5126 (tt0) cc_final: 0.4832 (tt0) REVERT: B 751 MET cc_start: 0.7479 (mmm) cc_final: 0.7046 (mmm) REVERT: B 883 HIS cc_start: 0.2626 (OUTLIER) cc_final: -0.0011 (m90) REVERT: C 192 GLU cc_start: 0.5929 (mt-10) cc_final: 0.5258 (mt-10) REVERT: C 328 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7325 (m-30) REVERT: C 686 ASP cc_start: 0.8012 (m-30) cc_final: 0.7783 (m-30) REVERT: C 765 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6718 (mtt180) REVERT: C 817 TYR cc_start: 0.7358 (m-80) cc_final: 0.7109 (m-80) REVERT: C 848 GLU cc_start: 0.7871 (mt-10) cc_final: 0.6471 (tp30) REVERT: D 192 GLU cc_start: 0.7466 (mp0) cc_final: 0.6651 (mp0) REVERT: D 230 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8644 (tt) REVERT: D 269 LEU cc_start: 0.8686 (mt) cc_final: 0.8445 (mm) REVERT: D 331 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.8279 (m-80) REVERT: D 361 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8392 (mm) REVERT: D 372 LEU cc_start: 0.8913 (mm) cc_final: 0.8642 (mm) REVERT: D 767 SER cc_start: 0.8894 (t) cc_final: 0.8471 (p) REVERT: E 203 ARG cc_start: 0.7263 (tpp-160) cc_final: 0.6549 (tpp80) REVERT: E 238 LEU cc_start: 0.8562 (pt) cc_final: 0.8188 (tp) REVERT: E 382 TYR cc_start: 0.8604 (m-10) cc_final: 0.7766 (m-10) REVERT: E 572 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8373 (ppp) REVERT: E 689 GLU cc_start: 0.7728 (pm20) cc_final: 0.7437 (pm20) REVERT: E 717 ASP cc_start: 0.7570 (t70) cc_final: 0.7366 (t0) REVERT: E 763 LEU cc_start: 0.7995 (mt) cc_final: 0.7405 (tp) REVERT: E 806 LEU cc_start: 0.6120 (mp) cc_final: 0.5839 (mt) REVERT: E 808 GLN cc_start: 0.7783 (mm-40) cc_final: 0.6875 (tm-30) REVERT: F 213 GLU cc_start: 0.5317 (mp0) cc_final: 0.4841 (pt0) REVERT: F 221 ILE cc_start: 0.7278 (mt) cc_final: 0.7022 (mt) REVERT: F 290 MET cc_start: 0.5452 (mmt) cc_final: 0.5004 (tmm) REVERT: F 337 LYS cc_start: 0.8461 (mtmm) cc_final: 0.8168 (mmtt) REVERT: F 585 ASP cc_start: 0.6686 (m-30) cc_final: 0.5810 (t0) REVERT: F 634 ASP cc_start: 0.7307 (t0) cc_final: 0.7039 (t0) REVERT: F 678 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.6294 (mmtm) REVERT: F 808 GLN cc_start: 0.6361 (mm-40) cc_final: 0.5068 (mm-40) outliers start: 105 outliers final: 66 residues processed: 656 average time/residue: 0.1686 time to fit residues: 178.5582 Evaluate side-chains 612 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 536 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 274 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 766 ILE 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 E residue 312 VAL Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 712 GLN Chi-restraints excluded: chain E residue 719 SER Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 830 ARG Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 209 CYS 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 615 LEU Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain F residue 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 25 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 189 optimal weight: 0.4980 chunk 118 optimal weight: 0.6980 chunk 342 optimal weight: 10.0000 chunk 235 optimal weight: 0.0010 chunk 224 optimal weight: 3.9990 chunk 331 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 ASN A 336 GLN ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS D 362 HIS F 287 HIS ** 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 = 0.3920 r_free = 0.3920 target = 0.151425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127451 restraints weight = 51964.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.130119 restraints weight = 31477.