Starting phenix.real_space_refine on Mon Sep 14 01:44:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5vya_8746/09_2026/5vya_8746.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vya_8746/09_2026/5vya_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/5vya_8746/09_2026/5vya_8746.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5vya_8746/09_2026/5vya_8746.cif" model { file = "/net/cci-nas-00/data/ceres_data/5vya_8746/09_2026/5vya_8746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vya_8746/09_2026/5vya_8746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5vya_8746/09_2026/5vya_8746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vya_8746/09_2026/5vya_8746.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.67, per 1000 atoms: 0.20 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: 2.22 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: 0.95 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: 5.24 Time building geometry restraints manager: 2.84 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: 17004 34.38 - 68.75: 263 68.75 - 103.12: 25 103.12 - 137.50: 7 137.50 - 171.87: 2 Dihedral angle restraints: 17301 sinusoidal: 7182 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 17298 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: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 23.630 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 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 : 12.340 171.874 10749 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/Z covalent geometry : bond 0.02393 / 1.30 (28050) covalent geometry : angle 1.94239 / 1.30 (37841) SS BOND : bond 0.00879 / 0.46 ( 2) SS BOND : angle 6.13179 / 3.21 ( 4) hydrogen bonds : bond 0.16815 / 11.42 ( 1384) hydrogen bonds : angle 7.98178 / 5.75 ( 3867) Misc. bond : bond 0.32486 / 19.17 ( 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 : 1.065 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: 0.2090 time to fit residues: 389.1628 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 : 0.812 ------------------------------------------------------------------------------- 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... ** 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 F 737 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.126305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.105691 restraints weight = 63212.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.108653 restraints weight = 34931.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.110659 restraints weight = 22412.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.112026 restraints weight = 16032.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112788 restraints weight = 12484.291| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 28059 Z= 0.272 Angle : 0.926 12.949 37845 Z= 0.482 Chirality : 0.052 0.254 4383 Planarity : 0.007 0.251 4839 Dihedral : 10.839 155.253 3920 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.56 % Favored : 93.83 % Rotamer: Outliers : 3.76 % Allowed : 13.55 % Favored : 82.70 % 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: -0.71 (0.14), residues: 3438 helix: -0.05 (0.12), residues: 1765 sheet: -0.79 (0.25), residues: 362 loop : -0.76 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D 826 TYR 0.039 0.003 TYR F 650 PHE 0.030 0.003 PHE F 630 HIS 0.012 0.002 HIS A 692 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.27 (28050) covalent geometry : angle 0.92461 / 0.48 (37841) SS BOND : bond 0.02003 / 1.05 ( 2) SS BOND : angle 4.52565 / 2.42 ( 4) hydrogen bonds : bond 0.06090 / 4.06 ( 1384) hydrogen bonds : angle 6.56661 / 4.75 ( 3867) Misc. bond : bond 0.00210 / 0.13 ( 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 928 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 816 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7088 (mm-30) REVERT: A 387 ARG cc_start: 0.7518 (mmm-85) cc_final: 0.7243 (mmm-85) REVERT: A 572 MET cc_start: 0.8995 (ptm) cc_final: 0.8768 (ptm) REVERT: A 762 PHE cc_start: 0.8145 (t80) cc_final: 0.7928 (t80) REVERT: A 813 PHE cc_start: 0.5910 (t80) cc_final: 0.4887 (t80) REVERT: B 211 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8521 (mt) REVERT: B 257 TYR cc_start: 0.7678 (m-80) cc_final: 0.7385 (m-80) REVERT: B 290 MET cc_start: 0.7273 (ttm) cc_final: 0.6836 (ttm) REVERT: B 299 ASN cc_start: 0.6909 (m-40) cc_final: 0.6704 (m110) REVERT: B 333 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7642 (tpt170) REVERT: B 359 TYR cc_start: 0.8202 (m-80) cc_final: 0.7862 (m-10) REVERT: B 387 ARG cc_start: 0.8591 (mmp80) cc_final: 0.7626 (mmm160) REVERT: B 572 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7812 (ppp) REVERT: B 632 PHE cc_start: 0.7745 (m-80) cc_final: 0.7445 (m-80) REVERT: B 635 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7205 (pt0) REVERT: B 637 MET cc_start: 0.7271 (tpt) cc_final: 0.6981 (tpt) REVERT: B 689 GLU cc_start: 0.8428 (pm20) cc_final: 0.7932 (pm20) REVERT: B 708 ILE cc_start: 0.8285 (mt) cc_final: 0.7282 (mt) REVERT: B 725 MET cc_start: 0.8482 (mtm) cc_final: 0.8276 (mtt) REVERT: B 819 TYR cc_start: 0.7399 (t80) cc_final: 0.7173 (t80) REVERT: C 173 ASP cc_start: 0.8405 (t0) cc_final: 0.8132 (t0) REVERT: C 192 GLU cc_start: 0.7330 (mp0) cc_final: 0.7019 (mp0) REVERT: C 266 LYS cc_start: 0.8775 (tttp) cc_final: 0.8354 (ttmt) REVERT: C 288 MET cc_start: 0.8090 (mmm) cc_final: 0.7428 (mmm) REVERT: C 310 LEU cc_start: 0.8870 (mt) cc_final: 0.8638 (mt) REVERT: C 372 LEU cc_start: 0.9152 (mt) cc_final: 0.8949 (mt) REVERT: C 387 ARG cc_start: 0.8907 (mmp80) cc_final: 0.8559 (mmt-90) REVERT: C 560 LYS cc_start: 0.8414 (mttt) cc_final: 0.8064 (mtmm) REVERT: C 654 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8498 (ttmm) REVERT: C 675 LEU cc_start: 0.8927 (mm) cc_final: 0.8527 (mt) REVERT: C 684 LEU cc_start: 0.9356 (tp) cc_final: 0.9138 (tt) REVERT: C 690 LYS cc_start: 0.8305 (mmmt) cc_final: 0.7784 (mmtt) REVERT: C 751 MET cc_start: 0.8692 (mmm) cc_final: 0.8333 (mmm) REVERT: C 789 LYS cc_start: 0.9083 (mttp) cc_final: 0.8788 (ttmm) REVERT: C 807 THR cc_start: 0.8392 (m) cc_final: 0.7970 (p) REVERT: C 842 LEU cc_start: 0.9181 (tp) cc_final: 0.8820 (pp) REVERT: D 204 ILE cc_start: 0.8738 (mm) cc_final: 0.8514 (tp) REVERT: D 223 GLU cc_start: 0.8005 (tt0) cc_final: 0.7710 (tt0) REVERT: D 290 MET cc_start: 0.6098 (mtm) cc_final: 0.5804 (mtm) REVERT: D 579 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7570 (mt-10) REVERT: D 583 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7325 (mm-40) REVERT: D 618 SER cc_start: 0.8886 (p) cc_final: 0.8629 (t) REVERT: D 620 LYS cc_start: 0.8659 (mtmt) cc_final: 0.8366 (mtmm) REVERT: D 623 LEU cc_start: 0.9371 (tp) cc_final: 0.9106 (tt) REVERT: D 626 LYS cc_start: 0.9155 (mmtt) cc_final: 0.8786 (mmmt) REVERT: D 694 ASP cc_start: 0.8049 (m-30) cc_final: 0.7633 (m-30) REVERT: D 786 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8348 (mm) REVERT: D 802 TYR cc_start: 0.6583 (p90) cc_final: 0.6329 (p90) REVERT: E 223 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7927 (mt-10) REVERT: E 238 LEU cc_start: 0.8852 (tp) cc_final: 0.8613 (tt) REVERT: E 247 ASP cc_start: 0.8273 (t0) cc_final: 0.8054 (t0) REVERT: E 322 ARG cc_start: 0.8263 (mtm-85) cc_final: 0.7671 (mtm-85) REVERT: E 572 MET cc_start: 0.8682 (ttm) cc_final: 0.8473 (ttm) REVERT: E 626 LYS cc_start: 0.8921 (tptt) cc_final: 0.8443 (tptp) REVERT: E 790 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: F 170 TYR cc_start: 0.7293 (m-10) cc_final: 0.7059 (m-10) REVERT: F 209 CYS cc_start: 0.8362 (t) cc_final: 0.7866 (p) REVERT: F 223 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8101 (tt0) REVERT: F 232 ASP cc_start: 0.6377 (t0) cc_final: 0.5640 (t70) REVERT: F 262 GLU cc_start: 0.8571 (tt0) cc_final: 0.7843 (tp30) REVERT: F 283 ILE cc_start: 0.8293 (mm) cc_final: 0.8013 (mp) REVERT: F 285 GLU cc_start: 0.6488 (mp0) cc_final: 0.6063 (mp0) REVERT: F 290 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.5851 (mtp) REVERT: F 380 LYS cc_start: 0.9309 (tppt) cc_final: 0.8584 (tttt) REVERT: F 381 ARG cc_start: 0.8173 (ttt180) cc_final: 0.7548 (tpm170) REVERT: F 393 LEU cc_start: 0.9403 (mm) cc_final: 0.9195 (mm) REVERT: F 605 ARG cc_start: 0.6616 (mmm-85) cc_final: 0.6284 (mmm160) REVERT: F 634 ASP cc_start: 0.7264 (t0) cc_final: 0.7047 (t0) REVERT: F 682 VAL cc_start: 0.8674 (p) cc_final: 0.8183 (t) REVERT: F 837 LEU cc_start: 0.9361 (mt) cc_final: 0.9147 (mm) REVERT: F 838 ASN cc_start: 0.8441 (m-40) cc_final: 0.8070 (p0) outliers start: 112 outliers final: 63 residues processed: 885 average time/residue: 0.1787 time to fit residues: 248.0051 Evaluate side-chains 677 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 608 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 290 MET 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: 2.9990 chunk 215 optimal weight: 4.9990 chunk 339 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 257 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 299 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 GLN ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 HIS ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN ** 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** E 363 HIS ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 712 GLN F 781 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.121662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.100550 restraints weight = 64123.