Starting phenix.real_space_refine on Wed Mar 4 10:15:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tth_26115/03_2026/7tth_26115.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tth_26115/03_2026/7tth_26115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tth_26115/03_2026/7tth_26115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tth_26115/03_2026/7tth_26115.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tth_26115/03_2026/7tth_26115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tth_26115/03_2026/7tth_26115.map" } resolution = 3.25 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= -0.000 sd= 0.114 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 K 2 8.98 5 S 82 5.16 5 C 8296 2.51 5 N 2114 2.21 5 O 2204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12698 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 875, 6292 Classifications: {'peptide': 875} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'CIS': 3, 'PTRANS': 38, 'TRANS': 833} Chain breaks: 1 Unresolved non-hydrogen bonds: 496 Unresolved non-hydrogen angles: 618 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 28, 'GLN:plan1': 9, 'PHE:plan': 5, 'ASN:plan1': 7, 'ARG:plan': 9, 'HIS:plan': 6, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 333 Chain: "B" Number of atoms: 6292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 875, 6292 Classifications: {'peptide': 875} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'CIS': 3, 'PTRANS': 38, 'TRANS': 833} Chain breaks: 1 Unresolved non-hydrogen bonds: 496 Unresolved non-hydrogen angles: 618 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 28, 'GLN:plan1': 9, 'PHE:plan': 5, 'ASN:plan1': 7, 'ARG:plan': 9, 'HIS:plan': 6, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 333 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.23, per 1000 atoms: 0.25 Number of scatterers: 12698 At special positions: 0 Unit cell: (114.66, 95.004, 149.604, 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) K 2 19.00 S 82 16.00 O 2204 8.00 N 2114 7.00 C 8296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.04 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.04 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " 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 Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 361 " " NAG E 1 " - " ASN B 312 " " NAG F 1 " - " ASN B 361 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 516.9 milliseconds 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 6 sheets defined 58.9% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 141 through 177 removed outlier: 6.965A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 198 through 227 removed outlier: 3.726A pdb=" N ALA A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 269 removed outlier: 4.319A pdb=" N ALA A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 298 removed outlier: 4.067A pdb=" N SER A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.523A pdb=" N SER A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.800A pdb=" N MET A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 removed outlier: 3.568A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 446 through 477 removed outlier: 3.927A pdb=" N ILE A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Proline residue: A 452 - end of helix Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.542A pdb=" N GLY A 487 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 488' Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'A' and resid 503 through 537 removed outlier: 4.245A pdb=" N ILE A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 543 through 547 removed outlier: 3.976A pdb=" N HIS A 547 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 570 Processing helix chain 'A' and resid 573 through 602 Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.562A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 661 Processing helix chain 'A' and resid 666 through 680 removed outlier: 3.651A pdb=" N ALA A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 720 removed outlier: 3.756A pdb=" N LEU A 712 " --> pdb=" O TYR A 708 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 756 removed outlier: 3.796A pdb=" N ILE A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 756 " --> pdb=" O MET A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 781 removed outlier: 4.206A pdb=" N GLN A 779 " --> pdb=" O ALA A 775 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N CYS A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 821 removed outlier: 3.922A pdb=" N THR A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 Processing helix chain 'A' and resid 854 through 859 removed outlier: 3.859A pdb=" N LEU A 858 " --> pdb=" O ASP A 854 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET A 859 " --> pdb=" O GLY A 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 854 through 859' Processing helix chain 'A' and resid 860 through 867 removed outlier: 4.115A pdb=" N GLN A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 902 removed outlier: 3.790A pdb=" N LYS A 893 " --> pdb=" O ILE A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1034 removed outlier: 3.947A pdb=" N VAL A1023 " --> pdb=" O MET A1019 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A1028 " --> pdb=" O LYS A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1064 removed outlier: 4.287A pdb=" N GLU A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL A1062 " --> pdb=" O GLU A1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 141 through 177 removed outlier: 6.999A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 198 through 227 removed outlier: 3.755A pdb=" N ALA B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 269 removed outlier: 4.130A pdb=" N ALA B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 298 removed outlier: 4.043A pdb=" N SER B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 removed outlier: 3.516A pdb=" N SER B 340 " --> pdb=" O THR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.697A pdb=" N MET B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.587A pdb=" N LEU B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 433 through 439 removed outlier: 