Starting phenix.real_space_refine on Wed Nov 19 20:20:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vya_8746/11_2025/5vya_8746.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vya_8746/11_2025/5vya_8746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5vya_8746/11_2025/5vya_8746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vya_8746/11_2025/5vya_8746.map" model { file = "/net/cci-nas-00/data/ceres_data/5vya_8746/11_2025/5vya_8746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vya_8746/11_2025/5vya_8746.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= 0.005 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 17303 2.51 5 N 4852 2.21 5 O 5380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27691 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: 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: "P" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 139 Classifications: {'peptide': 28} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 27} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 28} Unresolved non-hydrogen planarities: 28 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: 6.79, per 1000 atoms: 0.25 Number of scatterers: 27691 At special positions: 0 Unit cell: (129, 144, 137, 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 5380 8.00 N 4852 7.00 C 17303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 721 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 721 " distance=2.03 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 Atom "HETATM27532 O5' AGS D1002 .*. O " rejected from bonding due to valence issues. Atom "HETATM27594 O5' AGS E1001 .*. O " rejected from bonding due to valence issues. Atom "HETATM27528 O3A AGS D1002 .*. O " rejected from bonding due to valence issues. Atom "HETATM27653 O3B AGS F1001 .*. O " rejected from bonding due to valence issues. Atom "HETATM27532 O5' AGS D1002 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6546 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 24 sheets defined 60.0% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.539A pdb=" N TYR A 170 " --> pdb=" O TYR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 Processing helix chain 'A' and resid 189 through 201 Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.786A pdb=" N ILE A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 298 through 306 Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 318 through 329 Processing helix chain 'A' and resid 330 through 334 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 Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 556 through 560 Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 583 through 598 removed outlier: 3.576A pdb=" N ILE A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 601 No H-bonds generated for 'chain 'A' and resid 599 through 601' Processing helix chain 'A' and resid 619 through 633 Processing helix chain 'A' and resid 644 through 646 No H-bonds generated for 'chain 'A' and resid 644 through 646' 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 699 Processing helix chain 'A' and resid 699 through 704 Processing helix chain 'A' and resid 730 through 735 Processing helix chain 'A' and resid 745 through 758 removed outlier: 3.528A pdb=" N HIS A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 764 Processing helix chain 'A' and resid 775 through 795 Processing helix chain 'A' and resid 806 through 817 Processing helix chain 'A' and resid 825 through 835 Processing helix chain 'A' and resid 835 through 846 Processing helix chain 'B' and resid 165 through 169 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 231 Processing helix chain 'B' and resid 235 through 240 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 290 Processing helix chain 'B' and resid 300 through 306 removed outlier: 4.270A pdb=" N ALA B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 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 removed outlier: 3.751A pdb=" N LEU B 393 " --> pdb=" O PRO B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 555 Processing helix chain 'B' and resid 556 through 561 Processing helix chain 'B' and resid 562 through 564 No H-bonds generated for 'chain 'B' and resid 562 through 564' Processing helix chain 'B' and resid 565 through 580 removed outlier: 5.351A pdb=" N GLU B 573 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B 579 " --> pdb=" O ASP B 575 " (cutoff:3.500A) 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 removed outlier: 3.794A pdb=" N MET B 638 " --> pdb=" O GLU B 635 " (cutoff:3.500A) 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 651 through 657 removed outlier: 3.842A pdb=" N LEU B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 676 Processing helix chain 'B' and resid 687 through 691 Processing helix chain 'B' and resid 692 through 703 removed outlier: 3.572A pdb=" N LEU B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN B 701 " --> pdb=" O THR B 697 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET B 702 " --> pdb=" O VAL B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 735 Processing helix chain 'B' and resid 745 through 756 Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 776 through 795 removed outlier: 3.594A pdb=" N PHE B 795 " --> pdb=" O ILE B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 817 Processing helix chain 'B' and resid 825 through 836 Processing helix chain 'B' and resid 836 through 846 Processing helix chain 'C' and resid 165 through 169 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 290 Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 317 through 329 removed outlier: 4.529A pdb=" N LYS C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 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 410 Processing helix chain 'C' and resid 542 through 555 Processing helix chain 'C' and resid 556 through 561 removed outlier: 3.570A pdb=" N LEU C 561 " --> pdb=" O VAL C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 564 No H-bonds generated for 'chain 'C' and resid 562 through 564' Processing helix chain 'C' and resid 565 through 580 removed outlier: 5.137A pdb=" N GLU C 573 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ARG C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 599 Processing helix chain 'C' and resid 619 through 633 Processing helix chain 'C' and resid 634 through 638 Processing helix chain 'C' and resid 647 through 657 removed outlier: 4.821A pdb=" N VAL C 652 " --> pdb=" O GLU C 648 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N SER C 653 " --> pdb=" O LYS C 649 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 655 " --> pdb=" O ALA C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 676 Processing helix chain 'C' and resid 687 through 691 Processing helix chain 'C' and resid 692 through 703 removed outlier: 3.566A pdb=" N LEU C 696 " --> pdb=" O HIS C 692 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN C 701 " --> pdb=" O THR C 697 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET C 702 " --> pdb=" O VAL C 698 " (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 removed outlier: 3.539A pdb=" N LYS C 782 " --> pdb=" O LYS C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 806 through 818 Processing helix chain 'C' and resid 820 through 824 Processing helix chain 'C' and resid 825 through 836 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 235 through 240 removed outlier: 3.529A pdb=" N GLY D 240 " --> pdb=" O THR D 236 " (cutoff:3.500A) 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 removed outlier: 4.317A pdb=" N GLY D 291 " --> pdb=" O MET D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 318 through 328 Processing helix chain 'D' and resid 329 through 335 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 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 564 No H-bonds generated for 'chain 'D' and resid 562 through 564' Processing helix chain 'D' and resid 565 through 578 removed outlier: 5.514A pdb=" N GLU D 573 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ARG D 574 " --> pdb=" O ILE D 570 " (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 642 through 646 Processing helix chain 'D' and resid 650 through 657 Processing helix chain 'D' and resid 670 through 678 removed outlier: 3.836A pdb=" N TYR D 677 " --> pdb=" O ASN D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 703 removed outlier: 3.528A pdb=" N GLN D 701 " --> pdb=" O THR D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 735 Processing helix chain 'D' and resid 745 through 758 Processing helix chain 'D' and resid 759 through 764 Processing helix chain 'D' and resid 776 through 795 removed outlier: 3.598A pdb=" N LYS D 782 " --> pdb=" O LYS D 778 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP D 785 " --> pdb=" O HIS D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 818 Processing helix chain 'D' and resid 820 through 824 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 201 Processing helix chain 'E' and resid 217 through 231 Processing helix chain 'E' and resid 235 through 240 removed outlier: 4.393A pdb=" N GLY E 240 " --> pdb=" O THR E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 253 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 285 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 317 through 322 Processing helix chain 'E' and resid 323 through 329 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 410 Processing helix chain 'E' and resid 542 through 555 Processing helix chain 'E' and resid 556 through 561 Processing helix chain 'E' and resid 562 through 564 No H-bonds generated for 'chain 'E' and resid 562 through 564' Processing helix chain 'E' and resid 565 through 571 Processing helix chain 'E' and resid 571 through 577 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 Processing helix chain 'E' and resid 650 through 656 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 removed outlier: 4.024A pdb=" N GLN E 701 " --> pdb=" O THR E 697 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET E 702 " --> pdb=" O VAL E 698 " (cutoff:3.500A) Processing helix chain 'E' and resid 730 through 735 Processing helix chain 'E' and resid 745 through 756 Processing helix chain 'E' and resid 759 through 765 removed outlier: 3.689A pdb=" N ARG E 765 " --> pdb=" O GLU E 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 776 through 794 Processing helix chain 'E' and resid 808 through 818 Processing helix chain 'E' and resid 820 through 825 removed outlier: 7.780A pdb=" N ALA E 825 " --> pdb=" O ASP E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 826 through 836 removed outlier: 3.557A pdb=" N ARG E 830 " --> pdb=" O ARG E 826 " (cutoff:3.500A) Processing helix chain 'E' and resid 836 through 846 Processing helix chain 'F' and resid 166 through 171 Processing helix chain 'F' and resid 174 through 180 Processing helix chain 'F' and resid 189 through 201 Processing helix chain 'F' and resid 217 through 231 Processing helix chain 'F' and resid 235 through 240 Processing helix chain 'F' and resid 248 through 253 Processing helix chain 'F' and resid 259 through 272 removed outlier: 3.939A pdb=" N GLY F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL F 268 " --> pdb=" O ARG F 264 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS F 270 " --> pdb=" O LYS F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 289 Processing helix chain 'F' and resid 300 through 306 Processing helix chain 'F' and resid 318 through 329 Processing helix chain 'F' and resid 329 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 408 removed outlier: 4.185A pdb=" N LEU F 