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.103588 restraints weight = 34839.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.105582 restraints weight = 22110.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.106973 restraints weight = 15801.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107799 restraints weight = 12335.999| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 28059 Z= 0.252 Angle : 0.839 10.533 37845 Z= 0.433 Chirality : 0.050 0.225 4383 Planarity : 0.006 0.058 4839 Dihedral : 10.655 145.079 3907 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.40 % Favored : 93.05 % Rotamer: Outliers : 4.96 % Allowed : 16.97 % Favored : 78.07 % 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: -0.73 (0.14), residues: 3438 helix: 0.07 (0.12), residues: 1759 sheet: -1.11 (0.25), residues: 362 loop : -0.88 (0.18), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 843 TYR 0.032 0.003 TYR F 817 PHE 0.022 0.002 PHE F 282 HIS 0.012 0.002 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.25 (28050) covalent geometry : angle 0.83821 / 0.43 (37841) SS BOND : bond 0.00409 / 0.21 ( 2) SS BOND : angle 3.45962 / 1.86 ( 4) hydrogen bonds : bond 0.05202 / 3.51 ( 1384) hydrogen bonds : angle 6.40976 / 4.61 ( 3867) Misc. bond : bond 0.00628 / 0.31 ( 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 798 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 650 time to evaluate : 1.026 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 287 HIS cc_start: 0.8086 (p90) cc_final: 0.7705 (p-80) REVERT: A 288 MET cc_start: 0.8571 (mmm) cc_final: 0.8302 (mtp) REVERT: A 359 TYR cc_start: 0.5741 (m-80) cc_final: 0.5018 (m-80) REVERT: A 640 ARG cc_start: 0.6910 (ptm-80) cc_final: 0.6701 (ptm-80) REVERT: A 733 PHE cc_start: 0.7214 (m-80) cc_final: 0.6747 (m-10) REVERT: A 749 LEU cc_start: 0.8018 (mt) cc_final: 0.7658 (tp) REVERT: A 767 SER cc_start: 0.8345 (m) cc_final: 0.7927 (t) REVERT: B 205 LYS cc_start: 0.8379 (ttpt) cc_final: 0.8153 (ttpt) REVERT: B 257 TYR cc_start: 0.7831 (m-80) cc_final: 0.7433 (m-80) REVERT: B 290 MET cc_start: 0.7150 (ttm) cc_final: 0.6902 (tpp) REVERT: B 387 ARG cc_start: 0.8394 (mmp80) cc_final: 0.8032 (mmt180) REVERT: B 584 MET cc_start: 0.7840 (mpp) cc_final: 0.7572 (tpp) REVERT: B 635 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7252 (pt0) REVERT: B 662 TYR cc_start: 0.8603 (m-10) cc_final: 0.8374 (m-10) REVERT: B 708 ILE cc_start: 0.8253 (mt) cc_final: 0.8004 (mt) REVERT: B 722 ILE cc_start: 0.9350 (mm) cc_final: 0.9079 (mm) REVERT: B 762 PHE cc_start: 0.9214 (t80) cc_final: 0.8915 (t80) REVERT: B 765 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8073 (mtt90) REVERT: B 833 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8391 (tm-30) REVERT: B 843 ARG cc_start: 0.7357 (mmt-90) cc_final: 0.7101 (mmt-90) REVERT: C 173 ASP cc_start: 0.8534 (t0) cc_final: 0.8297 (t0) REVERT: C 266 LYS cc_start: 0.8858 (tttp) cc_final: 0.8613 (ttpt) REVERT: C 269 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8557 (mt) REVERT: C 332 GLU cc_start: 0.7734 (tp30) cc_final: 0.7532 (tp30) REVERT: C 372 LEU cc_start: 0.9108 (mt) cc_final: 0.8891 (mt) REVERT: C 387 ARG cc_start: 0.8984 (mmp80) cc_final: 0.8549 (mmt-90) REVERT: C 549 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8969 (p) REVERT: C 560 LYS cc_start: 0.8415 (mttt) cc_final: 0.8160 (mtmm) REVERT: C 654 LYS cc_start: 0.8987 (ttmm) cc_final: 0.8675 (ttmm) REVERT: C 684 LEU cc_start: 0.9350 (tp) cc_final: 0.9063 (tp) REVERT: C 715 THR cc_start: 0.8500 (m) cc_final: 0.8090 (p) REVERT: C 789 LYS cc_start: 0.9055 (mttp) cc_final: 0.8851 (tmmt) REVERT: C 807 THR cc_start: 0.8291 (m) cc_final: 0.7815 (p) REVERT: D 204 ILE cc_start: 0.8812 (mm) cc_final: 0.8493 (tp) REVERT: D 290 MET cc_start: 0.6164 (mtm) cc_final: 0.5788 (mtm) REVERT: D 321 TYR cc_start: 0.8332 (t80) cc_final: 0.8067 (t80) REVERT: D 332 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7283 (tp30) REVERT: D 333 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8059 (tmt170) REVERT: D 572 MET cc_start: 0.8501 (ptm) cc_final: 0.8291 (ptp) REVERT: D 579 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7519 (mp0) REVERT: D 694 ASP cc_start: 0.7964 (m-30) cc_final: 0.7612 (m-30) REVERT: D 717 ASP cc_start: 0.8182 (m-30) cc_final: 0.7909 (t70) REVERT: E 169 LYS cc_start: 0.8783 (tttt) cc_final: 0.8560 (tppt) REVERT: E 223 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8112 (mt-10) REVERT: E 263 GLU cc_start: 0.8315 (pp20) cc_final: 0.7998 (pt0) REVERT: E 322 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.7801 (mtm-85) REVERT: E 345 VAL cc_start: 0.9207 (m) cc_final: 0.8931 (t) REVERT: E 646 LEU cc_start: 0.8970 (mt) cc_final: 0.8606 (mt) REVERT: E 761 GLU cc_start: 0.8053 (pm20) cc_final: 0.7788 (pm20) REVERT: F 209 CYS cc_start: 0.8536 (t) cc_final: 0.8127 (p) REVERT: F 211 ILE cc_start: 0.7935 (mt) cc_final: 0.7518 (pt) REVERT: F 223 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8074 (mt-10) REVERT: F 232 ASP cc_start: 0.6489 (t0) cc_final: 0.5866 (t70) REVERT: F 262 GLU cc_start: 0.8602 (tt0) cc_final: 0.7899 (tp30) REVERT: F 270 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8092 (tppt) REVERT: F 285 GLU cc_start: 0.6491 (mp0) cc_final: 0.6162 (mp0) REVERT: F 380 LYS cc_start: 0.9247 (tppt) cc_final: 0.8493 (tttt) REVERT: F 390 ASP cc_start: 0.8476 (p0) cc_final: 0.7829 (t0) REVERT: F 634 ASP cc_start: 0.7172 (t0) cc_final: 0.6892 (t0) REVERT: F 643 CYS cc_start: 0.7660 (m) cc_final: 0.7443 (t) REVERT: F 686 ASP cc_start: 0.7699 (t0) cc_final: 0.7357 (t70) REVERT: F 699 MET cc_start: 0.8913 (tpp) cc_final: 0.8653 (tpp) outliers start: 148 outliers final: 86 residues processed: 753 average time/residue: 0.1814 time to fit residues: 215.2306 Evaluate side-chains 641 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 550 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain A residue 252 THR 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 659 THR 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 268 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 324 ILE 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 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 543 SER Chi-restraints excluded: chain C residue 549 THR 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 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 332 GLU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 403 VAL 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 695 VAL Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 704 ASP 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 378 LEU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 627 VAL 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 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 882 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 240 optimal weight: 1.9990 chunk 310 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 331 optimal weight: 8.9990 chunk 260 optimal weight: 4.9990 chunk 303 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 188 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN A 701 GLN A 781 HIS A 883 HIS B 299 ASN ** B 571 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** ** 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 712 GLN F 712 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.123403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.102222 restraints weight = 63165.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105282 restraints weight = 34455.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.107318 restraints weight = 21845.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.108655 restraints weight = 15623.