3.518A pdb=" N SER B 438 " --> pdb=" O MET B 435 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 439 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 477 removed outlier: 3.934A pdb=" N ILE B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Proline residue: B 452 - end of helix Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.507A pdb=" N GLY B 487 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B 488 " --> pdb=" O LYS B 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 484 through 488' Processing helix chain 'B' and resid 495 through 499 Processing helix chain 'B' and resid 503 through 537 removed outlier: 4.317A pdb=" N ILE B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 543 through 547 removed outlier: 3.849A pdb=" N HIS B 547 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 570 Processing helix chain 'B' and resid 573 through 602 removed outlier: 3.530A pdb=" N ALA B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Proline residue: B 579 - end of helix Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.559A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 661 Processing helix chain 'B' and resid 666 through 680 removed outlier: 3.637A pdb=" N ALA B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 720 removed outlier: 3.778A pdb=" N LEU B 712 " --> pdb=" O TYR B 708 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 719 " --> pdb=" O ALA B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 756 removed outlier: 3.504A pdb=" N ALA B 742 " --> pdb=" O SER B 738 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 756 " --> pdb=" O MET B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 781 removed outlier: 4.201A pdb=" N GLN B 779 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N CYS B 781 " --> pdb=" O LEU B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 821 removed outlier: 3.774A pdb=" N THR B 810 " --> pdb=" O ARG B 806 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N PHE B 811 " --> pdb=" O ALA B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 834 Processing helix chain 'B' and resid 854 through 859 removed outlier: 3.839A pdb=" N LEU B 858 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET B 859 " --> pdb=" O GLY B 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 854 through 859' Processing helix chain 'B' and resid 860 through 867 removed outlier: 4.117A pdb=" N GLN B 867 " --> pdb=" O PHE B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 874 removed outlier: 4.323A pdb=" N LYS B 873 " --> pdb=" O VAL B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 902 removed outlier: 3.588A pdb=" N LYS B 893 " --> pdb=" O ILE B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1034 removed outlier: 3.905A pdb=" N VAL B1023 " --> pdb=" O MET B1019 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B1028 " --> pdb=" O LYS B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1064 removed outlier: 4.460A pdb=" N GLU B1061 " --> pdb=" O MET B1057 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL B1062 " --> pdb=" O GLU B1058 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AA3, first strand: chain 'A' and resid 761 through 767 removed outlier: 6.511A pdb=" N THR A 725 " --> pdb=" O PHE A 761 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN A 763 " --> pdb=" O THR A 725 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 727 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL A 765 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER A 729 " --> pdb=" O VAL A 765 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA A 767 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE A 731 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU A 694 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLY A 728 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 696 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N VAL A 730 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU A 695 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL A1070 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A1039 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL A1073 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU A1041 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP A 847 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ASN A1042 " --> pdb=" O ASP A 847 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N TRP A 849 " --> pdb=" O ASN A1042 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AA5, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AA6, first strand: chain 'B' and resid 761 through 767 removed outlier: 6.382A pdb=" N THR B 725 " --> pdb=" O PHE B 761 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLN B 763 " --> pdb=" O THR B 725 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL B 727 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL B 765 " --> pdb=" O VAL B 727 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER B 729 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ALA B 767 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE B 731 " --> pdb=" O ALA B 767 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU B 694 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLY B 728 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 696 " --> pdb=" O GLY B 728 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL B 730 " --> pdb=" O VAL B 696 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 695 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B1070 " --> pdb=" O LYS B 829 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B1039 " --> pdb=" O LEU B1071 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL B1073 " --> pdb=" O VAL B1039 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B1041 " --> pdb=" O VAL B1073 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASP B 847 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ASN B1042 " --> pdb=" O ASP B 847 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N TRP B 849 " --> pdb=" O ASN B1042 " (cutoff:3.500A) 707 hydrogen bonds defined for protein. 