393 " --> pdb=" O PRO F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 555 Processing helix chain 'F' and resid 556 through 560 Processing helix chain 'F' and resid 569 through 580 Processing helix chain 'F' and resid 583 through 596 Processing helix chain 'F' and resid 597 through 601 Processing helix chain 'F' and resid 621 through 632 Processing helix chain 'F' and resid 634 through 638 Processing helix chain 'F' and resid 652 through 657 Processing helix chain 'F' and resid 671 through 676 Processing helix chain 'F' and resid 687 through 691 Processing helix chain 'F' and resid 692 through 703 Processing helix chain 'F' and resid 730 through 735 Processing helix chain 'F' and resid 743 through 758 Processing helix chain 'F' and resid 759 through 764 Processing helix chain 'F' and resid 776 through 795 Processing helix chain 'F' and resid 806 through 818 Processing helix chain 'F' and resid 820 through 824 Processing helix chain 'F' and resid 825 through 836 removed outlier: 4.043A pdb=" N ASN F 829 " --> pdb=" O ALA F 825 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG F 830 " --> pdb=" O ARG F 826 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 846 Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 173 removed outlier: 6.327A pdb=" N LYS A 242 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE A 282 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A 244 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE A 313 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU A 281 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ALA A 315 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N THR A 316 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU A 210 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N CYS A 209 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 366 through 367 removed outlier: 7.262A 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 639 through 642 removed outlier: 6.149A pdb=" N LEU A 683 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR A 726 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N PHE A 685 " --> pdb=" O THR A 726 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER A 609 " --> pdb=" O SER A 768 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL A 770 " --> pdb=" O SER A 609 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU A 611 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE A 772 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU A 613 " --> pdb=" O PHE A 772 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 709 through 710 Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 173 removed outlier: 6.174A pdb=" N LYS B 242 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N PHE B 282 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE B 244 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 315 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 6.061A 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: 6.744A 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 Processing sheet with id=AA8, first strand: chain 'B' and resid 709 through 710 Processing sheet with id=AA9, first strand: chain 'B' and resid 802 through 804 removed outlier: 4.552A pdb=" N TYR B 802 " --> pdb=" O GLU B 853 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N VAL B 855 " --> pdb=" O TYR B 802 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU B 804 " --> pdb=" O VAL B 855 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N VAL B 857 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 171 through 173 removed outlier: 6.338A pdb=" N LYS C 242 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE C 282 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE C 244 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE C 313 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 281 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ALA C 315 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE C 283 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR C 316 " --> pdb=" O PRO C 208 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU C 210 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N CYS C 209 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 366 through 367 removed outlier: 6.814A pdb=" N ARG C 366 " --> pdb=" O VAL C 541 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 639 through 641 removed outlier: 6.083A pdb=" N LEU C 683 " --> pdb=" O ILE C 724 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR C 726 " --> pdb=" O LEU C 683 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE C 685 " --> pdb=" O THR C 726 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 802 through 804 removed outlier: 6.757A pdb=" N VAL C 855 " --> pdb=" O LYS C 803 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 171 through 173 removed outlier: 6.217A pdb=" N LYS D 242 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE D 282 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE D 244 " --> pdb=" O PHE D 282 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N ILE D 313 " --> pdb=" O ILE D 279 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU D 281 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ALA D 315 " --> pdb=" O LEU D 281 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE D 283 " --> pdb=" O ALA D 315 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N THR D 317 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N THR D 316 " --> pdb=" O PRO D 208 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU D 210 " --> pdb=" O THR D 316 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 366 through 367 removed outlier: 6.794A pdb=" N ARG D 366 " --> pdb=" O VAL D 541 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 639 through 641 Processing sheet with id=AB8, first strand: chain 'D' and resid 802 through 804 removed outlier: 4.555A pdb=" N TYR D 802 " --> pdb=" O GLU D 853 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL D 855 " --> pdb=" O TYR D 802 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU D 804 " --> pdb=" O VAL D 855 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL D 857 " --> pdb=" O LEU D 804 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 171 through 173 removed outlier: 6.189A pdb=" N LYS E 242 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE E 282 " --> pdb=" O LYS E 242 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE E 244 " --> pdb=" O PHE E 282 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 366 through 367 removed outlier: 6.648A pdb=" N ARG E 366 " --> pdb=" O VAL E 541 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 639 through 641 removed outlier: 6.649A pdb=" N SER E 609 " --> pdb=" O SER E 768 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL E 770 " --> pdb=" O SER E 609 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU E 611 " --> pdb=" O VAL E 770 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 802 through 804 removed outlier: 6.740A pdb=" N VAL E 855 " --> pdb=" O LYS E 803 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 172 through 173 removed outlier: 6.346A pdb=" N LYS F 242 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE F 282 " --> pdb=" O LYS F 242 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE F 244 " --> pdb=" O PHE F 282 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE F 313 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU F 281 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ALA F 315 " --> pdb=" O LEU F 281 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE F 283 " --> pdb=" O ALA F 315 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N THR F 317 " --> pdb=" O ILE F 283 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 366 through 367 removed outlier: 7.182A pdb=" N ARG F 366 " --> pdb=" O VAL F 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 639 through 641 removed outlier: 6.304A pdb=" N ALA F 608 " --> pdb=" O VAL F 723 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N MET F 725 " --> pdb=" O ALA F 608 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE F 610 " --> pdb=" O MET F 725 " (cutoff:3.500A) 1384 hydrogen bonds defined for protein. 3867 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: 5.72 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.34: 9359 1.34 - 1.52: 15983 1.52 - 1.70: 2523 1.70 - 1.88: 173 1.88 - 2.06: 12 Bond restraints: 28050 Sorted by residual: bond pdb=" C4 AGS A1002 " pdb=" C5 AGS A1002 " ideal model delta sigma weight residual 1.386 1.476 -0.090 1.00e-02 1.00e+04 8.03e+01 bond pdb=" CB HIS E 287 " pdb=" CG HIS E 287 " ideal model delta sigma weight residual 1.497 1.375 0.122 1.40e-02 5.10e+03 7.65e+01 bond pdb=" C4 AGS F1002 " pdb=" C5 AGS F1002 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 7.02e+01 bond pdb=" C4 AGS C1002 " pdb=" C5 AGS C1002 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" CB ASN F 673 " pdb=" CG ASN F 673 " ideal model delta sigma weight residual 1.516 1.309 0.207 2.50e-02 1.60e+03 6.83e+01 ... (remaining 28045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.58: 36592 4.58 - 9.17: 1157 9.17 - 13.75: 66 13.75 - 18.34: 24 18.34 - 22.92: 2 Bond angle restraints: 37841 Sorted by residual: angle pdb=" N LYS F 266 " pdb=" CA LYS F 266 " pdb=" C LYS F 266 " ideal model delta sigma weight residual 112.38 130.85 -18.47 1.22e+00 6.72e-01 2.29e+02 angle pdb=" C5 AGS E1002 " pdb=" C4 AGS E1002 " pdb=" N3 AGS E1002 " ideal model delta sigma weight residual 126.80 117.84 8.96 7.41e-01 1.82e+00 1.46e+02 angle pdb=" C5 AGS A1002 " pdb=" C4 AGS A1002 " pdb=" N3 AGS A1002 " ideal model delta sigma weight residual 126.80 117.92 8.88 7.41e-01 1.82e+00 1.44e+02 angle pdb=" C5 AGS D1002 " pdb=" C4 AGS D1002 " pdb=" N3 AGS D1002 " ideal model delta sigma weight residual 126.80 117.93 8.87 7.41e-01 1.82e+00 1.43e+02 angle pdb=" C5 AGS F1002 " pdb=" C4 AGS F1002 " pdb=" N3 AGS F1002 " ideal model delta sigma weight residual 126.80 118.10 8.70 7.41e-01 1.82e+00 1.38e+02 ... (remaining 37836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 17097 34.38 - 68.75: 301 68.75 - 103.12: 26 103.12 - 137.50: 7 137.50 - 171.87: 2 Dihedral angle restraints: 17433 sinusoidal: 7314 harmonic: 10119 Sorted by residual: dihedral pdb=" N LYS F 266 " pdb=" C LYS F 266 " pdb=" CA LYS F 266 " pdb=" CB LYS F 266 " ideal model delta harmonic sigma weight residual 122.80 140.71 -17.91 0 2.50e+00 1.60e-01 5.13e+01 dihedral pdb=" C LYS F 266 " pdb=" N LYS F 266 " pdb=" CA LYS F 266 " pdb=" CB LYS F 266 " ideal model delta harmonic sigma weight residual -122.60 -138.13 15.53 0 2.50e+00 1.60e-01 3.86e+01 dihedral pdb=" O1B AGS F1001 " pdb=" O3B AGS F1001 " pdb=" PB AGS F1001 " pdb=" PG AGS F1001 " ideal model delta sinusoidal sigma weight residual 68.91 -102.96 171.87 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 17430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.204: 4152 0.204 - 0.408: 226 0.408 - 0.611: 4 0.611 - 0.815: 0 0.815 - 1.019: 1 Chirality restraints: 4383 Sorted by residual: chirality pdb=" CA LYS F 266 " pdb=" N LYS F 266 " pdb=" C LYS F 266 " pdb=" CB LYS F 266 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CA LEU C 388 " pdb=" N LEU C 388 " pdb=" C LEU C 388 " pdb=" CB LEU C 388 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CB ILE F 272 " pdb=" CA ILE F 272 " pdb=" CG1 ILE F 272 " pdb=" CG2 ILE F 272 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 4380 not shown) Planarity restraints: 4839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 170 " 0.077 2.00e-02 2.50e+03 4.16e-02 3.47e+01 pdb=" CG TYR A 170 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 