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131979 restraints weight = 21456.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.133002 restraints weight = 16193.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133785 restraints weight = 13429.627| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.7071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27943 Z= 0.160 Angle : 0.810 27.287 37682 Z= 0.407 Chirality : 0.049 0.418 4368 Planarity : 0.005 0.094 4817 Dihedral : 8.490 126.990 3877 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.82 % Favored : 93.86 % Rotamer: Outliers : 3.03 % Allowed : 24.18 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3421 helix: 0.26 (0.12), residues: 1793 sheet: -1.00 (0.25), residues: 396 loop : -0.98 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 334 TYR 0.046 0.002 TYR E 170 PHE 0.055 0.002 PHE B 261 HIS 0.013 0.001 HIS C 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (27932) covalent geometry : angle 0.81004 / 0.41 (37680) SS BOND : bond 0.00722 / 0.38 ( 1) SS BOND : angle 2.09716 / 1.11 ( 2) hydrogen bonds : bond 0.04074 / 2.73 ( 1432) hydrogen bonds : angle 5.84667 / 4.20 ( 4035) Misc. bond : bond 0.00570 / 0.31 ( 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 680 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 590 time to evaluate : 1.106 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: 0.8579 (mm) cc_final: 0.8248 (mm) REVERT: A 173 ASP cc_start: 0.7817 (t0) cc_final: 0.7570 (t70) REVERT: A 216 ILE cc_start: 0.9295 (pt) cc_final: 0.8999 (mt) REVERT: A 236 THR cc_start: 0.8023 (p) cc_final: 0.7677 (t) REVERT: A 262 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: A 270 LYS cc_start: 0.8331 (mmtt) cc_final: 0.7859 (mtmm) REVERT: A 274 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6320 (pp20) REVERT: A 287 HIS cc_start: 0.7108 (p90) cc_final: 0.6477 (t-90) REVERT: A 319 ASN cc_start: 0.6762 (m110) cc_final: 0.6375 (t0) REVERT: A 397 ASP cc_start: 0.7789 (t70) cc_final: 0.7584 (t70) REVERT: A 635 GLU cc_start: 0.6972 (mm-30) cc_final: 0.5850 (mt-10) REVERT: A 640 ARG cc_start: 0.7193 (mtt90) cc_final: 0.6976 (mtm-85) REVERT: A 662 TYR cc_start: 0.8047 (m-80) cc_final: 0.7695 (m-80) REVERT: A 693 PRO cc_start: 0.8358 (Cg_exo) cc_final: 0.8001 (Cg_endo) REVERT: A 705 ASP cc_start: 0.7355 (t0) cc_final: 0.6757 (p0) REVERT: A 781 HIS cc_start: 0.6366 (m-70) cc_final: 0.5814 (m90) REVERT: A 812 ASP cc_start: 0.2732 (m-30) cc_final: 0.2293 (t0) REVERT: B 192 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8132 (mm-30) REVERT: B 377 GLN cc_start: 0.7216 (tt0) cc_final: 0.6979 (tt0) REVERT: B 692 HIS cc_start: 0.7742 (t-90) cc_final: 0.7435 (t-90) REVERT: B 883 HIS cc_start: 0.2520 (OUTLIER) cc_final: 0.0040 (m90) REVERT: C 192 GLU cc_start: 0.5934 (mt-10) cc_final: 0.5112 (mt-10) REVERT: C 542 ASP cc_start: 0.8026 (p0) cc_final: 0.7697 (p0) REVERT: C 765 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6615 (mtt180) REVERT: C 817 TYR cc_start: 0.7254 (m-80) cc_final: 0.6956 (m-80) REVERT: C 848 GLU cc_start: 0.7785 (mt-10) cc_final: 0.6381 (tp30) REVERT: D 192 GLU cc_start: 0.7462 (mp0) cc_final: 0.6697 (mp0) REVERT: D 230 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8610 (tt) REVERT: D 282 PHE cc_start: 0.8936 (t80) cc_final: 0.8674 (t80) REVERT: D 361 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8274 (mm) REVERT: D 372 LEU cc_start: 0.8952 (mm) cc_final: 0.8647 (mm) REVERT: D 702 MET cc_start: 0.8108 (tmm) cc_final: 0.7767 (tmm) REVERT: D 767 SER cc_start: 0.8943 (t) cc_final: 0.8526 (p) REVERT: D 826 ARG cc_start: 0.8028 (mtt-85) cc_final: 0.7783 (mtp85) REVERT: E 174 MET cc_start: 0.8756 (mmm) cc_final: 0.8464 (mmt) REVERT: E 183 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7918 (pt) REVERT: E 192 GLU cc_start: 0.6970 (mp0) cc_final: 0.6161 (mp0) REVERT: E 203 ARG cc_start: 0.7198 (tpp-160) cc_final: 0.6480 (tpp80) REVERT: E 238 LEU cc_start: 0.8570 (pt) cc_final: 0.8262 (tp) REVERT: E 572 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7948 (ppp) REVERT: E 689 GLU cc_start: 0.7672 (pm20) cc_final: 0.7286 (pm20) REVERT: E 699 MET cc_start: 0.8660 (mmm) cc_final: 0.8355 (mmm) REVERT: E 717 ASP cc_start: 0.7638 (t70) cc_final: 0.7391 (t0) REVERT: E 763 LEU cc_start: 0.7990 (mt) cc_final: 0.7400 (tp) REVERT: E 806 LEU cc_start: 0.5830 (mp) cc_final: 0.5523 (mt) REVERT: E 808 GLN cc_start: 0.7781 (mm-40) cc_final: 0.6876 (tm-30) REVERT: F 179 ARG cc_start: 0.6744 (tpm170) cc_final: 0.6340 (ptm-80) REVERT: F 221 ILE cc_start: 0.7261 (mt) cc_final: 0.6984 (mt) REVERT: F 290 MET cc_start: 0.5300 (mmt) cc_final: 0.5048 (tmm) REVERT: F 337 LYS cc_start: 0.8567 (mtmm) cc_final: 0.8053 (mmtt) REVERT: F 585 ASP cc_start: 0.6564 (m-30) cc_final: 0.5770 (t0) REVERT: F 634 ASP cc_start: 0.7269 (t0) cc_final: 0.6976 (t0) REVERT: F 707 ARG cc_start: 0.7024 (mtt90) cc_final: 0.6490 (mmm160) outliers start: 90 outliers final: 61 residues processed: 639 average time/residue: 0.1733 time to fit residues: 179.8351 Evaluate side-chains 603 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 534 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 773 ASN Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 712 GLN Chi-restraints excluded: chain E residue 719 SER Chi-restraints excluded: chain E residue 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 317 THR Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 750 VAL 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 14 optimal weight: 1.9990 chunk 233 optimal weight: 0.5980 chunk 306 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 297 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 757 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.152017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.128505 restraints weight = 51937.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131086 restraints weight = 31549.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132701 restraints weight = 21651.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134053 restraints weight = 16645.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134716 restraints weight = 13576.595| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.7232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27943 Z= 0.162 Angle : 0.818 23.578 37682 Z= 0.409 Chirality : 0.048 0.399 4368 Planarity : 0.005 0.094 4817 Dihedral : 8.376 123.679 3877 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.55 % Favored : 94.15 % Rotamer: Outliers : 2.69 % Allowed : 25.40 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.14), residues: 3421 helix: 0.24 (0.12), residues: 1816 sheet: -1.01 (0.25), residues: 395 loop : -0.99 (0.19), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 787 TYR 0.034 0.002 TYR D 382 PHE 0.071 0.002 PHE B 261 HIS 0.013 0.001 HIS C 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (27932) covalent geometry : angle 0.81806 / 0.41 (37680) SS BOND : bond 0.00632 / 0.33 ( 1) SS BOND : angle 1.61238 / 0.86 ( 2) hydrogen bonds : bond 0.04051 / 2.73 ( 1432) hydrogen bonds : angle 5.81815 / 4.17 ( 4035) Misc. bond : bond 0.00557 / 0.30 ( 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 