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.109471 restraints weight = 12244.293| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28059 Z= 0.180 Angle : 0.749 9.840 37845 Z= 0.387 Chirality : 0.047 0.381 4383 Planarity : 0.005 0.068 4839 Dihedral : 10.334 137.444 3907 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.28 % Favored : 93.25 % Rotamer: Outliers : 4.33 % Allowed : 19.58 % Favored : 76.09 % 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: -0.68 (0.14), residues: 3438 helix: 0.13 (0.12), residues: 1769 sheet: -1.03 (0.25), residues: 377 loop : -0.92 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 333 TYR 0.029 0.002 TYR F 321 PHE 0.040 0.002 PHE F 282 HIS 0.016 0.002 HIS F 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (28050) covalent geometry : angle 0.74803 / 0.39 (37841) SS BOND : bond 0.01201 / 0.63 ( 2) SS BOND : angle 3.37390 / 1.83 ( 4) hydrogen bonds : bond 0.04640 / 3.13 ( 1384) hydrogen bonds : angle 6.20327 / 4.47 ( 3867) Misc. bond : bond 0.00209 / 0.15 ( 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 768 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 639 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6182 (mp0) REVERT: A 359 TYR cc_start: 0.5924 (m-80) cc_final: 0.5132 (m-80) REVERT: A 699 MET cc_start: 0.8698 (tpp) cc_final: 0.8463 (tpp) REVERT: A 733 PHE cc_start: 0.7213 (m-80) cc_final: 0.6735 (m-10) REVERT: A 749 LEU cc_start: 0.7972 (mt) cc_final: 0.7595 (tp) REVERT: A 751 MET cc_start: 0.8868 (tmm) cc_final: 0.8643 (tmm) REVERT: B 257 TYR cc_start: 0.7730 (m-80) cc_final: 0.7367 (m-80) REVERT: B 263 GLU cc_start: 0.7911 (pt0) cc_final: 0.7641 (pt0) REVERT: B 266 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8280 (mttm) REVERT: B 280 VAL cc_start: 0.9502 (t) cc_final: 0.9230 (m) REVERT: B 290 MET cc_start: 0.7161 (ttm) cc_final: 0.6918 (tpp) REVERT: B 336 GLN cc_start: 0.8616 (tp40) cc_final: 0.8325 (tp-100) REVERT: B 348 THR cc_start: 0.9258 (m) cc_final: 0.9009 (p) REVERT: B 635 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7285 (pt0) REVERT: B 702 MET cc_start: 0.7867 (mmm) cc_final: 0.7547 (mmm) REVERT: B 722 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.9035 (mm) REVERT: B 725 MET cc_start: 0.8710 (mtm) cc_final: 0.7472 (mtm) REVERT: B 765 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8072 (mtp85) REVERT: B 833 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8428 (tm-30) REVERT: B 843 ARG cc_start: 0.7429 (mmt-90) cc_final: 0.7195 (mmt-90) REVERT: C 387 ARG cc_start: 0.8936 (mmp80) cc_final: 0.8578 (mmt-90) REVERT: C 560 LYS cc_start: 0.8343 (mttt) cc_final: 0.8072 (mtmm) REVERT: C 654 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8459 (ttmm) REVERT: C 684 LEU cc_start: 0.9304 (tp) cc_final: 0.8990 (tp) REVERT: C 702 MET cc_start: 0.8945 (tpp) cc_final: 0.8514 (tpt) REVERT: C 715 THR cc_start: 0.8448 (m) cc_final: 0.7798 (p) REVERT: C 755 ARG cc_start: 0.8239 (mtp-110) cc_final: 0.7925 (mtp-110) REVERT: C 789 LYS cc_start: 0.9053 (mttp) cc_final: 0.8817 (ttmm) REVERT: C 807 THR cc_start: 0.8215 (m) cc_final: 0.7707 (p) REVERT: D 282 PHE cc_start: 0.8573 (t80) cc_final: 0.8317 (t80) REVERT: D 287 HIS cc_start: 0.8687 (p-80) cc_final: 0.8374 (p90) REVERT: D 321 TYR cc_start: 0.8295 (t80) cc_final: 0.7908 (t80) REVERT: D 332 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7267 (tp30) REVERT: D 333 ARG cc_start: 0.8369 (ttp80) cc_final: 0.7949 (tmt-80) REVERT: D 694 ASP cc_start: 0.7978 (m-30) cc_final: 0.7679 (m-30) REVERT: D 800 LYS cc_start: 0.6076 (mptt) cc_final: 0.5774 (mptt) REVERT: E 169 LYS cc_start: 0.8792 (tttt) cc_final: 0.8554 (tppt) REVERT: E 174 MET cc_start: 0.8733 (mtp) cc_final: 0.8499 (mtp) REVERT: E 223 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7980 (mt-10) REVERT: E 263 GLU cc_start: 0.8109 (pp20) cc_final: 0.7694 (pt0) REVERT: E 827 PRO cc_start: 0.9553 (Cg_endo) cc_final: 0.9309 (Cg_exo) REVERT: E 880 LEU cc_start: 0.8428 (mp) cc_final: 0.8159 (mp) REVERT: F 209 CYS cc_start: 0.8567 (t) cc_final: 0.7982 (p) REVERT: F 211 ILE cc_start: 0.7802 (mt) cc_final: 0.7401 (pt) REVERT: F 262 GLU cc_start: 0.8558 (tt0) cc_final: 0.7355 (tp30) REVERT: F 290 MET cc_start: 0.6483 (tmm) cc_final: 0.5673 (ttm) REVERT: F 321 TYR cc_start: 0.8762 (t80) cc_final: 0.8354 (t80) REVERT: F 380 LYS cc_start: 0.9181 (tppt) cc_final: 0.8465 (tttt) REVERT: F 390 ASP cc_start: 0.8473 (p0) cc_final: 0.7676 (t0) REVERT: F 634 ASP cc_start: 0.7218 (t0) cc_final: 0.6830 (t0) REVERT: F 699 MET cc_start: 0.8986 (tpp) cc_final: 0.8657 (tpp) REVERT: F 719 SER cc_start: 0.8997 (p) cc_final: 0.8638 (t) REVERT: F 838 ASN cc_start: 0.8292 (m-40) cc_final: 0.7919 (p0) outliers start: 129 outliers final: 82 residues processed: 718 average time/residue: 0.1707 time to fit residues: 194.4214 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 : 1.090 ------------------------------------------------------------------------------- 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 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 725 MET 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 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 541 VAL 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 703 LEU Chi-restraints excluded: chain B residue 722 ILE 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 B residue 801 HIS Chi-restraints excluded: chain B residue 878 GLU 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 273 GLU 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 577 SER Chi-restraints excluded: chain C residue 720 ASN 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 168 SER 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 332 GLU 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 721 CYS Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 814 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 400 CYS Chi-restraints excluded: chain E residue 653 SER Chi-restraints excluded: chain E residue 665 TYR 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 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 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: 10.0000 chunk 94 optimal weight: 0.2980 chunk 324 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 287 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 155 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 GLN A 363 HIS A 538 GLN A 676 GLN A 829 ASN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS D 720 ASN ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 882 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.123190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.101964 restraints weight = 63368.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.104985 restraints weight = 34515.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.107014 restraints weight = 21913.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.108315 restraints weight = 15644.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.109188 restraints weight = 12295.744| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.6282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 28059 Z= 0.172 Angle : 0.740 14.043 37845 Z= 0.377 Chirality : 0.047 0.309 4383 Planarity : 0.005 0.064 4839 Dihedral : 10.216 138.833 3907 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.28 % Favored : 93.19 % Rotamer: Outliers : 4.33 % Allowed : 20.22 % 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: 0.17 (0.12), residues: 1770 sheet: -0.99 (0.25), residues: 379 loop : -0.91 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 552 TYR 0.030 0.002 TYR B 802 PHE 0.037 0.002 PHE F 282 HIS 0.011 0.001 HIS C 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (28050) covalent geometry : angle 0.73938 / 0.38 (37841) SS BOND : bond 0.00399 / 0.21 ( 2) SS BOND : angle 2.94443 / 1.58 ( 4) hydrogen bonds : bond 0.04336 / 2.91 ( 1384) hydrogen bonds : angle 6.07602 / 4.39 ( 3867) Misc. bond : bond 0.00047 / 0.03 ( 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 726 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 597 time to evaluate : 1.053 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: A 287 HIS cc_start: 0.8167 (p90) cc_final: 0.7957 (p-80) REVERT: A 333 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8038 (ptm160) REVERT: A 359 TYR cc_start: 0.5708 (m-80) cc_final: 0.4999 (m-80) REVERT: A 733 PHE cc_start: 0.7257 (m-80) cc_final: 0.6730 (m-10) REVERT: A 749 LEU cc_start: 0.7994 (mt) cc_final: 0.7622 (tp) REVERT: B 257 TYR cc_start: 0.7697 (m-80) cc_final: 0.7325 (m-80) REVERT: B 263 GLU cc_start: 0.7891 (pt0) cc_final: 0.7562 (pt0) REVERT: B 280 VAL cc_start: 0.9511 (t) cc_final: 0.9271 (m) REVERT: B 336 GLN cc_start: 0.8619 (tp40) cc_final: 0.8366 (tp-100) REVERT: B 387 ARG cc_start: 0.8446 (mmp80) cc_final: 0.8218 (mmt180) REVERT: B 584 MET cc_start: 0.8055 (tpp) cc_final: 0.7727 (tpp) REVERT: B 635 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7250 (pt0) REVERT: B 662 TYR cc_start: 0.8506 (m-10) cc_final: 0.8293 (m-10) REVERT: B 722 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8966 (mm) REVERT: B 765 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8075 (mtp85) REVERT: B 837 LEU cc_start: 0.9138 (tp) cc_final: 0.8831 (tp) REVERT: B 877 LEU cc_start: 0.8173 (mm) cc_final: 0.7758 (mt) REVERT: C 387 ARG cc_start: 0.8940 (mmp80) cc_final: 0.8405 (mmt-90) REVERT: C 654 LYS cc_start: 0.8728 (ttmm) cc_final: 0.8467 (ttmm) REVERT: C 684 LEU cc_start: 0.9195 (tp) cc_final: 0.8959 (tp) REVERT: C 715 THR cc_start: 0.8496 (m) cc_final: 0.8058 (p) REVERT: C 755 ARG cc_start: 0.8233 (mtp-110) cc_final: 0.7929 (mtp-110) REVERT: C 789 LYS cc_start: 0.9053 (mttp) cc_final: 0.8829 (ttmm) REVERT: C 821 ASP cc_start: 0.7971 (p0) cc_final: 0.7644 (p0) REVERT: C 848 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: D 321 TYR cc_start: 0.8352 (t80) cc_final: 0.7811 (t80) REVERT: D 332 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7216 (tp30) REVERT: D 694 ASP cc_start: 0.7977 (m-30) cc_final: 0.7706 (m-30) REVERT: D 828 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8882 (tp) REVERT: E 169 LYS cc_start: 0.8804 (tttt) cc_final: 0.8556 (tppt) REVERT: E 223 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7951 (mt-10) REVERT: E 263 GLU cc_start: 0.8115 (pp20) cc_final: 0.7715 (pt0) REVERT: E 759 ARG cc_start: 0.7869 (ttm110) cc_final: 0.7399 (ttm-80) REVERT: F 209 CYS cc_start: 0.8639 (t) cc_final: 0.8158 (p) REVERT: F 211 ILE cc_start: 0.7845 (mt) cc_final: 0.7457 (pt) REVERT: F 262 GLU cc_start: 0.8539 (tt0) cc_final: 0.7768 (tp30) REVERT: F 288 MET cc_start: 0.8380 (mmp) cc_final: 0.8148 (tpt) REVERT: F 380 LYS cc_start: 0.9124 (tppt) cc_final: 0.8433 (tttt) REVERT: F 390 ASP cc_start: 0.8330 (p0) cc_final: 0.7489 (t0) REVERT: F 634 ASP cc_start: 0.7230 (t0) cc_final: 0.6905 (t0) REVERT: F 699 MET cc_start: 0.9009 (tpp) cc_final: 0.8727 (tpp) REVERT: F 719 SER cc_start: 0.8947 (p) cc_final: 0.8478 (t) REVERT: F 816 LYS cc_start: 0.7726 (pttt) cc_final: 0.7522 (tptt) outliers start: 129 outliers final: 90 residues processed: 675 average time/residue: 0.1751 time to fit residues: 187.7293 Evaluate side-chains 624 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 528 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 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 168 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 299 ASN 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 541 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 722 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 175 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 248 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 543 SER Chi-restraints excluded: chain C residue 552 ARG Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 727 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 848 GLU 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 324 ILE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 372 LEU 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 721 CYS 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 196 THR Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 ASP 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 393 LEU Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain F residue 232 ASP 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 399 SER Chi-restraints excluded: chain F residue 554 THR Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 638 MET 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 720 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 50 optimal weight: 6.9990 chunk 167 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 232 optimal weight: 6.9990 chunk 297 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 281 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 GLN ** A 692 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 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E 712 GLN F 781 HIS F 882 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.120854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099688 restraints weight = 63783.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102614 restraints weight = 35194.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.104543 restraints weight = 22627.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.105750 restraints weight = 16366.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.106722 restraints weight = 13039.684| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.6641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 28059 Z= 0.223 Angle : 0.778 13.874 37845 Z= 0.397 Chirality : 0.048 0.245 4383 Planarity : 0.005 0.064 4839 Dihedral : 10.349 142.430 3907 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.25 % Favored : 93.22 % Rotamer: Outliers : 5.03 % Allowed : 21.13 % Favored : 73.84 % 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: -0.72 (0.14), residues: 3438 helix: 0.12 (0.12), residues: 1775 sheet: -1.01 (0.27), residues: 353 loop : -1.00 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 264 TYR 0.030 0.002 TYR D 677 PHE 0.026 0.002 PHE D 630 HIS 0.015 0.002 HIS D 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (28050) covalent geometry : angle 0.77783 / 0.40 (37841) SS BOND : bond 0.00572 / 0.29 ( 2) SS BOND : angle 2.99902 / 1.61 ( 4) hydrogen bonds : bond 0.04380 / 2.94 ( 1384) hydrogen bonds : angle 6.06858 / 4.38 ( 3867) Misc. bond : bond 0.00076 / 0.05 ( 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 718 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 568 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LYS cc_start: 0.8861 (mmtp) cc_final: 0.8560 (mttt) REVERT: A 294 LYS cc_start: 0.8246 (mttt) cc_final: 0.7756 (mtmm) REVERT: A 333 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8094 (ptm160) REVERT: A 699 MET cc_start: 0.8829 (tpp) cc_final: 0.8592 (tpp) REVERT: A 721 CYS cc_start: 0.8563 (p) cc_final: 0.7156 (p) REVERT: A 733 PHE cc_start: 0.7407 (m-80) cc_final: 0.6841 (m-10) REVERT: A 749 LEU cc_start: 0.7988 (mt) cc_final: 0.7622 (tp) REVERT: B 205 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8342 (ttpt) REVERT: B 211 ILE cc_start: 0.9150 (mm) cc_final: 0.8873 (mt) REVERT: B 257 TYR cc_start: 0.7851 (m-80) cc_final: 0.7477 (m-80) REVERT: B 263 GLU cc_start: 0.7919 (pt0) cc_final: 0.7549 (pt0) REVERT: B 280 VAL cc_start: 0.9532 (t) cc_final: 0.9217 (m) REVERT: B 387 ARG cc_start: 0.8400 (mmp80) cc_final: 0.8073 (mmt180) REVERT: B 584 MET cc_start: 0.7922 (tpp) cc_final: 0.7610 (tpp) REVERT: B 722 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8920 (mm) REVERT: B 765 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8325 (mtp85) REVERT: B 813 PHE cc_start: 0.7897 (t80) cc_final: 0.7529 (t80) REVERT: B 837 LEU cc_start: 0.9212 (tp) cc_final: 0.8893 (tp) REVERT: C 282 PHE cc_start: 0.9315 (t80) cc_final: 0.9112 (t80) REVERT: C 307 ARG cc_start: 0.8043 (mmp-170) cc_final: 0.7251 (mmp-170) REVERT: C 387 ARG cc_start: 0.8952 (mmp80) cc_final: 0.8489 (mmt-90) REVERT: C 654 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8630 (ttmm) REVERT: C 684 LEU cc_start: 0.9282 (tp) cc_final: 0.9034 (tp) REVERT: C 715 THR cc_start: 0.8521 (m) cc_final: 0.8097 (p) REVERT: C 755 ARG cc_start: 0.8350 (mtp-110) cc_final: 0.8002 (mtp-110) REVERT: C 789 LYS cc_start: 0.9066 (mttp) cc_final: 0.8843 (tmmt) REVERT: C 848 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: D 321 TYR cc_start: 0.8319 (t80) cc_final: 0.7508 (t80) REVERT: D 332 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7243 (tp30) REVERT: D 333 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7801 (tmt170) REVERT: D 579 GLU cc_start: 0.6866 (mp0) cc_final: 0.6614 (mp0) REVERT: D 694 ASP cc_start: 0.7940 (m-30) cc_final: 0.7730 (m-30) REVERT: D 699 MET cc_start: 0.8047 (mmp) cc_final: 0.7235 (mmp) REVERT: D 785 ASP cc_start: 0.8487 (p0) cc_final: 0.7669 (t0) REVERT: D 828 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8897 (tp) REVERT: E 169 LYS cc_start: 0.8911 (tttt) cc_final: 0.8664 (tppt) REVERT: E 223 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8008 (mt-10) REVERT: E 263 GLU cc_start: 0.8151 (pp20) cc_final: 0.7709 (pt0) REVERT: E 638 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8480 (ttm) REVERT: E 665 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6676 (m-10) REVERT: F 209 CYS cc_start: 0.8611 (t) cc_final: 0.7941 (p) REVERT: F 211 ILE cc_start: 0.7859 (mt) cc_final: 0.7522 (pt) REVERT: F 223 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8383 (mt-10) REVERT: F 262 GLU cc_start: 0.8506 (tt0) cc_final: 0.7750 (tp30) REVERT: F 287 HIS cc_start: 0.9208 (p-80) cc_final: 0.8965 (p-80) REVERT: F 321 TYR cc_start: 0.8825 (t80) cc_final: 0.8429 (t80) REVERT: F 390 ASP cc_start: 0.8303 (p0) cc_final: 0.7726 (t0) REVERT: F 634 ASP cc_start: 0.7320 (t0) cc_final: 0.6971 (t0) REVERT: F 673 ASN cc_start: 0.7741 (m-40) cc_final: 0.7383 (t0) REVERT: F 699 MET cc_start: 0.8962 (tpp) cc_final: 0.8667 (tpp) REVERT: F 719 SER cc_start: 0.8961 (p) cc_final: 0.8611 (t) REVERT: F 738 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6566 (pm20) REVERT: F 816 LYS cc_start: 0.7790 (pttt) cc_final: 0.7498 (tptt) REVERT: F 838 ASN cc_start: 0.8348 (m-40) cc_final: 0.7880 (p0) outliers start: 150 outliers final: 108 residues processed: 656 average time/residue: 0.1693 time to fit residues: 178.0779 Evaluate side-chains 642 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 524 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain A residue 246 LEU 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 835 GLU 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 221 ILE 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 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 324 ILE 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 637 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 703 LEU Chi-restraints excluded: chain B residue 722 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 248 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 278 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 399 SER Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 552 ARG Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 727 SER 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 848 GLU 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 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 372 LEU 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 672 THR 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 721 CYS Chi-restraints excluded: chain D residue 727 SER Chi-restraints excluded: chain D residue 763 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 261 PHE Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 ASP 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 388 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 638 MET Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 554 THR Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 638 MET 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 720 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 8 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 309 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 GLN ** A 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.121880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100805 restraints weight = 63192.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.103788 restraints weight = 34757.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105743 restraints weight = 22249.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.107013 restraints weight = 16069.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.107941 restraints weight = 12722.507| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28059 Z= 0.183 Angle : 0.750 17.170 37845 Z= 0.380 Chirality : 0.047 0.231 4383 Planarity : 0.005 0.064 4839 Dihedral : 10.238 142.657 3907 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.20 % Favored : 93.31 % Rotamer: Outliers : 4.63 % Allowed : 22.64 % Favored : 72.74 % 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: 0.19 (0.12), residues: 1766 sheet: -1.05 (0.26), residues: 372 loop : -0.96 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 264 TYR 0.032 0.002 TYR D 677 PHE 0.020 0.002 PHE D 630 HIS 0.011 0.001 HIS D 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (28050) covalent geometry : angle 0.74928 / 0.38 (37841) SS BOND : bond 0.00610 / 0.32 ( 2) SS BOND : angle 3.34507 / 1.81 ( 4) hydrogen bonds : bond 0.04173 / 2.81 ( 1384) hydrogen bonds : angle 5.96591 / 4.31 ( 3867) Misc. bond : bond 0.00039 / 0.02 ( 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 702 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 564 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LYS cc_start: 0.8860 (mmtp) cc_final: 0.8619 (mttt) REVERT: A 285 GLU cc_start: 0.6273 (mp0) cc_final: 0.5712 (mp0) REVERT: A 294 LYS cc_start: 0.8297 (mttt) cc_final: 0.7875 (mtmm) REVERT: A 721 CYS cc_start: 0.8602 (p) cc_final: 0.7189 (p) REVERT: A 733 PHE cc_start: 0.7409 (m-80) cc_final: 0.6851 (m-10) REVERT: A 749 LEU cc_start: 0.8037 (mt) cc_final: 0.7652 (tp) REVERT: B 205 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8284 (ttpt) REVERT: B 211 ILE cc_start: 0.9070 (mm) cc_final: 0.8845 (mt) REVERT: B 257 TYR cc_start: 0.7820 (m-80) cc_final: 0.7476 (m-80) REVERT: B 263 GLU cc_start: 0.7868 (pt0) cc_final: 0.7450 (pt0) REVERT: B 280 VAL cc_start: 0.9288 (t) cc_final: 0.9009 (m) REVERT: B 331 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.8017 (m-10) REVERT: B 387 ARG cc_start: 0.8351 (mmp80) cc_final: 0.8089 (mmt180) REVERT: B 584 MET cc_start: 0.7909 (tpp) cc_final: 0.7549 (tpp) REVERT: B 765 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8334 (mtp85) REVERT: B 813 PHE cc_start: 0.7993 (t80) cc_final: 0.7690 (t80) REVERT: B 837 LEU cc_start: 0.9193 (tp) cc_final: 0.8978 (mp) REVERT: B 877 LEU cc_start: 0.7508 (mt) cc_final: 0.7152 (mp) REVERT: C 191 GLU cc_start: 0.8379 (pp20) cc_final: 0.8063 (pp20) REVERT: C 288 MET cc_start: 0.8867 (mmt) cc_final: 0.8632 (mmt) REVERT: C 307 ARG cc_start: 0.8010 (mmp-170) cc_final: 0.7177 (mmp-170) REVERT: C 387 ARG cc_start: 0.8960 (mmp80) cc_final: 0.8461 (mmt-90) REVERT: C 654 LYS cc_start: 0.8898 (ttmm) cc_final: 0.8528 (ttmm) REVERT: C 715 THR cc_start: 0.8389 (m) cc_final: 0.8089 (p) REVERT: C 755 ARG cc_start: 0.8340 (mtp-110) cc_final: 0.8013 (mtp-110) REVERT: C 789 LYS cc_start: 0.9043 (mttp) cc_final: 0.8832 (tmmt) REVERT: D 278 LEU cc_start: 0.8571 (tp) cc_final: 0.8294 (tp) REVERT: D 694 ASP cc_start: 0.7906 (m-30) cc_final: 0.7602 (m-30) REVERT: D 699 MET cc_start: 0.7932 (mmp) cc_final: 0.7099 (mmp) REVERT: D 828 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8834 (tp) REVERT: E 263 GLU cc_start: 0.8115 (pp20) cc_final: 0.7554 (pt0) REVERT: E 638 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8456 (ttm) REVERT: F 174 MET cc_start: 0.8479 (mmm) cc_final: 0.8217 (mmt) REVERT: F 209 CYS cc_start: 0.8503 (t) cc_final: 0.8067 (p) REVERT: F 211 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7516 (pt) REVERT: F 223 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8380 (mt-10) REVERT: F 262 GLU cc_start: 0.8466 (tt0) cc_final: 0.7703 (tp30) REVERT: F 290 MET cc_start: 0.6193 (tmm) cc_final: 0.5452 (ttm) REVERT: F 380 LYS cc_start: 0.9285 (tppt) cc_final: 0.8520 (tttt) REVERT: F 634 ASP cc_start: 0.7364 (t0) cc_final: 0.7034 (t0) REVERT: F 673 ASN cc_start: 0.7618 (m-40) cc_final: 0.7275 (t0) REVERT: F 699 MET cc_start: 0.8965 (tpp) cc_final: 0.8702 (tpp) REVERT: F 719 SER cc_start: 0.8938 (p) cc_final: 0.8566 (t) REVERT: F 816 LYS cc_start: 0.7787 (pttt) cc_final: 0.7456 (tptt) REVERT: F 831 LEU cc_start: 0.9320 (tp) cc_final: 0.9048 (tp) REVERT: F 835 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7320 (mt-10) REVERT: F 838 ASN cc_start: 0.8343 (m-40) cc_final: 0.7835 (p0) outliers start: 138 outliers final: 103 residues processed: 646 average time/residue: 0.1665 time to fit residues: 174.4887 Evaluate side-chains 626 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 518 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 236 THR 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 672 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 MET 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 221 ILE Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 637 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 703 LEU 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 C residue 238 LEU Chi-restraints excluded: chain C residue 248 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 399 SER Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 552 ARG 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 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 324 ILE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 553 LEU 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 672 THR 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 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 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 295 ASP 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 393 LEU Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 638 MET Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 279 ILE 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 554 THR Chi-restraints excluded: chain F residue 556 ILE 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 680 TYR Chi-restraints excluded: chain F residue 720 ASN 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: 0.9980 chunk 138 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 340 optimal weight: 0.5980 chunk 309 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 GLN ** A 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 GLN B 571 HIS ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 HIS C 363 HIS ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.123652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.103029 restraints weight = 63551.