170 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR A 170 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR A 170 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR A 170 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 170 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 170 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 819 " -0.058 2.00e-02 2.50e+03 3.49e-02 2.44e+01 pdb=" CG TYR C 819 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR C 819 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR C 819 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR C 819 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR C 819 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR C 819 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR C 819 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 321 " 0.064 2.00e-02 2.50e+03 3.34e-02 2.23e+01 pdb=" CG TYR B 321 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR B 321 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR B 321 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 321 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 321 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR B 321 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 321 " 0.044 2.00e-02 2.50e+03 ... (remaining 4836 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 25 1.86 - 2.62: 743 2.62 - 3.38: 40836 3.38 - 4.14: 71075 4.14 - 4.90: 128571 Nonbonded interactions: 241250 Sorted by model distance: nonbonded pdb=" OE2 GLU D 213 " pdb=" CD ARG D 387 " model vdw 1.095 3.440 nonbonded pdb=" NZ LYS F 205 " pdb=" NH2 ARG F 333 " model vdw 1.130 3.200 nonbonded pdb=" OE2 GLU D 213 " pdb=" CG ARG D 387 " model vdw 1.178 3.440 nonbonded pdb=" CD GLU D 213 " pdb=" NE ARG D 387 " model vdw 1.267 3.350 nonbonded pdb=" OH TYR B 662 " pdb=" O LYS C 649 " model vdw 1.272 3.040 ... (remaining 241245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 26.160 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 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 : 0.024 0.532 28059 Z= 1.401 Angle : 1.943 22.921 37845 Z= 1.303 Chirality : 0.104 1.019 4383 Planarity : 0.010 0.087 4839 Dihedral : 12.779 171.874 10881 Min Nonbonded Distance : 1.095 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 1.37 % Allowed : 4.57 % Favored : 94.07 % Rotamer: Outliers : 0.77 % Allowed : 1.01 % Favored : 98.22 % Cbeta Deviations : 0.03 % 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: -1.01 (0.14), residues: 3438 helix: -0.68 (0.11), residues: 1756 sheet: -0.45 (0.24), residues: 370 loop : -0.43 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 179 TYR 0.077 0.009 TYR A 170 PHE 0.042 0.006 PHE A 685 HIS 0.016 0.003 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.02393 (28050) covalent geometry : angle 1.94239 (37841) SS BOND : bond 0.00879 ( 2) SS BOND : angle 6.13179 ( 4) hydrogen bonds : bond 0.16815 ( 1384) hydrogen bonds : angle 7.98178 ( 3867) Misc. bond : bond 0.32486 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1233 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 HIS cc_start: 0.7075 (p90) cc_final: 0.5863 (p-80) REVERT: A 288 MET cc_start: 0.6997 (mmm) cc_final: 0.6697 (mmm) REVERT: A 643 CYS cc_start: 0.4925 (m) cc_final: 0.4586 (m) REVERT: A 762 PHE cc_start: 0.4939 (t80) cc_final: 0.4046 (t80) REVERT: B 174 MET cc_start: 0.6619 (mmm) cc_final: 0.5797 (tpp) REVERT: B 333 ARG cc_start: 0.5961 (OUTLIER) cc_final: 0.5672 (tpt90) REVERT: B 658 THR cc_start: 0.9287 (p) cc_final: 0.8976 (t) REVERT: B 704 ASP cc_start: 0.7079 (t0) cc_final: 0.6627 (t0) REVERT: B 708 ILE cc_start: 0.7204 (mt) cc_final: 0.6725 (mt) REVERT: B 877 LEU cc_start: 0.5045 (mt) cc_final: 0.4699 (mm) REVERT: B 879 VAL cc_start: 0.7057 (t) cc_final: 0.6283 (t) REVERT: C 206 SER cc_start: 0.8422 (m) cc_final: 0.8163 (p) REVERT: C 387 ARG cc_start: 0.8542 (mmp80) cc_final: 0.7892 (mmp80) REVERT: C 684 LEU cc_start: 0.9089 (tp) cc_final: 0.8859 (tp) REVERT: C 697 THR cc_start: 0.8493 (m) cc_final: 0.8191 (m) REVERT: C 718 CYS cc_start: 0.7171 (m) cc_final: 0.5402 (m) REVERT: C 751 MET cc_start: 0.7433 (mmm) cc_final: 0.7226 (mmm) REVERT: D 272 ILE cc_start: 0.7866 (mt) cc_final: 0.7363 (mt) REVERT: D 290 MET cc_start: 0.5522 (mtm) cc_final: 0.5297 (mtm) REVERT: D 618 SER cc_start: 0.8390 (p) cc_final: 0.8185 (t) REVERT: D 620 LYS cc_start: 0.8328 (mtmt) cc_final: 0.8057 (mtmm) REVERT: D 654 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7770 (ttmt) REVERT: D 694 ASP cc_start: 0.7355 (m-30) cc_final: 0.6951 (m-30) REVERT: D 696 LEU cc_start: 0.8613 (mt) cc_final: 0.8274 (mt) REVERT: D 800 LYS cc_start: 0.5582 (mmtm) cc_final: 0.5316 (mptt) REVERT: D 817 TYR cc_start: 0.6148 (m-80) cc_final: 0.5857 (m-10) REVERT: E 187 ILE cc_start: 0.7552 (mp) cc_final: 0.7321 (mm) REVERT: E 223 GLU cc_start: 0.6496 (mt-10) cc_final: 0.6257 (mt-10) REVERT: E 355 LEU cc_start: 0.7159 (mt) cc_final: 0.6852 (mt) REVERT: E 587 ILE cc_start: 0.8698 (mt) cc_final: 0.8480 (mm) REVERT: E 686 ASP cc_start: 0.6826 (m-30) cc_final: 0.6310 (t0) REVERT: E 819 TYR cc_start: 0.6850 (t80) cc_final: 0.6223 (t80) REVERT: F 183 LEU cc_start: 0.8248 (mt) cc_final: 0.7537 (mt) REVERT: F 232 ASP cc_start: 0.3847 (t0) cc_final: 0.3586 (t70) outliers start: 23 outliers final: 10 residues processed: 1249 average time/residue: 0.2303 time to fit residues: 424.5703 Evaluate side-chains 674 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 663 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 765 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN B 701 GLN ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 180 GLN C 362 HIS D 177 GLN ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN D 756 GLN ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN F 583 GLN F 606 GLN F 701 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.126418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.105325 restraints weight = 63373.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.108423 restraints weight = 34225.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.110536 restraints weight = 21681.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.111921 restraints weight = 15333.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112769 restraints weight = 11906.074| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 28059 Z= 0.268 Angle : 0.930 13.145 37845 Z= 0.484 Chirality : 0.053 0.345 4383 Planarity : 0.007 0.250 4839 Dihedral : 11.989 151.418 4052 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.50 % Favored : 93.89 % Rotamer: Outliers : 3.76 % Allowed : 13.51 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.72 (0.14), residues: 3438 helix: -0.06 (0.12), residues: 1765 sheet: -0.78 (0.25), residues: 362 loop : -0.77 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG D 826 TYR 0.038 0.004 TYR F 650 PHE 0.033 0.003 PHE F 630 HIS 0.012 0.002 HIS F 692 Details of bonding type rmsd covalent geometry : bond 0.00595 (28050) covalent geometry : angle 0.92838 (37841) SS BOND : bond 0.02199 ( 2) SS BOND : angle 4.80839 ( 4) hydrogen bonds : bond 0.06062 ( 1384) hydrogen bonds : angle 6.56538 ( 3867) Misc. bond : bond 0.00809 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 814 time to evaluate : 1.134 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: A 285 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7102 (mm-30) REVERT: A 572 MET cc_start: 0.9007 (ptm) cc_final: 0.8769 (ptm) REVERT: A 762 PHE cc_start: 0.8192 (t80) cc_final: 0.7969 (t80) REVERT: A 813 PHE cc_start: 0.5935 (t80) cc_final: 0.4911 (t80) REVERT: B 211 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8422 (mt) REVERT: B 257 TYR cc_start: 0.7694 (m-80) cc_final: 0.7391 (m-80) REVERT: B 290 MET cc_start: 0.7189 (ttm) cc_final: 0.6751 (ttm) REVERT: B 299 ASN cc_start: 0.6917 (m-40) cc_final: 0.6711 (m110) REVERT: B 333 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7443 (tmt170) REVERT: B 359 TYR cc_start: 0.8257 (m-80) cc_final: 0.7912 (m-10) REVERT: B 387 ARG cc_start: 0.8609 (mmp80) cc_final: 0.7647 (mmm160) REVERT: B 572 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7847 (ppp) REVERT: B 584 MET cc_start: 0.7748 (mpp) cc_final: 0.7494 (mpp) REVERT: B 632 PHE cc_start: 0.7773 (m-80) cc_final: 0.7456 (m-80) REVERT: B 635 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7188 (pt0) REVERT: B 637 MET cc_start: 0.7297 (tpt) cc_final: 0.6997 (tpt) REVERT: B 689 GLU cc_start: 0.8420 (pm20) cc_final: 0.7931 (pm20) REVERT: B 708 ILE cc_start: 0.8271 (mt) cc_final: 0.7258 (mt) REVERT: B 762 PHE cc_start: 0.9120 (t80) cc_final: 0.8892 (t80) REVERT: B 819 TYR cc_start: 0.7414 (t80) cc_final: 0.7173 (t80) REVERT: C 173 ASP cc_start: 0.8468 (t0) cc_final: 0.8175 (t0) REVERT: C 266 LYS cc_start: 0.8794 (tttp) cc_final: 0.8359 (ttmt) REVERT: C 288 MET cc_start: 0.8107 (mmm) cc_final: 0.7434 (mmm) REVERT: C 310 LEU cc_start: 0.8876 (mt) cc_final: 0.8639 (mt) REVERT: C 387 ARG cc_start: 0.8902 (mmp80) cc_final: 0.8539 (mmt-90) REVERT: C 560 LYS cc_start: 0.8434 (mttt) cc_final: 0.8067 (mtmm) REVERT: C 654 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8494 (ttmm) REVERT: C 675 LEU cc_start: 0.8945 (mm) cc_final: 0.8548 (mt) REVERT: C 684 LEU cc_start: 0.9361 (tp) cc_final: 0.9140 (tt) REVERT: C 690 LYS cc_start: 0.8330 (mmmt) cc_final: 0.7812 (mmtt) REVERT: C 751 MET cc_start: 0.8718 (mmm) cc_final: 0.8361 (mmm) REVERT: C 789 LYS cc_start: 0.9110 (mttp) cc_final: 0.8819 (ttmm) REVERT: C 807 THR cc_start: 0.8403 (m) cc_final: 0.7973 (p) REVERT: C 842 LEU cc_start: 0.9182 (tp) cc_final: 0.8740 (pp) REVERT: D 223 GLU cc_start: 0.8039 (tt0) cc_final: 0.7752 (tt0) REVERT: D 290 MET cc_start: 0.6095 (mtm) cc_final: 0.5804 (mtm) REVERT: D 579 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7605 (mt-10) REVERT: D 583 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7321 (mm-40) REVERT: D 618 SER cc_start: 0.8887 (p) cc_final: 0.8629 (t) REVERT: D 620 LYS cc_start: 0.8627 (mtmt) cc_final: 0.8340 (mtmm) REVERT: D 623 LEU cc_start: 0.9382 (tp) cc_final: 0.9116 (tt) REVERT: D 626 LYS cc_start: 0.9163 (mmtt) cc_final: 0.8793 (mmmt) REVERT: D 694 ASP cc_start: 0.8065 (m-30) cc_final: 0.7658 (m-30) REVERT: D 786 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8373 (mm) REVERT: D 802 TYR cc_start: 0.6626 (p90) cc_final: 0.6359 (p90) REVERT: E 223 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8088 (mt-10) REVERT: E 238 LEU cc_start: 0.8869 (tp) cc_final: 0.8628 (tt) REVERT: E 247 ASP cc_start: 0.8286 (t0) cc_final: 0.8066 (t0) REVERT: E 322 ARG cc_start: 0.8270 (mtm-85) cc_final: 0.7664 (mtm-85) REVERT: E 572 MET cc_start: 0.8715 (ttm) cc_final: 0.8497 (ttm) REVERT: E 626 LYS cc_start: 0.8939 (tptt) cc_final: 0.8453 (tptp) REVERT: E 790 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: F 170 TYR cc_start: 0.7316 (m-10) cc_final: 0.7088 (m-10) REVERT: F 209 CYS cc_start: 0.8401 (t) cc_final: 0.7868 (p) REVERT: F 223 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8122 (tt0) REVERT: F 232 ASP cc_start: 0.6374 (t0) cc_final: 0.5627 (t70) REVERT: F 262 GLU cc_start: 0.8609 (tt0) cc_final: 0.7864 (tp30) REVERT: F 283 ILE cc_start: 0.8425 (mm) cc_final: 0.8151 (mp) REVERT: F 285 GLU cc_start: 0.6516 (mp0) cc_final: 0.6095 (mp0) REVERT: F 290 MET cc_start: 0.6613 (tmm) cc_final: 0.5834 (mtp) REVERT: F 380 LYS cc_start: 0.9309 (tppt) cc_final: 0.8576 (tttt) REVERT: F 381 ARG cc_start: 0.8194 (ttt180) cc_final: 0.7536 (tpm170) REVERT: F 393 LEU cc_start: 0.9424 (mm) cc_final: 0.9213 (mm) REVERT: F 605 ARG cc_start: 0.6635 (mmm-85) cc_final: 0.6286 (mmm160) REVERT: F 634 ASP cc_start: 0.7290 (t0) cc_final: 0.7056 (t0) REVERT: F 682 VAL cc_start: 0.8665 (p) cc_final: 0.8201 (t) REVERT: F 837 LEU cc_start: 0.9369 (mt) cc_final: 0.9149 (mm) REVERT: F 838 ASN cc_start: 0.8475 (m-40) cc_final: 0.8099 (p0) REVERT: F 846 LYS cc_start: 0.9118 (mttt) cc_final: 0.8819 (ptmt) REVERT: F 848 GLU cc_start: 0.5488 (mm-30) cc_final: 0.4094 (mm-30) outliers start: 112 outliers final: 63 residues processed: 883 average time/residue: 0.1964 time to fit residues: 268.9030 Evaluate side-chains 674 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 606 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 801 HIS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 786 ILE Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 790 GLU Chi-restraints excluded: chain E residue 828 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 720 ASN Chi-restraints excluded: chain F residue 738 GLN Chi-restraints excluded: chain F residue 876 CYS Chi-restraints excluded: chain F residue 882 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 240 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 339 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 257 optimal weight: 2.9990 chunk 280 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 299 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 238 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN A 701 GLN A 781 HIS ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN C 566 ASN ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 756 GLN ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS F 781 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.124824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.103764 restraints weight = 63573.