654 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 574 time to evaluate : 1.110 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: 0.8551 (mm) cc_final: 0.8271 (mm) REVERT: A 173 ASP cc_start: 0.7801 (t0) cc_final: 0.7536 (t70) REVERT: A 216 ILE cc_start: 0.9320 (pt) cc_final: 0.9037 (mt) REVERT: A 236 THR cc_start: 0.7962 (p) cc_final: 0.7639 (t) REVERT: A 270 LYS cc_start: 0.8332 (mmtt) cc_final: 0.7848 (mtmm) REVERT: A 274 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6456 (pp20) REVERT: A 287 HIS cc_start: 0.7282 (p90) cc_final: 0.6475 (t-90) REVERT: A 319 ASN cc_start: 0.6726 (m110) cc_final: 0.6423 (t0) REVERT: A 388 LEU cc_start: 0.8334 (mm) cc_final: 0.7988 (mm) REVERT: A 635 GLU cc_start: 0.7012 (mm-30) cc_final: 0.5750 (mt-10) REVERT: A 662 TYR cc_start: 0.8006 (m-80) cc_final: 0.7665 (m-80) REVERT: A 705 ASP cc_start: 0.7301 (t0) cc_final: 0.6745 (p0) REVERT: A 781 HIS cc_start: 0.6277 (m-70) cc_final: 0.5754 (m90) REVERT: A 812 ASP cc_start: 0.2521 (m-30) cc_final: 0.2191 (t0) REVERT: B 192 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8090 (mm-30) REVERT: B 377 GLN cc_start: 0.7410 (tt0) cc_final: 0.7191 (tt0) REVERT: B 692 HIS cc_start: 0.7705 (t-90) cc_final: 0.7231 (t-90) REVERT: B 694 ASP cc_start: 0.8252 (p0) cc_final: 0.7750 (p0) REVERT: B 883 HIS cc_start: 0.2390 (OUTLIER) cc_final: -0.0047 (m90) REVERT: C 192 GLU cc_start: 0.5655 (mt-10) cc_final: 0.5406 (mt-10) REVERT: C 307 ARG cc_start: 0.8516 (mmp-170) cc_final: 0.8263 (mmp-170) REVERT: C 649 LYS cc_start: 0.6344 (ttpt) cc_final: 0.6007 (ttpt) REVERT: C 765 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6842 (mtt180) REVERT: C 817 TYR cc_start: 0.7171 (m-80) cc_final: 0.6859 (m-80) REVERT: C 848 GLU cc_start: 0.7755 (mt-10) cc_final: 0.6358 (tp30) REVERT: D 192 GLU cc_start: 0.7442 (mp0) cc_final: 0.6751 (mp0) REVERT: D 198 ARG cc_start: 0.8802 (ttm-80) cc_final: 0.8459 (ttm170) REVERT: D 230 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8571 (tt) REVERT: D 331 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.8171 (m-80) REVERT: D 334 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.5976 (mtm-85) REVERT: D 361 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8312 (mm) REVERT: D 372 LEU cc_start: 0.8894 (mm) cc_final: 0.8595 (mm) REVERT: D 626 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8577 (mmmt) REVERT: D 702 MET cc_start: 0.8093 (tmm) cc_final: 0.7792 (tmm) REVERT: D 767 SER cc_start: 0.8934 (t) cc_final: 0.8522 (p) REVERT: D 822 ASP cc_start: 0.8058 (p0) cc_final: 0.7849 (p0) REVERT: E 170 TYR cc_start: 0.8840 (m-10) cc_final: 0.8628 (m-10) REVERT: E 174 MET cc_start: 0.8802 (mmm) cc_final: 0.8498 (mmt) REVERT: E 192 GLU cc_start: 0.6938 (mp0) cc_final: 0.6032 (mp0) REVERT: E 203 ARG cc_start: 0.7313 (tpp-160) cc_final: 0.6595 (tpp80) REVERT: E 238 LEU cc_start: 0.8535 (pt) cc_final: 0.8256 (tp) REVERT: E 572 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7801 (ppp) REVERT: E 689 GLU cc_start: 0.7701 (pm20) cc_final: 0.7340 (pm20) REVERT: E 699 MET cc_start: 0.8568 (mmm) cc_final: 0.8290 (mmm) REVERT: E 717 ASP cc_start: 0.7672 (t70) cc_final: 0.7418 (t0) REVERT: E 763 LEU cc_start: 0.7981 (mt) cc_final: 0.7406 (tp) REVERT: E 806 LEU cc_start: 0.5622 (mp) cc_final: 0.5348 (mt) REVERT: E 808 GLN cc_start: 0.7816 (mm-40) cc_final: 0.6930 (tm-30) REVERT: F 179 ARG cc_start: 0.6649 (tpm170) cc_final: 0.6349 (ptm-80) REVERT: F 213 GLU cc_start: 0.5209 (mp0) cc_final: 0.4763 (pt0) REVERT: F 221 ILE cc_start: 0.7197 (mt) cc_final: 0.6942 (mt) REVERT: F 290 MET cc_start: 0.5314 (mmt) cc_final: 0.5072 (tmm) REVERT: F 337 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8090 (mmtt) REVERT: F 585 ASP cc_start: 0.6504 (m-30) cc_final: 0.5737 (t0) REVERT: F 634 ASP cc_start: 0.7273 (t0) cc_final: 0.7038 (t0) REVERT: F 678 LYS cc_start: 0.6677 (OUTLIER) cc_final: 0.6385 (mmtt) REVERT: F 707 ARG cc_start: 0.7072 (mtt90) cc_final: 0.6509 (mmm160) REVERT: F 747 LYS cc_start: 0.7188 (pttt) cc_final: 0.6111 (tptt) outliers start: 80 outliers final: 59 residues processed: 620 average time/residue: 0.1665 time to fit residues: 168.8378 Evaluate side-chains 605 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 537 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 763 LEU 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 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 700 LEU Chi-restraints excluded: chain B residue 883 HIS Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 665 TYR Chi-restraints excluded: chain C residue 680 TYR 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 D residue 225 VAL Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 665 TYR Chi-restraints excluded: chain D residue 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 848 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain E residue 712 GLN Chi-restraints excluded: chain E residue 719 SER Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 830 ARG Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 209 CYS Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 678 LYS Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 699 MET Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 750 VAL 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 218 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 306 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 180 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 GLN ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS ** F 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 834 ASN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.151560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.128012 restraints weight = 51955.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.130648 restraints weight = 32190.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.132175 restraints weight = 22134.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 75)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133483 restraints weight = 17150.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134134 restraints weight = 14104.523| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.7358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27943 Z= 0.166 Angle : 0.813 22.285 37682 Z= 0.406 Chirality : 0.049 0.391 4368 Planarity : 0.005 0.085 4817 Dihedral : 8.326 120.532 3877 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.85 % Favored : 93.86 % Rotamer: Outliers : 2.69 % Allowed : 26.03 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.15), residues: 3421 helix: 0.25 (0.12), residues: 1821 sheet: -0.96 (0.25), residues: 409 loop : -0.94 (0.19), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 787 TYR 0.026 0.002 TYR E 677 PHE 0.054 0.002 PHE B 261 HIS 0.012 0.001 HIS C 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (27932) covalent geometry : angle 0.81282 / 0.41 (37680) SS BOND : bond 0.00640 / 0.34 ( 1) SS BOND : angle 1.42550 / 0.76 ( 2) hydrogen bonds : bond 0.04017 / 2.69 ( 1432) hydrogen bonds : angle 5.77047 / 4.14 ( 4035) Misc. bond : bond 0.00455 / 0.25 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5138.88 seconds wall clock time: 89 minutes 53.15 seconds (5393.15 seconds total)