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.106030 restraints weight = 34740.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.108049 restraints weight = 22122.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.109316 restraints weight = 15762.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110239 restraints weight = 12428.471| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.7103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 28059 Z= 0.153 Angle : 0.728 13.997 37845 Z= 0.371 Chirality : 0.046 0.250 4383 Planarity : 0.005 0.064 4839 Dihedral : 10.011 140.469 3903 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.37 % Favored : 93.14 % Rotamer: Outliers : 3.72 % Allowed : 23.47 % Favored : 72.80 % 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: -0.53 (0.14), residues: 3438 helix: 0.34 (0.12), residues: 1737 sheet: -0.97 (0.26), residues: 374 loop : -0.95 (0.18), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 322 TYR 0.037 0.002 TYR D 677 PHE 0.025 0.002 PHE D 244 HIS 0.010 0.001 HIS C 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (28050) covalent geometry : angle 0.72768 / 0.37 (37841) SS BOND : bond 0.00848 / 0.44 ( 2) SS BOND : angle 2.99074 / 1.61 ( 4) hydrogen bonds : bond 0.03961 / 2.67 ( 1384) hydrogen bonds : angle 5.89527 / 4.25 ( 3867) Misc. bond : bond 0.00045 / 0.03 ( 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 692 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 581 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LYS cc_start: 0.8846 (mmtp) cc_final: 0.8616 (mttt) REVERT: A 285 GLU cc_start: 0.6275 (mp0) cc_final: 0.5708 (mp0) REVERT: A 692 HIS cc_start: 0.7665 (t70) cc_final: 0.7312 (t70) REVERT: A 699 MET cc_start: 0.8462 (tpp) cc_final: 0.8050 (tpt) REVERT: A 721 CYS cc_start: 0.8640 (p) cc_final: 0.7282 (p) REVERT: A 733 PHE cc_start: 0.7373 (m-80) cc_final: 0.6782 (m-10) REVERT: A 749 LEU cc_start: 0.7995 (mt) cc_final: 0.7626 (tp) REVERT: B 205 LYS cc_start: 0.8714 (ttpt) cc_final: 0.8293 (ttpt) REVERT: B 211 ILE cc_start: 0.9037 (mm) cc_final: 0.8835 (mt) REVERT: B 257 TYR cc_start: 0.7648 (m-80) cc_final: 0.7313 (m-80) REVERT: B 263 GLU cc_start: 0.7756 (pt0) cc_final: 0.7478 (pt0) REVERT: B 331 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8129 (m-10) REVERT: B 387 ARG cc_start: 0.8252 (mmp80) cc_final: 0.8002 (mmt180) REVERT: B 579 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7890 (pm20) REVERT: B 584 MET cc_start: 0.7805 (tpp) cc_final: 0.7459 (tpp) REVERT: B 662 TYR cc_start: 0.8584 (m-10) cc_final: 0.8345 (m-10) REVERT: B 722 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8739 (mm) REVERT: B 759 ARG cc_start: 0.8198 (tpp80) cc_final: 0.7729 (ttt180) REVERT: B 765 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8426 (mtp85) REVERT: B 813 PHE cc_start: 0.7964 (t80) cc_final: 0.7762 (t80) REVERT: B 837 LEU cc_start: 0.9211 (tp) cc_final: 0.8990 (mp) REVERT: B 877 LEU cc_start: 0.7311 (mt) cc_final: 0.6935 (mp) REVERT: C 191 GLU cc_start: 0.8357 (pp20) cc_final: 0.8057 (pp20) REVERT: C 288 MET cc_start: 0.8865 (mmt) cc_final: 0.8639 (mmt) REVERT: C 307 ARG cc_start: 0.7937 (mmp-170) cc_final: 0.7121 (mmp-170) REVERT: C 552 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8455 (tmm-80) REVERT: C 577 SER cc_start: 0.8999 (OUTLIER) cc_final: 0.8633 (p) REVERT: C 654 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8453 (ttmm) REVERT: C 789 LYS cc_start: 0.9071 (mttp) cc_final: 0.8802 (ttmm) REVERT: C 877 LEU cc_start: 0.8106 (tp) cc_final: 0.7813 (tp) REVERT: D 191 GLU cc_start: 0.8304 (tp30) cc_final: 0.8103 (tp30) REVERT: D 278 LEU cc_start: 0.8600 (tp) cc_final: 0.8265 (tp) REVERT: D 321 TYR cc_start: 0.8275 (t80) cc_final: 0.7438 (t80) REVERT: D 332 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7349 (tp30) REVERT: D 333 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7653 (tmt170) REVERT: D 694 ASP cc_start: 0.7921 (m-30) cc_final: 0.7532 (m-30) REVERT: D 699 MET cc_start: 0.7878 (mmp) cc_final: 0.7029 (mmp) REVERT: D 828 LEU cc_start: 0.9193 (tt) cc_final: 0.8879 (tp) REVERT: E 263 GLU cc_start: 0.8049 (pp20) cc_final: 0.7553 (pt0) REVERT: F 174 MET cc_start: 0.8539 (mmm) cc_final: 0.8285 (mmt) REVERT: F 209 CYS cc_start: 0.8361 (t) cc_final: 0.8055 (p) REVERT: F 211 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7453 (pt) REVERT: F 223 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8462 (mt-10) REVERT: F 262 GLU cc_start: 0.8479 (tt0) cc_final: 0.7686 (tp30) REVERT: F 300 ILE cc_start: 0.7459 (pt) cc_final: 0.7119 (mm) REVERT: F 337 LYS cc_start: 0.8815 (ptpp) cc_final: 0.8446 (mttm) REVERT: F 380 LYS cc_start: 0.9283 (tppt) cc_final: 0.8561 (tttt) REVERT: F 390 ASP cc_start: 0.8193 (p0) cc_final: 0.7401 (t0) REVERT: F 634 ASP cc_start: 0.7302 (t0) cc_final: 0.6957 (t0) REVERT: F 665 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.7467 (t80) REVERT: F 673 ASN cc_start: 0.7485 (m-40) cc_final: 0.7161 (t0) REVERT: F 699 MET cc_start: 0.8949 (tpp) cc_final: 0.8688 (tpp) REVERT: F 816 LYS cc_start: 0.7817 (pttt) cc_final: 0.7459 (tptt) REVERT: F 831 LEU cc_start: 0.9278 (tp) cc_final: 0.9025 (tp) REVERT: F 835 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7260 (mt-10) REVERT: F 838 ASN cc_start: 0.8311 (m-40) cc_final: 0.7905 (p0) REVERT: F 877 LEU cc_start: 0.7859 (mp) cc_final: 0.7407 (tt) outliers start: 111 outliers final: 88 residues processed: 647 average time/residue: 0.1707 time to fit residues: 176.3113 Evaluate side-chains 632 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 534 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 672 THR Chi-restraints excluded: chain A residue 695 VAL 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 184 ASP Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 637 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 703 LEU Chi-restraints excluded: chain B residue 722 ILE 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 878 GLU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 248 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 399 SER Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 552 ARG Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 749 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 324 ILE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 553 LEU 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 672 THR Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 697 THR 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 261 PHE 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 393 LEU Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 546 ILE Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 232 ASP 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 554 THR Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 643 CYS Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 665 TYR Chi-restraints excluded: chain F residue 680 TYR Chi-restraints excluded: chain F residue 720 ASN Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 789 LYS Chi-restraints excluded: chain F residue 876 CYS Chi-restraints excluded: chain F residue 883 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 263 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 290 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 304 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 319 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 ASN A 538 GLN A 676 GLN ** A 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 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** ** F 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 882 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.124371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103977 restraints weight = 63036.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.106985 restraints weight = 34491.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.108960 restraints weight = 21921.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110297 restraints weight = 15637.