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.106908 restraints weight = 34219.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.108941 restraints weight = 21498.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.110261 restraints weight = 15314.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.111240 restraints weight = 12002.546| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 28059 Z= 0.200 Angle : 0.801 13.248 37845 Z= 0.413 Chirality : 0.049 0.312 4383 Planarity : 0.005 0.081 4839 Dihedral : 11.843 140.604 4039 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.99 % Favored : 93.46 % Rotamer: Outliers : 4.66 % Allowed : 16.77 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.66 (0.14), residues: 3438 helix: 0.11 (0.12), residues: 1760 sheet: -1.02 (0.25), residues: 362 loop : -0.84 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 333 TYR 0.027 0.003 TYR F 321 PHE 0.021 0.002 PHE F 630 HIS 0.012 0.002 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00449 (28050) covalent geometry : angle 0.80008 (37841) SS BOND : bond 0.00392 ( 2) SS BOND : angle 3.42758 ( 4) hydrogen bonds : bond 0.05103 ( 1384) hydrogen bonds : angle 6.37686 ( 3867) Misc. bond : bond 0.00759 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 676 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.8527 (mmm) cc_final: 0.8295 (mtp) REVERT: A 336 GLN cc_start: 0.7822 (mm-40) cc_final: 0.6833 (mm110) REVERT: A 359 TYR cc_start: 0.5584 (m-80) cc_final: 0.4632 (m-80) REVERT: A 393 LEU cc_start: 0.7708 (pp) cc_final: 0.6792 (tp) REVERT: A 572 MET cc_start: 0.8988 (ptm) cc_final: 0.8740 (ptm) REVERT: A 733 PHE cc_start: 0.7153 (m-80) cc_final: 0.6694 (m-80) REVERT: A 749 LEU cc_start: 0.8007 (mt) cc_final: 0.7703 (tp) REVERT: A 767 SER cc_start: 0.8185 (m) cc_final: 0.7731 (t) REVERT: B 211 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8442 (mt) REVERT: B 257 TYR cc_start: 0.7653 (m-80) cc_final: 0.7264 (m-80) REVERT: B 281 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9009 (tp) REVERT: B 290 MET cc_start: 0.7055 (ttm) cc_final: 0.6807 (tpp) REVERT: B 299 ASN cc_start: 0.6937 (m-40) cc_final: 0.6691 (m110) REVERT: B 321 TYR cc_start: 0.7805 (t80) cc_final: 0.7437 (t80) REVERT: B 342 GLU cc_start: 0.7441 (tt0) cc_final: 0.7099 (tp30) REVERT: B 348 THR cc_start: 0.9229 (m) cc_final: 0.8915 (p) REVERT: B 386 ARG cc_start: 0.7415 (mtm-85) cc_final: 0.7205 (mmm-85) REVERT: B 387 ARG cc_start: 0.8387 (mmp80) cc_final: 0.7605 (mmt180) REVERT: B 394 ASP cc_start: 0.7346 (m-30) cc_final: 0.6967 (t0) REVERT: B 572 MET cc_start: 0.8324 (ppp) cc_final: 0.8099 (ppp) REVERT: B 632 PHE cc_start: 0.7837 (m-80) cc_final: 0.7387 (m-80) REVERT: B 635 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7213 (pt0) REVERT: B 704 ASP cc_start: 0.8375 (t0) cc_final: 0.7736 (t0) REVERT: B 708 ILE cc_start: 0.8126 (mt) cc_final: 0.7723 (mt) REVERT: B 765 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7800 (mtt90) REVERT: B 833 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8325 (tm-30) REVERT: C 173 ASP cc_start: 0.8390 (t0) cc_final: 0.8106 (t0) REVERT: C 192 GLU cc_start: 0.7491 (mp0) cc_final: 0.7072 (mp0) REVERT: C 266 LYS cc_start: 0.8815 (tttp) cc_final: 0.8575 (ttmt) REVERT: C 269 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8575 (mt) REVERT: C 282 PHE cc_start: 0.8944 (t80) cc_final: 0.8671 (t80) REVERT: C 356 GLN cc_start: 0.8234 (tt0) cc_final: 0.7897 (tp40) REVERT: C 387 ARG cc_start: 0.8985 (mmp80) cc_final: 0.8514 (mmt-90) REVERT: C 560 LYS cc_start: 0.8344 (mttt) cc_final: 0.8121 (mtmm) REVERT: C 684 LEU cc_start: 0.9305 (tp) cc_final: 0.9097 (tt) REVERT: C 702 MET cc_start: 0.8850 (tpp) cc_final: 0.8289 (tpt) REVERT: C 751 MET cc_start: 0.8647 (mmm) cc_final: 0.8383 (mmm) REVERT: C 789 LYS cc_start: 0.9038 (mttp) cc_final: 0.8801 (ttmm) REVERT: C 807 THR cc_start: 0.8300 (m) cc_final: 0.7810 (p) REVERT: C 842 LEU cc_start: 0.9110 (tp) cc_final: 0.8693 (pp) REVERT: D 174 MET cc_start: 0.8021 (ttt) cc_final: 0.7086 (ttp) REVERT: D 290 MET cc_start: 0.6129 (mtm) cc_final: 0.5692 (mtm) REVERT: D 332 GLU cc_start: 0.7907 (tt0) cc_final: 0.7217 (tp30) REVERT: D 333 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7828 (tmt-80) REVERT: D 372 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8929 (mp) REVERT: D 579 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7498 (mp0) REVERT: D 620 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8218 (mtmm) REVERT: D 694 ASP cc_start: 0.7977 (m-30) cc_final: 0.7577 (m-30) REVERT: D 717 ASP cc_start: 0.8143 (m-30) cc_final: 0.7888 (t70) REVERT: D 729 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8277 (mp) REVERT: E 169 LYS cc_start: 0.8718 (tttt) cc_final: 0.8498 (tppt) REVERT: E 223 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8184 (mt-10) REVERT: E 238 LEU cc_start: 0.8806 (tp) cc_final: 0.8522 (tt) REVERT: E 263 GLU cc_start: 0.8210 (pp20) cc_final: 0.7938 (pt0) REVERT: E 322 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7597 (ttm110) REVERT: E 334 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.5813 (mtm-85) REVERT: E 572 MET cc_start: 0.8675 (ttm) cc_final: 0.8456 (ttm) REVERT: E 827 PRO cc_start: 0.9503 (Cg_endo) cc_final: 0.9060 (Cg_exo) REVERT: F 209 CYS cc_start: 0.8405 (t) cc_final: 0.8028 (p) REVERT: F 211 ILE cc_start: 0.7820 (mt) cc_final: 0.7381 (pt) REVERT: F 223 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8060 (mt-10) REVERT: F 262 GLU cc_start: 0.8538 (tt0) cc_final: 0.7885 (tp30) REVERT: F 285 GLU cc_start: 0.6451 (mp0) cc_final: 0.6031 (mp0) REVERT: F 290 MET cc_start: 0.6541 (tmm) cc_final: 0.5804 (mtp) REVERT: F 305 LEU cc_start: 0.6285 (tp) cc_final: 0.5757 (tp) REVERT: F 380 LYS cc_start: 0.9184 (tppt) cc_final: 0.8465 (tttt) REVERT: F 381 ARG cc_start: 0.8182 (ttt180) cc_final: 0.7316 (tpp-160) REVERT: F 390 ASP cc_start: 0.8511 (p0) cc_final: 0.7836 (t0) REVERT: F 699 MET cc_start: 0.8880 (tpp) cc_final: 0.8665 (tpp) outliers start: 139 outliers final: 80 residues processed: 769 average time/residue: 0.1870 time to fit residues: 225.3114 Evaluate side-chains 677 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 589 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 747 LYS Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 801 HIS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 876 CYS Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 704 ASP Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 786 ILE Chi-restraints excluded: chain D residue 826 ARG Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 828 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 720 ASN Chi-restraints excluded: chain F residue 738 GLN Chi-restraints excluded: chain F residue 781 HIS Chi-restraints excluded: chain F residue 789 LYS Chi-restraints excluded: chain F residue 876 CYS Chi-restraints excluded: chain F residue 882 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 240 optimal weight: 0.9990 chunk 310 optimal weight: 3.9990 chunk 81 optimal weight: 0.0010 chunk 331 optimal weight: 5.9990 chunk 260 optimal weight: 5.9990 chunk 303 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN A 781 HIS ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 ASN ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.122902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.102101 restraints weight = 63187.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105003 restraints weight = 35115.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.106923 restraints weight = 22574.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.108214 restraints weight = 16264.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.108923 restraints weight = 12832.776| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28059 Z= 0.200 Angle : 0.763 10.475 37845 Z= 0.393 Chirality : 0.048 0.414 4383 Planarity : 0.005 0.067 4839 Dihedral : 11.687 138.006 4039 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.37 % Favored : 93.16 % Rotamer: Outliers : 4.66 % Allowed : 18.61 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.69 (0.14), residues: 3438 helix: 0.10 (0.12), residues: 1774 sheet: -1.06 (0.25), residues: 362 loop : -0.88 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 333 TYR 0.027 0.002 TYR F 321 PHE 0.041 0.002 PHE F 282 HIS 0.017 0.002 HIS F 781 Details of bonding type rmsd covalent geometry : bond 0.00454 (28050) covalent geometry : angle 0.76260 (37841) SS BOND : bond 0.00413 ( 2) SS BOND : angle 3.12509 ( 4) hydrogen bonds : bond 0.04669 ( 1384) hydrogen bonds : angle 6.19262 ( 3867) Misc. bond : bond 0.00164 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 633 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLU cc_start: 0.6700 (mm-30) cc_final: 0.6203 (mp0) REVERT: A 336 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7454 (mm110) REVERT: A 359 TYR cc_start: 0.5772 (m-80) cc_final: 0.5043 (m-80) REVERT: A 393 LEU cc_start: 0.7619 (pp) cc_final: 0.7364 (pp) REVERT: A 733 PHE cc_start: 0.7226 (m-80) cc_final: 0.6754 (m-10) REVERT: A 749 LEU cc_start: 0.7996 (mt) cc_final: 0.7621 (tp) REVERT: B 246 LEU cc_start: 0.8985 (tp) cc_final: 0.8733 (tt) REVERT: B 257 TYR cc_start: 0.7728 (m-80) cc_final: 0.7344 (m-80) REVERT: B 263 GLU cc_start: 0.7880 (pt0) cc_final: 0.7347 (pt0) REVERT: B 266 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8212 (tttm) REVERT: B 290 MET cc_start: 0.7181 (ttm) cc_final: 0.6771 (ttm) REVERT: B 299 ASN cc_start: 0.7009 (m-40) cc_final: 0.6664 (m-40) REVERT: B 321 TYR cc_start: 0.7837 (t80) cc_final: 0.7479 (t80) REVERT: B 333 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7350 (ttt90) REVERT: B 386 ARG cc_start: 0.7384 (mtm-85) cc_final: 0.7177 (mtm-85) REVERT: B 387 ARG cc_start: 0.8033 (mmp80) cc_final: 0.7797 (mmt180) REVERT: B 635 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7254 (pt0) REVERT: B 662 TYR cc_start: 0.8545 (m-10) cc_final: 0.8272 (m-10) REVERT: B 702 MET cc_start: 0.7788 (mmm) cc_final: 