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.111050 restraints weight = 12209.327| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.7278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 28059 Z= 0.148 Angle : 0.741 15.081 37845 Z= 0.373 Chirality : 0.046 0.274 4383 Planarity : 0.005 0.064 4839 Dihedral : 9.902 139.605 3903 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.34 % Favored : 93.22 % Rotamer: Outliers : 3.66 % Allowed : 24.48 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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: -0.47 (0.14), residues: 3438 helix: 0.38 (0.12), residues: 1742 sheet: -0.91 (0.27), residues: 373 loop : -0.93 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 202 TYR 0.026 0.002 TYR F 680 PHE 0.022 0.002 PHE D 244 HIS 0.016 0.002 HIS D 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (28050) covalent geometry : angle 0.74100 / 0.37 (37841) SS BOND : bond 0.01554 / 0.82 ( 2) SS BOND : angle 2.61390 / 1.43 ( 4) hydrogen bonds : bond 0.03877 / 2.61 ( 1384) hydrogen bonds : angle 5.86176 / 4.23 ( 3867) Misc. bond : bond 0.00050 / 0.03 ( 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 698 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 589 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLU cc_start: 0.6242 (mp0) cc_final: 0.5517 (mp0) REVERT: A 346 ARG cc_start: 0.7001 (tpt170) cc_final: 0.6497 (tpp-160) REVERT: A 553 LEU cc_start: 0.8293 (tp) cc_final: 0.7925 (mm) REVERT: A 692 HIS cc_start: 0.7727 (t70) cc_final: 0.7419 (t70) REVERT: A 699 MET cc_start: 0.8384 (tpp) cc_final: 0.8178 (tpt) REVERT: A 721 CYS cc_start: 0.8634 (p) cc_final: 0.7354 (p) REVERT: A 733 PHE cc_start: 0.7366 (m-80) cc_final: 0.6798 (m-10) REVERT: A 749 LEU cc_start: 0.7952 (mt) cc_final: 0.7596 (tp) REVERT: B 205 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8261 (ttpt) REVERT: B 206 SER cc_start: 0.9155 (p) cc_final: 0.8874 (p) REVERT: B 257 TYR cc_start: 0.7652 (m-80) cc_final: 0.7337 (m-80) REVERT: B 263 GLU cc_start: 0.7766 (pt0) cc_final: 0.7483 (pt0) REVERT: B 331 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8140 (m-10) REVERT: B 373 VAL cc_start: 0.9154 (m) cc_final: 0.8887 (p) REVERT: B 387 ARG cc_start: 0.8195 (mmp80) cc_final: 0.7971 (mmt180) REVERT: B 584 MET cc_start: 0.7817 (tpp) cc_final: 0.7461 (tpp) REVERT: B 662 TYR cc_start: 0.8589 (m-10) cc_final: 0.8385 (m-10) REVERT: B 702 MET cc_start: 0.7929 (mpp) cc_final: 0.7450 (mmm) REVERT: B 722 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8854 (mm) REVERT: B 751 MET cc_start: 0.8618 (mtp) cc_final: 0.7430 (ttm) REVERT: B 759 ARG cc_start: 0.8244 (tpp80) cc_final: 0.7817 (ttt180) REVERT: B 765 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8455 (mtp85) REVERT: B 813 PHE cc_start: 0.7941 (t80) cc_final: 0.7638 (t80) REVERT: B 877 LEU cc_start: 0.7318 (mt) cc_final: 0.6917 (mp) REVERT: C 192 GLU cc_start: 0.7530 (pm20) cc_final: 0.7203 (pm20) REVERT: C 263 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7951 (tm-30) REVERT: C 307 ARG cc_start: 0.7944 (mmp-170) cc_final: 0.7128 (mmp-170) REVERT: C 312 VAL cc_start: 0.9543 (t) cc_final: 0.9314 (p) REVERT: C 577 SER cc_start: 0.8941 (t) cc_final: 0.8664 (p) REVERT: C 684 LEU cc_start: 0.9110 (tp) cc_final: 0.8815 (mt) REVERT: C 789 LYS cc_start: 0.9067 (mttp) cc_final: 0.8824 (tmmt) REVERT: C 877 LEU cc_start: 0.8074 (tp) cc_final: 0.7769 (tp) REVERT: D 278 LEU cc_start: 0.8538 (tp) cc_final: 0.8288 (tp) REVERT: D 680 TYR cc_start: 0.8017 (t80) cc_final: 0.7802 (t80) REVERT: D 694 ASP cc_start: 0.7808 (m-30) cc_final: 0.7476 (m-30) REVERT: D 699 MET cc_start: 0.7808 (mmp) cc_final: 0.6963 (mmp) REVERT: D 732 GLU cc_start: 0.7308 (mp0) cc_final: 0.7080 (mp0) REVERT: D 790 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7862 (tt0) REVERT: D 828 LEU cc_start: 0.9241 (tt) cc_final: 0.8910 (tp) REVERT: D 842 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8492 (tp) REVERT: E 263 GLU cc_start: 0.8039 (pp20) cc_final: 0.7521 (pt0) REVERT: E 271 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: F 174 MET cc_start: 0.8535 (mmm) cc_final: 0.8273 (mmt) REVERT: F 209 CYS cc_start: 0.8399 (t) cc_final: 0.7992 (p) REVERT: F 211 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7476 (pt) REVERT: F 223 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8463 (mt-10) REVERT: F 262 GLU cc_start: 0.8488 (tt0) cc_final: 0.7683 (tp30) REVERT: F 288 MET cc_start: 0.8383 (mmm) cc_final: 0.8140 (mmm) REVERT: F 300 ILE cc_start: 0.7470 (pt) cc_final: 0.7180 (mm) REVERT: F 337 LYS cc_start: 0.8793 (ptpp) cc_final: 0.8470 (mttm) REVERT: F 380 LYS cc_start: 0.9262 (tppt) cc_final: 0.8503 (tttt) REVERT: F 390 ASP cc_start: 0.8179 (p0) cc_final: 0.7350 (t0) REVERT: F 634 ASP cc_start: 0.7386 (t0) cc_final: 0.7047 (t0) REVERT: F 665 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7441 (t80) REVERT: F 699 MET cc_start: 0.8937 (tpp) cc_final: 0.8681 (tpp) REVERT: F 816 LYS cc_start: 0.7844 (pttt) cc_final: 0.7459 (tptt) REVERT: F 831 LEU cc_start: 0.9249 (tp) cc_final: 0.8980 (tp) REVERT: F 835 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7121 (mt-10) REVERT: F 838 ASN cc_start: 0.8348 (m-40) cc_final: 0.7950 (p0) REVERT: F 877 LEU cc_start: 0.7800 (mp) cc_final: 0.7341 (tt) outliers start: 109 outliers final: 90 residues processed: 657 average time/residue: 0.1717 time to fit residues: 182.1006 Evaluate side-chains 632 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 535 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE 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 261 PHE 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 845 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 637 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 703 LEU Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 722 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 878 GLU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 248 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 399 SER Chi-restraints excluded: chain C residue 552 ARG Chi-restraints excluded: chain C residue 749 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 233 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 553 LEU 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 672 THR 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 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 248 LEU Chi-restraints excluded: chain E residue 261 PHE Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 275 SER 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 393 LEU Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 546 ILE Chi-restraints excluded: chain E residue 596 LEU Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 232 ASP 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 554 THR Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 643 CYS Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 665 TYR Chi-restraints excluded: chain F residue 720 ASN 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: 8.9990 chunk 249 optimal weight: 0.9990 chunk 340 optimal weight: 0.0000 chunk 80 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 282 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 12 optimal weight: 0.0040 chunk 48 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN A 538 GLN ** A 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 ASN B 299 ASN B 319 ASN ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 GLN ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.123896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.103379 restraints weight = 63544.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.106423 restraints weight = 34555.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.108465 restraints weight = 21892.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.109836 restraints weight = 15545.