0.7409 (mmm) REVERT: B 704 ASP cc_start: 0.8288 (t0) cc_final: 0.7675 (t0) REVERT: B 722 ILE cc_start: 0.9346 (mm) cc_final: 0.9054 (mm) REVERT: B 762 PHE cc_start: 0.9115 (t80) cc_final: 0.8856 (t80) REVERT: B 765 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8064 (mtp85) REVERT: C 266 LYS cc_start: 0.8826 (tttp) cc_final: 0.8606 (ttmt) REVERT: C 282 PHE cc_start: 0.8944 (t80) cc_final: 0.8553 (t80) REVERT: C 325 VAL cc_start: 0.8282 (t) cc_final: 0.7186 (p) REVERT: C 332 GLU cc_start: 0.7686 (tp30) cc_final: 0.7478 (tp30) REVERT: C 356 GLN cc_start: 0.8158 (tt0) cc_final: 0.7898 (tp40) REVERT: C 387 ARG cc_start: 0.9039 (mmp80) cc_final: 0.8632 (mmt-90) REVERT: C 560 LYS cc_start: 0.8335 (mttt) cc_final: 0.8084 (mtmm) REVERT: C 690 LYS cc_start: 0.8335 (mmmt) cc_final: 0.8035 (mmtt) REVERT: C 702 MET cc_start: 0.8778 (tpp) cc_final: 0.8140 (tpt) REVERT: C 715 THR cc_start: 0.8458 (m) cc_final: 0.7972 (p) REVERT: C 789 LYS cc_start: 0.8963 (mttp) cc_final: 0.8747 (ttmm) REVERT: C 807 THR cc_start: 0.8182 (m) cc_final: 0.7680 (p) REVERT: C 842 LEU cc_start: 0.9122 (tp) cc_final: 0.8681 (pp) REVERT: D 287 HIS cc_start: 0.8720 (p-80) cc_final: 0.8347 (p90) REVERT: D 290 MET cc_start: 0.5975 (mtm) cc_final: 0.5672 (mtm) REVERT: D 332 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: D 694 ASP cc_start: 0.7978 (m-30) cc_final: 0.7601 (m-30) REVERT: D 699 MET cc_start: 0.7983 (mmp) cc_final: 0.7408 (mmm) REVERT: D 828 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9009 (tp) REVERT: D 854 THR cc_start: 0.8231 (m) cc_final: 0.7994 (p) REVERT: E 169 LYS cc_start: 0.8751 (tttt) cc_final: 0.8519 (tppt) REVERT: E 223 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7870 (mt-10) REVERT: E 263 GLU cc_start: 0.8115 (pp20) cc_final: 0.7770 (pt0) REVERT: E 288 MET cc_start: 0.8034 (mpp) cc_final: 0.7819 (mpp) REVERT: E 345 VAL cc_start: 0.9052 (m) cc_final: 0.8830 (t) REVERT: E 626 LYS cc_start: 0.8727 (tptt) cc_final: 0.8416 (tptp) REVERT: E 827 PRO cc_start: 0.9535 (Cg_endo) cc_final: 0.9226 (Cg_exo) REVERT: F 209 CYS cc_start: 0.8610 (t) cc_final: 0.8119 (p) REVERT: F 211 ILE cc_start: 0.7762 (mt) cc_final: 0.7367 (pt) REVERT: F 262 GLU cc_start: 0.8545 (tt0) cc_final: 0.7865 (tp30) REVERT: F 285 GLU cc_start: 0.6436 (mp0) cc_final: 0.6221 (mp0) REVERT: F 288 MET cc_start: 0.8320 (mmp) cc_final: 0.8102 (tpp) REVERT: F 380 LYS cc_start: 0.9173 (tppt) cc_final: 0.8435 (tttt) REVERT: F 390 ASP cc_start: 0.8463 (p0) cc_final: 0.7667 (t0) REVERT: F 634 ASP cc_start: 0.7434 (t0) cc_final: 0.7209 (t0) REVERT: F 682 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8505 (m) REVERT: F 699 MET cc_start: 0.8867 (tpp) cc_final: 0.8575 (tpp) REVERT: F 719 SER cc_start: 0.9003 (p) cc_final: 0.8486 (t) REVERT: F 838 ASN cc_start: 0.8250 (m-40) cc_final: 0.7884 (p0) outliers start: 139 outliers final: 91 residues processed: 718 average time/residue: 0.1937 time to fit residues: 217.1700 Evaluate side-chains 643 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 546 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 876 CYS Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 643 CYS Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 704 ASP Chi-restraints excluded: chain D residue 721 CYS Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 783 ILE Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 814 LEU Chi-restraints excluded: chain D residue 828 LEU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 880 LEU Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 643 CYS Chi-restraints excluded: chain F residue 647 SER Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 680 TYR Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 720 ASN Chi-restraints excluded: chain F residue 738 GLN Chi-restraints excluded: chain F residue 876 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 170 optimal weight: 8.9990 chunk 94 optimal weight: 0.4980 chunk 324 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 293 optimal weight: 0.4980 chunk 239 optimal weight: 0.9980 chunk 287 optimal weight: 4.9990 chunk 7 optimal weight: 0.0050 chunk 155 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 HIS A 538 GLN A 883 HIS B 299 ASN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 HIS ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 720 ASN ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 712 GLN F 781 HIS F 882 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.125465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.104678 restraints weight = 63152.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107833 restraints weight = 34202.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.109879 restraints weight = 21458.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.111116 restraints weight = 15215.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.112047 restraints weight = 12021.800| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28059 Z= 0.151 Angle : 0.734 15.074 37845 Z= 0.372 Chirality : 0.047 0.327 4383 Planarity : 0.005 0.136 4839 Dihedral : 11.429 138.606 4039 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.28 % Favored : 93.25 % Rotamer: Outliers : 4.23 % Allowed : 20.32 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.63 (0.14), residues: 3438 helix: 0.18 (0.12), residues: 1769 sheet: -0.97 (0.25), residues: 379 loop : -0.93 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 264 TYR 0.035 0.002 TYR E 802 PHE 0.035 0.002 PHE F 282 HIS 0.013 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00341 (28050) covalent geometry : angle 0.73296 (37841) SS BOND : bond 0.01145 ( 2) SS BOND : angle 3.31502 ( 4) hydrogen bonds : bond 0.04259 ( 1384) hydrogen bonds : angle 6.09443 ( 3867) Misc. bond : bond 0.00092 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 644 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.8334 (mmp) cc_final: 0.8063 (mtp) REVERT: A 639 ILE cc_start: 0.8702 (pt) cc_final: 0.8166 (pt) REVERT: A 699 MET cc_start: 0.8443 (tpp) cc_final: 0.8223 (tpp) REVERT: A 733 PHE cc_start: 0.7182 (m-80) cc_final: 0.6659 (m-10) REVERT: A 749 LEU cc_start: 0.7971 (mt) cc_final: 0.7612 (tp) REVERT: B 257 TYR cc_start: 0.7571 (m-80) cc_final: 0.7251 (m-80) REVERT: B 263 GLU cc_start: 0.7910 (pt0) cc_final: 0.7355 (pt0) REVERT: B 280 VAL cc_start: 0.9523 (t) cc_final: 0.9249 (m) REVERT: B 321 TYR cc_start: 0.7774 (t80) cc_final: 0.7540 (t80) REVERT: B 348 THR cc_start: 0.9194 (m) cc_final: 0.8952 (p) REVERT: B 635 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7210 (pt0) REVERT: B 658 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.9053 (t) REVERT: B 662 TYR cc_start: 0.8399 (m-10) cc_final: 0.8191 (m-10) REVERT: B 704 ASP cc_start: 0.8135 (t0) cc_final: 0.7417 (t0) REVERT: B 765 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7896 (mtp85) REVERT: B 837 LEU cc_start: 0.9089 (tp) cc_final: 0.8747 (tp) REVERT: B 855 VAL cc_start: 0.8182 (OUTLIER) cc_final: 0.7961 (t) REVERT: B 877 LEU cc_start: 0.7980 (mm) cc_final: 0.7432 (mt) REVERT: C 266 LYS cc_start: 0.8909 (tttp) cc_final: 0.8652 (ttpt) REVERT: C 282 PHE cc_start: 0.8837 (t80) cc_final: 0.8468 (t80) REVERT: C 325 VAL cc_start: 0.8388 (t) cc_final: 0.7897 (p) REVERT: C 356 GLN cc_start: 0.8110 (tt0) cc_final: 0.7537 (tp40) REVERT: C 387 ARG cc_start: 0.8967 (mmp80) cc_final: 0.8764 (mmm160) REVERT: C 577 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8536 (p) REVERT: C 702 MET cc_start: 0.8754 (tpp) cc_final: 0.8162 (tpt) REVERT: C 715 THR cc_start: 0.8338 (m) cc_final: 0.7713 (p) REVERT: C 789 LYS cc_start: 0.9034 (mttp) cc_final: 0.8783 (ttmm) REVERT: C 821 ASP cc_start: 0.7888 (p0) cc_final: 0.7568 (p0) REVERT: C 842 LEU cc_start: 0.8984 (tp) cc_final: 0.8635 (pp) REVERT: D 166 TYR cc_start: 0.7999 (m-80) cc_final: 0.7584 (m-80) REVERT: D 192 GLU cc_start: 0.8218 (mp0) cc_final: 0.7993 (mp0) REVERT: D 265 PHE cc_start: 0.9269 (t80) cc_final: 0.8939 (t80) REVERT: D 321 TYR cc_start: 0.8250 (t80) cc_final: 0.7582 (t80) REVERT: D 332 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7329 (tp30) REVERT: D 694 ASP cc_start: 0.8104 (m-30) cc_final: 0.7750 (m-30) REVERT: D 699 MET cc_start: 0.7829 (mmp) cc_final: 0.7062 (mmp) REVERT: D 790 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8040 (tp30) REVERT: D 828 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9006 (tp) REVERT: E 169 LYS cc_start: 0.8730 (tttt) cc_final: 0.8476 (tppt) REVERT: E 174 MET cc_start: 0.8624 (mtp) cc_final: 0.8315 (mtt) REVERT: E 223 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7838 (mt-10) REVERT: E 263 GLU cc_start: 0.8008 (pp20) cc_final: 0.7661 (pt0) REVERT: E 288 MET cc_start: 0.8045 (mpp) cc_final: 0.7755 (mpp) REVERT: E 393 LEU cc_start: 0.9035 (tt) cc_final: 0.8511 (mm) REVERT: E 572 MET cc_start: 0.8739 (ttm) cc_final: 0.8355 (tmm) REVERT: E 584 MET cc_start: 0.7644 (mmm) cc_final: 0.7331 (mtt) REVERT: F 209 CYS cc_start: 0.8528 (t) cc_final: 0.8042 (p) REVERT: F 211 ILE cc_start: 0.7694 (mt) cc_final: 0.7383 (pt) REVERT: F 262 GLU cc_start: 0.8564 (tt0) cc_final: 0.7926 (tp30) REVERT: F 285 GLU cc_start: 0.6577 (mp0) cc_final: 0.6297 (mp0) REVERT: F 290 MET cc_start: 0.6360 (tmm) cc_final: 0.5535 (ttm) REVERT: F 307 ARG cc_start: 0.7235 (pmt-80) cc_final: 0.6992 (mpp-170) REVERT: F 380 LYS cc_start: 0.9085 (tppt) cc_final: 0.8374 (tttt) REVERT: F 634 ASP cc_start: 0.7510 (t0) cc_final: 0.7194 (t0) REVERT: F 682 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8466 (t) REVERT: F 699 MET cc_start: 0.9026 (tpp) cc_final: 0.8691 (tpp) REVERT: F 719 SER cc_start: 0.8843 (p) cc_final: 0.8410 (t) REVERT: F 816 LYS cc_start: 0.7638 (pttp) cc_final: 0.7261 (tptt) REVERT: F 819 TYR cc_start: 0.7983 (t80) cc_final: 0.7649 (t80) outliers start: 126 outliers final: 79 residues processed: 723 average time/residue: 0.1913 time to fit residues: 216.4924 Evaluate side-chains 636 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 550 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 801 HIS Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 876 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 643 CYS Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 704 ASP Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 828 LEU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 880 LEU Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 643 CYS Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 738 GLN Chi-restraints excluded: chain F residue 789 LYS Chi-restraints excluded: chain F residue 876 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 50 optimal weight: 0.0050 chunk 167 optimal weight: 0.0980 chunk 171 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 232 optimal weight: 6.9990 chunk 297 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 281 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 GLN A 538 GLN B 377 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 HIS ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 856 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.125251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.104831 restraints weight = 63201.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.107954 restraints weight = 34028.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.110003 restraints weight = 21280.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.111376 restraints weight = 14992.