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.110693 restraints weight = 12079.959| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.7411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 28059 Z= 0.152 Angle : 0.765 14.951 37845 Z= 0.386 Chirality : 0.047 0.319 4383 Planarity : 0.005 0.068 4839 Dihedral : 9.873 139.489 3901 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.46 % Favored : 93.11 % Rotamer: Outliers : 3.62 % Allowed : 24.85 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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: -0.46 (0.15), residues: 3438 helix: 0.41 (0.12), residues: 1745 sheet: -0.90 (0.27), residues: 373 loop : -0.97 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 333 TYR 0.033 0.002 TYR D 677 PHE 0.050 0.002 PHE D 244 HIS 0.012 0.002 HIS C 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (28050) covalent geometry : angle 0.76477 / 0.39 (37841) SS BOND : bond 0.00211 / 0.10 ( 2) SS BOND : angle 2.82741 / 1.53 ( 4) hydrogen bonds : bond 0.03880 / 2.64 ( 1384) hydrogen bonds : angle 5.84482 / 4.22 ( 3867) Misc. bond : bond 0.00060 / 0.04 ( 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 668 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 560 time to evaluate : 0.772 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: A 279 ILE cc_start: 0.8502 (mm) cc_final: 0.8233 (tt) REVERT: A 346 ARG cc_start: 0.7072 (tpt170) cc_final: 0.6575 (tpp-160) REVERT: A 538 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7350 (pp30) REVERT: A 553 LEU cc_start: 0.8284 (tp) cc_final: 0.7955 (mm) REVERT: A 692 HIS cc_start: 0.7649 (t70) cc_final: 0.7373 (t70) REVERT: A 699 MET cc_start: 0.8468 (tpp) cc_final: 0.8118 (tpt) REVERT: A 721 CYS cc_start: 0.8676 (p) cc_final: 0.7427 (p) REVERT: A 733 PHE cc_start: 0.7365 (m-80) cc_final: 0.6813 (m-10) REVERT: A 749 LEU cc_start: 0.7951 (mt) cc_final: 0.7593 (tp) REVERT: B 205 LYS cc_start: 0.8693 (ttpt) cc_final: 0.8251 (ttpt) REVERT: B 206 SER cc_start: 0.9170 (p) cc_final: 0.8907 (p) REVERT: B 257 TYR cc_start: 0.7640 (m-80) cc_final: 0.7312 (m-80) REVERT: B 263 GLU cc_start: 0.7797 (pt0) cc_final: 0.7504 (pt0) REVERT: B 331 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.8123 (m-10) REVERT: B 373 VAL cc_start: 0.9101 (m) cc_final: 0.8845 (p) REVERT: B 387 ARG cc_start: 0.8198 (mmp80) cc_final: 0.7992 (mmt180) REVERT: B 584 MET cc_start: 0.7814 (tpp) cc_final: 0.7457 (tpp) REVERT: B 722 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8747 (mm) REVERT: B 759 ARG cc_start: 0.8297 (tpp80) cc_final: 0.7862 (ttt180) REVERT: B 765 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8444 (mtp85) REVERT: B 813 PHE cc_start: 0.7914 (t80) cc_final: 0.7584 (t80) REVERT: B 877 LEU cc_start: 0.7225 (mt) cc_final: 0.6779 (mp) REVERT: C 263 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7984 (tm-30) REVERT: C 307 ARG cc_start: 0.7887 (mmp-170) cc_final: 0.7068 (mmp-170) REVERT: C 312 VAL cc_start: 0.9498 (t) cc_final: 0.9246 (p) REVERT: C 332 GLU cc_start: 0.7687 (tp30) cc_final: 0.7395 (mm-30) REVERT: C 552 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8425 (tmm-80) REVERT: C 577 SER cc_start: 0.8962 (t) cc_final: 0.8648 (p) REVERT: C 584 MET cc_start: 0.7649 (mmt) cc_final: 0.7349 (mmm) REVERT: C 588 LYS cc_start: 0.9204 (mtpp) cc_final: 0.8962 (mttp) REVERT: C 684 LEU cc_start: 0.9030 (tp) cc_final: 0.8820 (mt) REVERT: C 789 LYS cc_start: 0.9088 (mttp) cc_final: 0.8847 (tmmt) REVERT: C 877 LEU cc_start: 0.8081 (tp) cc_final: 0.7791 (tp) REVERT: D 278 LEU cc_start: 0.8548 (tp) cc_final: 0.8299 (tp) REVERT: D 332 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7477 (tp30) REVERT: D 650 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.6658 (m-80) REVERT: D 699 MET cc_start: 0.7869 (mmp) cc_final: 0.7009 (mmp) REVERT: D 732 GLU cc_start: 0.7275 (mp0) cc_final: 0.7073 (mp0) REVERT: D 790 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7858 (tt0) REVERT: D 828 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8973 (tp) REVERT: D 842 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8480 (tp) REVERT: D 875 GLU cc_start: 0.7672 (tt0) cc_final: 0.7071 (tt0) REVERT: E 223 GLU cc_start: 0.8107 (tt0) cc_final: 0.7838 (tt0) REVERT: E 263 GLU cc_start: 0.8041 (pp20) cc_final: 0.7527 (pt0) REVERT: E 271 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: F 174 MET cc_start: 0.8516 (mmm) cc_final: 0.8275 (mmt) REVERT: F 209 CYS cc_start: 0.8406 (t) cc_final: 0.8016 (p) REVERT: F 211 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7507 (pt) REVERT: F 223 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8500 (mt-10) REVERT: F 262 GLU cc_start: 0.8519 (tt0) cc_final: 0.7724 (tp30) REVERT: F 288 MET cc_start: 0.8400 (mmm) cc_final: 0.8180 (mmm) REVERT: F 300 ILE cc_start: 0.7462 (pt) cc_final: 0.7187 (mm) REVERT: F 337 LYS cc_start: 0.8780 (ptpp) cc_final: 0.8519 (mttm) REVERT: F 380 LYS cc_start: 0.9246 (tppt) cc_final: 0.8471 (tttt) REVERT: F 390 ASP cc_start: 0.8162 (p0) cc_final: 0.7332 (t0) REVERT: F 634 ASP cc_start: 0.7347 (t0) cc_final: 0.6957 (t0) REVERT: F 665 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.7434 (t80) REVERT: F 673 ASN cc_start: 0.7513 (m-40) cc_final: 0.7234 (m-40) REVERT: F 699 MET cc_start: 0.8915 (tpp) cc_final: 0.8657 (tpp) REVERT: F 816 LYS cc_start: 0.7890 (pttt) cc_final: 0.7506 (tptt) REVERT: F 831 LEU cc_start: 0.9258 (tp) cc_final: 0.9001 (tp) REVERT: F 835 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7151 (mt-10) REVERT: F 838 ASN cc_start: 0.8342 (m-40) cc_final: 0.7944 (p0) REVERT: F 877 LEU cc_start: 0.7760 (mp) cc_final: 0.7296 (tt) outliers start: 108 outliers final: 84 residues processed: 623 average time/residue: 0.1621 time to fit residues: 163.4437 Evaluate side-chains 626 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 530 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 672 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 725 MET 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 184 ASP Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 637 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 703 LEU Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 722 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 878 GLU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 248 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 399 SER Chi-restraints excluded: chain C residue 552 ARG 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 233 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 553 LEU 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 672 THR Chi-restraints excluded: chain D residue 695 VAL Chi-restraints excluded: chain D residue 697 THR 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 172 ILE Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 261 PHE Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 275 SER 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 397 ASP Chi-restraints excluded: chain E residue 400 CYS Chi-restraints excluded: chain E residue 546 ILE Chi-restraints excluded: chain E residue 596 LEU Chi-restraints excluded: chain E residue 665 TYR Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 695 VAL Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 232 ASP 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 554 THR Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 643 CYS Chi-restraints excluded: chain F residue 650 TYR Chi-restraints excluded: chain F residue 665 TYR Chi-restraints excluded: chain F residue 720 ASN 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 250 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 228 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 168 optimal weight: 0.0870 chunk 243 optimal weight: 6.9990 chunk 256 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN ** A 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 829 ASN ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 801 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.124639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.104203 restraints weight = 63413.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107271 restraints weight = 34569.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.109348 restraints weight = 21856.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.110699 restraints weight = 15395.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.111465 restraints weight = 11941.156| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.7548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28059 Z= 0.148 Angle : 0.772 15.394 37845 Z= 0.387 Chirality : 0.047 0.372 4383 Planarity : 0.005 0.067 4839 Dihedral : 9.783 138.988 3901 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.40 % Favored : 93.19 % Rotamer: Outliers : 3.52 % Allowed : 25.42 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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: -0.41 (0.15), residues: 3438 helix: 0.48 (0.13), residues: 1729 sheet: -0.99 (0.27), residues: 371 loop : -0.92 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 755 TYR 0.031 0.002 TYR F 680 PHE 0.043 0.002 PHE D 244 HIS 0.018 0.002 HIS D 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (28050) covalent geometry : angle 0.77158 / 0.39 (37841) SS BOND : bond 0.00594 / 0.31 ( 2) SS BOND : angle 2.91199 / 1.58 ( 4) hydrogen bonds : bond 0.03830 / 2.60 ( 1384) hydrogen bonds : angle 5.83970 / 4.22 ( 3867) Misc. bond : bond 0.00059 / 0.04 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5009.03 seconds wall clock time: 87 minutes 27.97 seconds (5247.97 seconds total)