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.112298 restraints weight = 11598.718| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.6479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28059 Z= 0.152 Angle : 0.728 14.851 37845 Z= 0.369 Chirality : 0.046 0.293 4383 Planarity : 0.005 0.079 4839 Dihedral : 11.303 139.277 4039 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.08 % Favored : 93.46 % Rotamer: Outliers : 4.29 % Allowed : 21.70 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.59 (0.14), residues: 3438 helix: 0.25 (0.12), residues: 1766 sheet: -0.93 (0.26), residues: 373 loop : -0.97 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 777 TYR 0.038 0.002 TYR D 677 PHE 0.032 0.002 PHE B 632 HIS 0.011 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00342 (28050) covalent geometry : angle 0.72757 (37841) SS BOND : bond 0.00747 ( 2) SS BOND : angle 2.85677 ( 4) hydrogen bonds : bond 0.04098 ( 1384) hydrogen bonds : angle 6.00949 ( 3867) Misc. bond : bond 0.00118 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 607 time to evaluate : 1.084 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: A 287 HIS cc_start: 0.7903 (p-80) cc_final: 0.7660 (p-80) REVERT: A 336 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7426 (mm110) REVERT: A 359 TYR cc_start: 0.5891 (m-80) cc_final: 0.5166 (m-80) REVERT: A 637 MET cc_start: 0.7624 (tpp) cc_final: 0.7401 (tpp) REVERT: A 639 ILE cc_start: 0.8582 (pt) cc_final: 0.7982 (pt) REVERT: A 699 MET cc_start: 0.8538 (tpp) cc_final: 0.8251 (tpp) REVERT: A 733 PHE cc_start: 0.7219 (m-80) cc_final: 0.6671 (m-10) REVERT: A 749 LEU cc_start: 0.7941 (mt) cc_final: 0.7607 (tp) REVERT: B 211 ILE cc_start: 0.8942 (mm) cc_final: 0.8689 (mt) REVERT: B 263 GLU cc_start: 0.7897 (pt0) cc_final: 0.7602 (pt0) REVERT: B 280 VAL cc_start: 0.9502 (t) cc_final: 0.9291 (m) REVERT: B 299 ASN cc_start: 0.7299 (OUTLIER) cc_final: 0.6829 (p0) REVERT: B 632 PHE cc_start: 0.7494 (m-10) cc_final: 0.7200 (m-10) REVERT: B 662 TYR cc_start: 0.8398 (m-10) cc_final: 0.8191 (m-10) REVERT: B 704 ASP cc_start: 0.8104 (t0) cc_final: 0.7511 (t0) REVERT: B 759 ARG cc_start: 0.8114 (tpp80) cc_final: 0.7678 (ttt180) REVERT: B 765 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8189 (mtp85) REVERT: B 837 LEU cc_start: 0.9098 (tp) cc_final: 0.8722 (tp) REVERT: B 856 ASN cc_start: 0.8900 (t0) cc_final: 0.8416 (t0) REVERT: C 282 PHE cc_start: 0.8811 (t80) cc_final: 0.8391 (t80) REVERT: C 325 VAL cc_start: 0.8497 (t) cc_final: 0.7398 (p) REVERT: C 332 GLU cc_start: 0.7740 (tp30) cc_final: 0.7449 (tp30) REVERT: C 356 GLN cc_start: 0.8026 (tt0) cc_final: 0.7660 (tp40) REVERT: C 577 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8577 (p) REVERT: C 702 MET cc_start: 0.8637 (tpp) cc_final: 0.8416 (tpt) REVERT: C 704 ASP cc_start: 0.7023 (t0) cc_final: 0.6105 (t0) REVERT: C 715 THR cc_start: 0.8342 (m) cc_final: 0.7926 (p) REVERT: C 755 ARG cc_start: 0.8024 (mtp-110) cc_final: 0.7647 (mtp-110) REVERT: C 789 LYS cc_start: 0.9048 (mttp) cc_final: 0.8784 (ttmm) REVERT: C 821 ASP cc_start: 0.7860 (p0) cc_final: 0.7530 (p0) REVERT: C 842 LEU cc_start: 0.9021 (tp) cc_final: 0.8676 (pp) REVERT: D 166 TYR cc_start: 0.7936 (m-80) cc_final: 0.7648 (m-80) REVERT: D 192 GLU cc_start: 0.8228 (mp0) cc_final: 0.7955 (mp0) REVERT: D 265 PHE cc_start: 0.9263 (t80) cc_final: 0.9039 (t80) REVERT: D 321 TYR cc_start: 0.8262 (t80) cc_final: 0.7506 (t80) REVERT: D 332 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7318 (tp30) REVERT: D 333 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7598 (tmt-80) REVERT: D 694 ASP cc_start: 0.8085 (m-30) cc_final: 0.7771 (m-30) REVERT: D 699 MET cc_start: 0.7968 (mmp) cc_final: 0.7152 (mmp) REVERT: D 790 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7977 (tp30) REVERT: D 828 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9039 (tp) REVERT: E 169 LYS cc_start: 0.8755 (tttt) cc_final: 0.8495 (tppt) REVERT: E 174 MET cc_start: 0.8552 (mtp) cc_final: 0.8260 (mtt) REVERT: E 223 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7842 (mt-10) REVERT: E 263 GLU cc_start: 0.8026 (pp20) cc_final: 0.7716 (pt0) REVERT: E 285 GLU cc_start: 0.7692 (mp0) cc_final: 0.7430 (mp0) REVERT: E 288 MET cc_start: 0.8190 (mpp) cc_final: 0.7955 (mpp) REVERT: E 393 LEU cc_start: 0.9043 (tt) cc_final: 0.8595 (mm) REVERT: E 572 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8395 (tmm) REVERT: F 209 CYS cc_start: 0.8478 (t) cc_final: 0.7967 (p) REVERT: F 211 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7398 (pt) REVERT: F 223 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8053 (mt-10) REVERT: F 262 GLU cc_start: 0.8541 (tt0) cc_final: 0.7899 (tp30) REVERT: F 285 GLU cc_start: 0.6679 (mp0) cc_final: 0.6335 (mp0) REVERT: F 307 ARG cc_start: 0.7144 (pmt-80) cc_final: 0.6921 (mpp-170) REVERT: F 321 TYR cc_start: 0.8690 (t80) cc_final: 0.8127 (t80) REVERT: F 336 GLN cc_start: 0.8442 (tt0) cc_final: 0.8020 (tt0) REVERT: F 337 LYS cc_start: 0.8853 (ptpp) cc_final: 0.8512 (mttp) REVERT: F 380 LYS cc_start: 0.9079 (tppt) cc_final: 0.8381 (tttt) REVERT: F 634 ASP cc_start: 0.7359 (t0) cc_final: 0.7105 (t0) REVERT: F 643 CYS cc_start: 0.7422 (t) cc_final: 0.7107 (t) REVERT: F 682 VAL cc_start: 0.8840 (OUTLIER) cc_final: 0.8373 (t) REVERT: F 699 MET cc_start: 0.8998 (tpp) cc_final: 0.8745 (tpp) REVERT: F 719 SER cc_start: 0.8849 (p) cc_final: 0.8279 (t) REVERT: F 738 GLN cc_start: 0.6504 (OUTLIER) cc_final: 0.6285 (pm20) REVERT: F 816 LYS cc_start: 0.7511 (pttp) cc_final: 0.7240 (tptt) REVERT: F 819 TYR cc_start: 0.8006 (t80) cc_final: 0.7654 (t80) REVERT: F 838 ASN cc_start: 0.8293 (m-40) cc_final: 0.7807 (p0) outliers start: 128 outliers final: 90 residues processed: 682 average time/residue: 0.1852 time to fit residues: 200.2878 Evaluate side-chains 649 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 549 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 801 HIS Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 876 CYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 634 ASP Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 643 CYS Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 704 ASP Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 828 LEU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 625 LYS Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain E residue 849 ILE Chi-restraints excluded: chain E residue 880 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 596 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 647 SER Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 680 TYR Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 738 GLN Chi-restraints excluded: chain F residue 789 LYS Chi-restraints excluded: chain F residue 876 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 8 optimal weight: 0.0980 chunk 227 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 309 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 100 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN B 571 HIS B 781 HIS ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 829 ASN ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 756 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.124976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.104774 restraints weight = 62468.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107962 restraints weight = 33620.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.110008 restraints weight = 20764.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.111366 restraints weight = 14483.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.112180 restraints weight = 11124.271| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 28059 Z= 0.153 Angle : 0.726 14.446 37845 Z= 0.368 Chirality : 0.046 0.256 4383 Planarity : 0.004 0.063 4839 Dihedral : 11.169 139.674 4035 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.17 % Favored : 93.37 % Rotamer: Outliers : 4.29 % Allowed : 22.54 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.57 (0.14), residues: 3438 helix: 0.23 (0.12), residues: 1771 sheet: -0.83 (0.26), residues: 373 loop : -0.95 (0.18), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 264 TYR 0.030 0.002 TYR C 677 PHE 0.023 0.002 PHE D 335 HIS 0.011 0.001 HIS D 287 Details of bonding type rmsd covalent geometry : bond 0.00353 (28050) covalent geometry : angle 0.72531 (37841) SS BOND : bond 0.00475 ( 2) SS BOND : angle 2.79277 ( 4) hydrogen bonds : bond 0.04013 ( 1384) hydrogen bonds : angle 5.97877 ( 3867) Misc. bond : bond 0.00119 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 594 time to evaluate : 1.100 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: A 266 LYS cc_start: 0.8861 (mmtp) cc_final: 0.8617 (mttt) REVERT: A 637 MET cc_start: 0.7728 (tpp) cc_final: 0.7452 (tpp) REVERT: A 639 ILE cc_start: 0.8306 (pt) cc_final: 0.7897 (pt) REVERT: A 699 MET cc_start: 0.8519 (tpp) cc_final: 0.8313 (tpp) REVERT: A 702 MET cc_start: 0.7992 (mmm) cc_final: 0.7727 (mmt) REVERT: A 733 PHE cc_start: 0.7270 (m-80) cc_final: 0.6682 (m-10) REVERT: A 749 LEU cc_start: 0.7900 (mt) cc_final: 0.7542 (tp) REVERT: B 211 ILE cc_start: 0.8995 (mm) cc_final: 0.8743 (mt) REVERT: B 263 GLU cc_start: 0.7767 (pt0) cc_final: 0.7430 (pt0) REVERT: B 280 VAL cc_start: 0.9340 (t) cc_final: 0.9055 (m) REVERT: B 584 MET cc_start: 0.7920 (tpp) cc_final: 0.7609 (tpp) REVERT: B 632 PHE cc_start: 0.7378 (m-80) cc_final: 0.7090 (m-10) REVERT: B 704 ASP cc_start: 0.8111 (t0) cc_final: 0.7464 (t0) REVERT: B 759 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7690 (ttt180) REVERT: B 765 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8220 (mtp85) REVERT: B 813 PHE cc_start: 0.7835 (t80) cc_final: 0.7451 (t80) REVERT: C 282 PHE cc_start: 0.8856 (t80) cc_final: 0.8398 (t80) REVERT: C 325 VAL cc_start: 0.8504 (t) cc_final: 0.8099 (p) REVERT: C 356 GLN cc_start: 0.7980 (tt0) cc_final: 0.7649 (tp40) REVERT: C 577 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8557 (p) REVERT: C 684 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8900 (mt) REVERT: C 702 MET cc_start: 0.8694 (tpp) cc_final: 0.8433 (tpp) REVERT: C 715 THR cc_start: 0.8275 (m) cc_final: 0.7946 (p) REVERT: C 789 LYS cc_start: 0.8990 (mttp) cc_final: 0.8770 (tmmt) REVERT: C 842 LEU cc_start: 0.9032 (tp) cc_final: 0.8691 (pp) REVERT: D 192 GLU cc_start: 0.8195 (mp0) cc_final: 0.7944 (mp0) REVERT: D 265 PHE cc_start: 0.9275 (t80) cc_final: 0.9054 (t80) REVERT: D 321 TYR cc_start: 0.8217 (t80) cc_final: 0.7351 (t80) REVERT: D 332 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: D 699 MET cc_start: 0.7957 (mmp) cc_final: 0.7164 (mmp) REVERT: D 790 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7891 (tp30) REVERT: D 828 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8950 (tp) REVERT: E 174 MET cc_start: 0.8466 (mtp) cc_final: 0.8196 (mtt) REVERT: E 223 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7765 (mt-10) REVERT: E 247 ASP cc_start: 0.8090 (t0) cc_final: 0.7824 (m-30) REVERT: E 263 GLU cc_start: 0.8039 (pp20) cc_final: 0.7670 (pt0) REVERT: E 572 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8394 (tmm) REVERT: E 584 MET cc_start: 0.7669 (mmm) cc_final: 0.7136 (mtt) REVERT: E 601 LEU cc_start: 0.8315 (mp) cc_final: 0.8010 (mp) REVERT: E 665 TYR cc_start: 0.6703 (OUTLIER) cc_final: 0.6279 (m-80) REVERT: F 209 CYS cc_start: 0.8346 (t) cc_final: 0.7968 (p) REVERT: F 211 ILE cc_start: 0.7750 (mt) cc_final: 0.7381 (pt) REVERT: F 223 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8033 (mt-10) REVERT: F 262 GLU cc_start: 0.8406 (tt0) cc_final: 0.7767 (tp30) REVERT: F 321 TYR cc_start: 0.8672 (t80) cc_final: 0.8080 (t80) REVERT: F 336 GLN cc_start: 0.8458 (tt0) cc_final: 0.7922 (tt0) REVERT: F 337 LYS cc_start: 0.8829 (ptpp) cc_final: 0.8592 (mttp) REVERT: F 390 ASP cc_start: 0.8511 (p0) cc_final: 0.7715 (t0) REVERT: F 394 ASP cc_start: 0.8570 (p0) cc_final: 0.8238 (p0) REVERT: F 634 ASP cc_start: 0.7395 (t0) cc_final: 0.7098 (t0) REVERT: F 643 CYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7089 (t) REVERT: F 699 MET cc_start: 0.8970 (tpp) cc_final: 0.8746 (tpp) REVERT: F 738 GLN cc_start: 0.6591 (OUTLIER) cc_final: 0.6275 (pm20) REVERT: F 816 LYS cc_start: 0.7540 (pttp) cc_final: 0.7263 (tptt) REVERT: F 819 TYR cc_start: 0.8011 (t80) cc_final: 0.7605 (t80) outliers start: 128 outliers final: 93 residues processed: 668 average time/residue: 0.1823 time to fit residues: 194.5440 Evaluate side-chains 653 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 551 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 705 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 761 GLU Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 801 HIS Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 634 ASP Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 643 CYS Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 704 ASP Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 828 LEU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 820 SER Chi-restraints excluded: chain E residue 880 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 596 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 643 CYS Chi-restraints excluded: chain F residue 647 SER Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 738 GLN Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 789 LYS Chi-restraints excluded: chain F residue 876 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 236 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 340 optimal weight: 4.9990 chunk 309 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 120 optimal weight: 0.0050 chunk 86 optimal weight: 0.9980 chunk 215 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN A 676 GLN B 781 HIS C 287 HIS C 571 HIS ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS D 801 HIS ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 HIS ** 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 = 0.3722 r_free = 0.3722 target = 0.125882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105768 restraints weight = 62970.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.108960 restraints weight = 33724.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.111060 restraints weight = 20940.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.112277 restraints weight = 14581.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.113301 restraints weight = 11370.152| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.6927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 28059 Z= 0.149 Angle : 0.739 14.782 37845 Z= 0.371 Chirality : 0.046 0.275 4383 Planarity : 0.004 0.063 4839 Dihedral : 11.030 142.234 4035 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.17 % Favored : 93.34 % Rotamer: Outliers : 3.99 % Allowed : 22.40 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 3438 helix: 0.26 (0.12), residues: 1779 sheet: -0.85 (0.26), residues: 373 loop : -0.88 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG C 333 TYR 0.034 0.002 TYR C 677 PHE 0.022 0.002 PHE F 733 HIS 0.013 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00340 (28050) covalent geometry : angle 0.73876 (37841) SS BOND : bond 0.00411 ( 2) SS BOND : angle 2.70126 ( 4) hydrogen bonds : bond 0.03887 ( 1384) hydrogen bonds : angle 5.94128 ( 3867) Misc. bond : bond 0.00201 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 592 time to evaluate : 1.157 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: A 637 MET cc_start: 0.7641 (tpp) cc_final: 0.7392 (tpp) REVERT: A 639 ILE cc_start: 0.8333 (pt) cc_final: 0.8060 (pt) REVERT: A 692 HIS cc_start: 0.7445 (t70) cc_final: 0.7134 (t70) REVERT: A 699 MET cc_start: 0.8456 (tpp) cc_final: 0.8214 (tpp) REVERT: B 211 ILE cc_start: 0.9023 (mm) cc_final: 0.8792 (mt) REVERT: B 263 GLU cc_start: 0.7760 (pt0) cc_final: 0.7542 (pt0) REVERT: B 584 MET cc_start: 0.7933 (tpp) cc_final: 0.7576 (tpp) REVERT: B 585 ASP cc_start: 0.8310 (p0) cc_final: 0.8086 (p0) REVERT: B 662 TYR cc_start: 0.8419 (m-10) cc_final: 0.8191 (m-10) REVERT: B 704 ASP cc_start: 0.8123 (t0) cc_final: 0.7531 (t0) REVERT: B 759 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7673 (ttt180) REVERT: B 765 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8260 (mtp85) REVERT: B 813 PHE cc_start: 0.7837 (t80) cc_final: 0.7379 (t80) REVERT: C 191 GLU cc_start: 0.8279 (pp20) cc_final: 0.7929 (pp20) REVERT: C 192 GLU cc_start: 0.7800 (pm20) cc_final: 0.7379 (pm20) REVERT: C 282 PHE cc_start: 0.8789 (t80) cc_final: 0.8420 (t80) REVERT: C 356 GLN cc_start: 0.7997 (tt0) cc_final: 0.7679 (tp40) REVERT: C 577 SER cc_start: 0.8837 (OUTLIER) cc_final: 0.8502 (p) REVERT: C 685 PHE cc_start: 0.7372 (m-80) cc_final: 0.7101 (m-80) REVERT: C 702 MET cc_start: 0.8712 (tpp) cc_final: 0.8373 (tpp) REVERT: C 715 THR cc_start: 0.8303 (m) cc_final: 0.7940 (p) REVERT: C 789 LYS cc_start: 0.8967 (mttp) cc_final: 0.8758 (tmmt) REVERT: C 842 LEU cc_start: 0.9035 (tp) cc_final: 0.8709 (pp) REVERT: C 877 LEU cc_start: 0.8004 (tp) cc_final: 0.7737 (tp) REVERT: D 192 GLU cc_start: 0.8148 (mp0) cc_final: 0.7880 (mp0) REVERT: D 278 LEU cc_start: 0.8447 (tp) cc_final: 0.8154 (tp) REVERT: D 321 TYR cc_start: 0.8219 (t80) cc_final: 0.7362 (t80) REVERT: D 332 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7383 (tp30) REVERT: D 694 ASP cc_start: 0.8168 (m-30) cc_final: 0.7413 (m-30) REVERT: D 699 MET cc_start: 0.7823 (mmp) cc_final: 0.6966 (mmp) REVERT: D 732 GLU cc_start: 0.7215 (mp0) cc_final: 0.6977 (mp0) REVERT: D 793 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8199 (mm-30) REVERT: D 842 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8379 (tp) REVERT: E 174 MET cc_start: 0.8361 (mtp) cc_final: 0.8041 (mtt) REVERT: E 223 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7848 (mt-10) REVERT: E 247 ASP cc_start: 0.7956 (t0) cc_final: 0.7683 (m-30) REVERT: E 263 GLU cc_start: 0.7952 (pp20) cc_final: 0.7679 (pt0) REVERT: E 393 LEU cc_start: 0.8971 (tt) cc_final: 0.8533 (mm) REVERT: E 572 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8440 (tmm) REVERT: E 584 MET cc_start: 0.7725 (mmm) cc_final: 0.7210 (mtt) REVERT: E 665 TYR cc_start: 0.6567 (OUTLIER) cc_final: 0.6232 (m-80) REVERT: F 174 MET cc_start: 0.8225 (mmp) cc_final: 0.7821 (mmt) REVERT: F 209 CYS cc_start: 0.8056 (t) cc_final: 0.7808 (p) REVERT: F 211 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7388 (pt) REVERT: F 223 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8096 (mt-10) REVERT: F 262 GLU cc_start: 0.8391 (tt0) cc_final: 0.7750 (tp30) REVERT: F 321 TYR cc_start: 0.8650 (t80) cc_final: 0.8097 (t80) REVERT: F 336 GLN cc_start: 0.8461 (tt0) cc_final: 0.7989 (tt0) REVERT: F 337 LYS cc_start: 0.8737 (ptpp) cc_final: 0.8534 (mttp) REVERT: F 380 LYS cc_start: 0.9249 (tppt) cc_final: 0.8479 (tttt) REVERT: F 634 ASP cc_start: 0.7389 (t0) cc_final: 0.7040 (t0) REVERT: F 643 CYS cc_start: 0.7589 (t) cc_final: 0.7388 (t) REVERT: F 654 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8871 (ttmt) REVERT: F 682 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8474 (t) REVERT: F 699 MET cc_start: 0.9003 (tpp) cc_final: 0.8788 (tpp) REVERT: F 819 TYR cc_start: 0.7976 (t80) cc_final: 0.7568 (t80) outliers start: 119 outliers final: 93 residues processed: 659 average time/residue: 0.1776 time to fit residues: 188.1302 Evaluate side-chains 653 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 552 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 761 GLU Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 801 HIS Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 876 CYS Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 828 LEU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 880 LEU Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 596 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 647 SER Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 738 GLN Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 789 LYS Chi-restraints excluded: chain F residue 876 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 263 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 290 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 304 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 319 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN ** A 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN B 781 HIS C 363 HIS ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 GLN ** 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 = 0.3679 r_free = 0.3679 target = 0.122940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102157 restraints weight = 63177.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105190 restraints weight = 34383.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107165 restraints weight = 21841.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.108451 restraints weight = 15579.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.109326 restraints weight = 12266.097| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 28059 Z= 0.196 Angle : 0.775 14.602 37845 Z= 0.392 Chirality : 0.047 0.272 4383 Planarity : 0.005 0.063 4839 Dihedral : 11.107 141.876 4035 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.28 % Favored : 93.22 % Rotamer: Outliers : 3.72 % Allowed : 23.37 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.54 (0.15), residues: 3438 helix: 0.30 (0.12), residues: 1761 sheet: -0.94 (0.26), residues: 373 loop : -0.94 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 333 TYR 0.034 0.002 TYR F 680 PHE 0.021 0.002 PHE F 733 HIS 0.017 0.002 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00445 (28050) covalent geometry : angle 0.77459 (37841) SS BOND : bond 0.00484 ( 2) SS BOND : angle 2.83738 ( 4) hydrogen bonds : bond 0.04083 ( 1384) hydrogen bonds : angle 5.94531 ( 3867) Misc. bond : bond 0.00177 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 576 time to evaluate : 1.108 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 692 HIS cc_start: 0.7724 (t70) cc_final: 0.7498 (t70) REVERT: B 174 MET cc_start: 0.8124 (mtt) cc_final: 0.7911 (ttm) REVERT: B 223 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7921 (mm-30) REVERT: B 257 TYR cc_start: 0.7716 (m-80) cc_final: 0.7362 (m-80) REVERT: B 263 GLU cc_start: 0.7803 (pt0) cc_final: 0.7519 (pt0) REVERT: B 280 VAL cc_start: 0.9393 (t) cc_final: 0.9084 (m) REVERT: B 584 MET cc_start: 0.7958 (tpp) cc_final: 0.7551 (tpp) REVERT: B 585 ASP cc_start: 0.8380 (p0) cc_final: 0.8153 (p0) REVERT: B 704 ASP cc_start: 0.8332 (t0) cc_final: 0.7951 (t0) REVERT: B 722 ILE cc_start: 0.9131 (mm) cc_final: 0.8863 (mm) REVERT: B 765 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8454 (mtp85) REVERT: B 790 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7911 (mm-30) REVERT: B 813 PHE cc_start: 0.7955 (t80) cc_final: 0.7640 (t80) REVERT: B 837 LEU cc_start: 0.9041 (mp) cc_final: 0.8735 (tp) REVERT: C 191 GLU cc_start: 0.8411 (pp20) cc_final: 0.8086 (pp20) REVERT: C 192 GLU cc_start: 0.7956 (pm20) cc_final: 0.7570 (pm20) REVERT: C 282 PHE cc_start: 0.8856 (t80) cc_final: 0.8437 (t80) REVERT: C 577 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8673 (p) REVERT: C 715 THR cc_start: 0.8381 (m) cc_final: 0.8017 (p) REVERT: C 780 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8292 (mt) REVERT: C 789 LYS cc_start: 0.9034 (mttp) cc_final: 0.8807 (tmmt) REVERT: C 877 LEU cc_start: 0.8124 (tp) cc_final: 0.7843 (tp) REVERT: D 192 GLU cc_start: 0.8130 (mp0) cc_final: 0.7881 (mp0) REVERT: D 223 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8244 (mm-30) REVERT: D 278 LEU cc_start: 0.8583 (tp) cc_final: 0.8336 (tp) REVERT: D 290 MET cc_start: 0.3148 (OUTLIER) cc_final: 0.2542 (ttt) REVERT: D 307 ARG cc_start: 0.8060 (mmp-170) cc_final: 0.6864 (mmp-170) REVERT: D 332 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7258 (tp30) REVERT: D 642 ASP cc_start: 0.7744 (t0) cc_final: 0.7510 (t0) REVERT: D 699 MET cc_start: 0.8023 (mmp) cc_final: 0.7230 (mmp) REVERT: D 732 GLU cc_start: 0.7323 (mp0) cc_final: 0.7118 (mp0) REVERT: D 790 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7759 (tt0) REVERT: E 174 MET cc_start: 0.8557 (mtp) cc_final: 0.8287 (mtt) REVERT: E 223 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7843 (mt-10) REVERT: E 263 GLU cc_start: 0.8044 (pp20) cc_final: 0.7518 (pt0) REVERT: E 572 MET cc_start: 0.8817 (ttm) cc_final: 0.8450 (tmm) REVERT: E 584 MET cc_start: 0.7801 (mmm) cc_final: 0.7285 (mtt) REVERT: E 626 LYS cc_start: 0.8790 (tptt) cc_final: 0.8320 (tptt) REVERT: E 665 TYR cc_start: 0.6893 (OUTLIER) cc_final: 0.6538 (m-80) REVERT: E 852 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7395 (mmtt) REVERT: F 209 CYS cc_start: 0.8300 (t) cc_final: 0.7904 (p) REVERT: F 211 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7412 (pt) REVERT: F 223 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8164 (mt-10) REVERT: F 262 GLU cc_start: 0.8465 (tt0) cc_final: 0.7789 (tp30) REVERT: F 290 MET cc_start: 0.6437 (tmm) cc_final: 0.5622 (ttm) REVERT: F 321 TYR cc_start: 0.8733 (t80) cc_final: 0.8186 (t80) REVERT: F 336 GLN cc_start: 0.8585 (tt0) cc_final: 0.8110 (tt0) REVERT: F 337 LYS cc_start: 0.8832 (ptpp) cc_final: 0.8530 (mttp) REVERT: F 380 LYS cc_start: 0.9304 (tppt) cc_final: 0.8550 (tttt) REVERT: F 634 ASP cc_start: 0.7421 (t0) cc_final: 0.7108 (t0) REVERT: F 643 CYS cc_start: 0.7834 (t) cc_final: 0.7582 (t) REVERT: F 682 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8471 (t) REVERT: F 686 ASP cc_start: 0.7876 (t70) cc_final: 0.7521 (t0) REVERT: F 745 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8813 (p) outliers start: 111 outliers final: 90 residues processed: 642 average time/residue: 0.1805 time to fit residues: 186.2685 Evaluate side-chains 643 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 544 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 705 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 761 GLU Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 704 ASP Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 802 TYR Chi-restraints excluded: chain E residue 880 LEU Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 596 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 647 SER Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 680 TYR Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 789 LYS Chi-restraints excluded: chain F residue 876 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 6 optimal weight: 6.9990 chunk 249 optimal weight: 0.9990 chunk 340 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 chunk 310 optimal weight: 6.9990 chunk 12 optimal weight: 0.0000 chunk 48 optimal weight: 8.9990 chunk 183 optimal weight: 0.2980 overall best weight: 1.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN ** A 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 HIS ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.122554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101711 restraints weight = 63525.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.104767 restraints weight = 34726.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.106752 restraints weight = 22015.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107999 restraints weight = 15719.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.108939 restraints weight = 12423.575| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.7280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 28059 Z= 0.181 Angle : 0.781 18.512 37845 Z= 0.394 Chirality : 0.048 0.341 4383 Planarity : 0.005 0.063 4839 Dihedral : 11.048 142.665 4031 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.40 % Favored : 93.14 % Rotamer: Outliers : 3.79 % Allowed : 23.94 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.57 (0.14), residues: 3438 helix: 0.34 (0.12), residues: 1741 sheet: -1.07 (0.26), residues: 374 loop : -0.99 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 333 TYR 0.037 0.002 TYR C 677 PHE 0.025 0.002 PHE C 632 HIS 0.016 0.002 HIS D 287 Details of bonding type rmsd covalent geometry : bond 0.00415 (28050) covalent geometry : angle 0.78062 (37841) SS BOND : bond 0.00699 ( 2) SS BOND : angle 3.25953 ( 4) hydrogen bonds : bond 0.04021 ( 1384) hydrogen bonds : angle 5.93387 ( 3867) Misc. bond : bond 0.00126 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 572 time to evaluate : 1.179 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: B 174 MET cc_start: 0.8037 (mtt) cc_final: 0.7815 (ttm) REVERT: B 223 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7760 (mm-30) REVERT: B 257 TYR cc_start: 0.7662 (m-80) cc_final: 0.7339 (m-80) REVERT: B 263 GLU cc_start: 0.7819 (pt0) cc_final: 0.7551 (pt0) REVERT: B 584 MET cc_start: 0.7946 (tpp) cc_final: 0.7543 (tpp) REVERT: B 585 ASP cc_start: 0.8378 (p0) cc_final: 0.8166 (p0) REVERT: B 704 ASP cc_start: 0.8389 (t0) cc_final: 0.7963 (t0) REVERT: B 722 ILE cc_start: 0.9090 (mm) cc_final: 0.8820 (mm) REVERT: B 759 ARG cc_start: 0.8294 (tpp80) cc_final: 0.7841 (ttt180) REVERT: B 765 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8367 (mtp85) REVERT: B 790 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7877 (mm-30) REVERT: B 813 PHE cc_start: 0.7929 (t80) cc_final: 0.7609 (t80) REVERT: B 837 LEU cc_start: 0.9038 (mp) cc_final: 0.8769 (tp) REVERT: C 191 GLU cc_start: 0.8342 (pp20) cc_final: 0.8044 (pp20) REVERT: C 192 GLU cc_start: 0.7871 (pm20) cc_final: 0.7547 (pm20) REVERT: C 263 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7865 (tm-30) REVERT: C 282 PHE cc_start: 0.8751 (t80) cc_final: 0.8335 (t80) REVERT: C 307 ARG cc_start: 0.7815 (mmp-170) cc_final: 0.7179 (mmp-170) REVERT: C 332 GLU cc_start: 0.7491 (tp30) cc_final: 0.7136 (mm-30) REVERT: C 356 GLN cc_start: 0.8044 (tt0) cc_final: 0.7693 (tp40) REVERT: C 584 MET cc_start: 0.7716 (mmt) cc_final: 0.7345 (mmm) REVERT: C 588 LYS cc_start: 0.9184 (mtpp) cc_final: 0.8923 (mttp) REVERT: C 715 THR cc_start: 0.8271 (m) cc_final: 0.7927 (p) REVERT: C 780 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8268 (mt) REVERT: C 789 LYS cc_start: 0.9036 (mttp) cc_final: 0.8828 (tmmt) REVERT: D 192 GLU cc_start: 0.8087 (mp0) cc_final: 0.7862 (mp0) REVERT: D 278 LEU cc_start: 0.8511 (tp) cc_final: 0.8257 (tp) REVERT: D 290 MET cc_start: 0.3183 (OUTLIER) cc_final: 0.2442 (ttt) REVERT: D 307 ARG cc_start: 0.7970 (mmp-170) cc_final: 0.7138 (mmp-170) REVERT: D 321 TYR cc_start: 0.8212 (t80) cc_final: 0.7231 (t80) REVERT: D 332 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7379 (tp30) REVERT: D 333 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7530 (tmt170) REVERT: D 642 ASP cc_start: 0.7768 (t0) cc_final: 0.7535 (t0) REVERT: D 699 MET cc_start: 0.7912 (mmp) cc_final: 0.7111 (mmp) REVERT: D 790 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7843 (tt0) REVERT: D 828 LEU cc_start: 0.9318 (tt) cc_final: 0.8975 (tp) REVERT: E 174 MET cc_start: 0.8507 (mtp) cc_final: 0.8225 (mtt) REVERT: E 223 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7782 (mt-10) REVERT: E 263 GLU cc_start: 0.8059 (pp20) cc_final: 0.7598 (pt0) REVERT: E 320 GLU cc_start: 0.8437 (mp0) cc_final: 0.8110 (mp0) REVERT: E 572 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8453 (tmm) REVERT: E 584 MET cc_start: 0.7696 (mmm) cc_final: 0.7365 (mtt) REVERT: E 852 LYS cc_start: 0.7767 (mmtt) cc_final: 0.7390 (mmtt) REVERT: F 209 CYS cc_start: 0.8212 (t) cc_final: 0.7744 (p) REVERT: F 211 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7426 (pt) REVERT: F 223 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8159 (mt-10) REVERT: F 262 GLU cc_start: 0.8447 (tt0) cc_final: 0.7779 (tp30) REVERT: F 290 MET cc_start: 0.6301 (tmm) cc_final: 0.5555 (ttm) REVERT: F 300 ILE cc_start: 0.7327 (pt) cc_final: 0.7003 (mm) REVERT: F 320 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7949 (mm-30) REVERT: F 321 TYR cc_start: 0.8718 (t80) cc_final: 0.8175 (t80) REVERT: F 336 GLN cc_start: 0.8511 (tt0) cc_final: 0.8044 (tt0) REVERT: F 337 LYS cc_start: 0.8809 (ptpp) cc_final: 0.8529 (mttp) REVERT: F 380 LYS cc_start: 0.9295 (tppt) cc_final: 0.8538 (tttt) REVERT: F 634 ASP cc_start: 0.7302 (t0) cc_final: 0.6981 (t0) REVERT: F 673 ASN cc_start: 0.7658 (m-40) cc_final: 0.7011 (m-40) REVERT: F 682 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8488 (t) REVERT: F 745 SER cc_start: 0.9086 (OUTLIER) cc_final: 0.8828 (p) outliers start: 113 outliers final: 95 residues processed: 635 average time/residue: 0.1841 time to fit residues: 187.6960 Evaluate side-chains 648 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 544 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 705 ASP Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 761 GLU Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 786 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 704 ASP Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 261 PHE Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 334 ARG Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 596 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 802 TYR Chi-restraints excluded: chain E residue 880 LEU Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 596 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 789 LYS Chi-restraints excluded: chain F residue 835 GLU Chi-restraints excluded: chain F residue 876 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 250 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 228 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 243 optimal weight: 9.9990 chunk 256 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 538 GLN ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 HIS C 673 ASN ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 HIS ** 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 = 0.3703 r_free = 0.3703 target = 0.124622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.103892 restraints weight = 63035.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.106931 restraints weight = 34571.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.108978 restraints weight = 22033.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.110227 restraints weight = 15679.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111198 restraints weight = 12369.766| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.7432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28059 Z= 0.154 Angle : 0.761 15.795 37845 Z= 0.384 Chirality : 0.047 0.323 4383 Planarity : 0.004 0.062 4839 Dihedral : 10.917 145.498 4031 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.52 % Favored : 93.05 % Rotamer: Outliers : 3.49 % Allowed : 24.65 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.51 (0.14), residues: 3438 helix: 0.42 (0.12), residues: 1724 sheet: -1.13 (0.26), residues: 374 loop : -0.98 (0.18), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 333 TYR 0.035 0.002 TYR C 677 PHE 0.023 0.002 PHE D 630 HIS 0.016 0.001 HIS A 781 Details of bonding type rmsd covalent geometry : bond 0.00352 (28050) covalent geometry : angle 0.76026 (37841) SS BOND : bond 0.00309 ( 2) SS BOND : angle 2.59599 ( 4) hydrogen bonds : bond 0.03914 ( 1384) hydrogen bonds : angle 5.90490 ( 3867) Misc. bond : bond 0.00092 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5400.58 seconds wall clock time: 94 minutes 15.87 seconds (5655.87 seconds total)