2052 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: 2.09 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3956 1.35 - 1.47: 3367 1.47 - 1.60: 5549 1.60 - 1.72: 0 1.72 - 1.85: 124 Bond restraints: 12996 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.568 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C1 NAG D 2 " pdb=" C2 NAG D 2 " ideal model delta sigma weight residual 1.532 1.594 -0.062 2.00e-02 2.50e+03 9.48e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 ... (remaining 12991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 17533 2.41 - 4.83: 220 4.83 - 7.24: 34 7.24 - 9.65: 2 9.65 - 12.06: 3 Bond angle restraints: 17792 Sorted by residual: angle pdb=" CA LEU B 410 " pdb=" CB LEU B 410 " pdb=" CG LEU B 410 " ideal model delta sigma weight residual 116.30 128.36 -12.06 3.50e+00 8.16e-02 1.19e+01 angle pdb=" CA LEU A 410 " pdb=" CB LEU A 410 " pdb=" CG LEU A 410 " ideal model delta sigma weight residual 116.30 128.28 -11.98 3.50e+00 8.16e-02 1.17e+01 angle pdb=" C LEU A 625 " pdb=" N CYS A 626 " pdb=" CA CYS A 626 " ideal model delta sigma weight residual 122.38 116.31 6.07 1.81e+00 3.05e-01 1.13e+01 angle pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " pdb=" C5 NAG D 2 " ideal model delta sigma weight residual 113.21 123.27 -10.06 3.00e+00 1.11e-01 1.12e+01 angle pdb=" C LEU B 625 " pdb=" N CYS B 626 " pdb=" CA CYS B 626 " ideal model delta sigma weight residual 122.38 116.39 5.99 1.81e+00 3.05e-01 1.09e+01 ... (remaining 17787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.82: 7293 22.82 - 45.64: 299 45.64 - 68.46: 41 68.46 - 91.28: 11 91.28 - 114.10: 6 Dihedral angle restraints: 7650 sinusoidal: 2628 harmonic: 5022 Sorted by residual: dihedral pdb=" CA CYS B 626 " pdb=" C CYS B 626 " pdb=" N LEU B 627 " pdb=" CA LEU B 627 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA CYS A 626 " pdb=" C CYS A 626 " pdb=" N LEU A 627 " pdb=" CA LEU A 627 " ideal model delta harmonic sigma weight residual 180.00 154.42 25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CB CYS B 343 " pdb=" SG CYS B 343 " pdb=" SG CYS B 353 " pdb=" CB CYS B 353 " ideal model delta sinusoidal sigma weight residual 93.00 50.50 42.50 1 1.00e+01 1.00e-02 2.52e+01 ... (remaining 7647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2072 0.091 - 0.182: 105 0.182 - 0.273: 4 0.273 - 0.365: 0 0.365 - 0.456: 1 Chirality restraints: 2182 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 361 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" C4 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O4 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.26 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA CYS B 626 " pdb=" N CYS B 626 " pdb=" C CYS B 626 " pdb=" CB CYS B 626 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 2179 not shown) Planarity restraints: 2198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 626 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.28e+00 pdb=" C CYS B 626 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS B 626 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 627 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 626 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.12e+00 pdb=" C CYS A 626 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS A 626 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 627 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 539 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO A 540 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 540 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 540 " -0.024 5.00e-02 4.00e+02 ... (remaining 2195 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 3668 2.81 - 3.40: 14430 3.40 - 3.98: 21980 3.98 - 4.56: 29989 4.56 - 5.14: 44539 Nonbonded interactions: 114606 Sorted by model distance: nonbonded pdb=" OG1 THR B 604 " pdb=" NH1 ARG B 679 " model vdw 2.232 3.120 nonbonded pdb=" O GLY B 517 " pdb=" NE2 GLN B 521 " model vdw 2.239 3.120 nonbonded pdb=" O GLY A 517 " pdb=" NE2 GLN A 521 " model vdw 2.253 3.120 nonbonded pdb=" OE1 GLN A 599 " pdb=" OG1 THR A 604 " model vdw 2.261 3.040 nonbonded pdb=" O ALA A 399 " pdb=" O6 NAG C 1 " model vdw 2.274 3.040 ... (remaining 114601 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.300 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 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 : 0.004 0.162 13010 Z= 0.180 Angle : 0.733 13.265 17828 Z= 0.383 Chirality : 0.046 0.456 2182 Planarity : 0.004 0.043 2194 Dihedral : 13.053 114.098 4416 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.21), residues: 1742 helix: 1.66 (0.18), residues: 862 sheet: -0.66 (0.45), residues: 142 loop : -2.00 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 528 TYR 0.013 0.001 TYR B 216 PHE 0.016 0.001 PHE A 591 TRP 0.017 0.001 TRP B 556 HIS 0.003 0.001 HIS A 788 Details of bonding type rmsd covalent geometry : bond 0.00363 (12996) covalent geometry : angle 0.70486 (17792) SS BOND : bond 0.00683 ( 6) SS BOND : angle 1.85366 ( 12) hydrogen bonds : bond 0.16076 ( 707) hydrogen bonds : angle 6.09337 ( 2052) link_BETA1-4 : bond 0.01701 ( 4) link_BETA1-4 : angle 3.89388 ( 12) link_NAG-ASN : bond 0.01645 ( 4) link_NAG-ASN : angle 6.48773 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 231 PRO cc_start: 0.6054 (Cg_exo) cc_final: 0.5843 (Cg_endo) REVERT: A 478 GLU cc_start: 0.6811 (pm20) cc_final: 0.6497 (pm20) REVERT: A 484 ASP cc_start: 0.7610 (t0) cc_final: 0.7166 (t0) REVERT: A 556 TRP cc_start: 0.7055 (m-90) cc_final: 0.6762 (m100) REVERT: A 1042 ASN cc_start: 0.7189 (t0) cc_final: 0.6852 (m-40) REVERT: A 1059 PHE cc_start: 0.4331 (p90) cc_final: 0.3508 (m-80) REVERT: B 312 ASN cc_start: 0.7680 (t0) cc_final: 0.7378 (t0) REVERT: B 484 ASP cc_start: 0.7566 (t0) cc_final: 0.7258 (t0) REVERT: B 1059 PHE cc_start: 0.4312 (p90) cc_final: 0.3800 (m-80) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1118 time to fit residues: 40.1442 Evaluate side-chains 167 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 537 ASN B 537 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.192782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.165204 restraints weight = 16680.976| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.46 r_work: 0.3913 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13010 Z= 0.139 Angle : 0.661 12.047 17828 Z= 0.317 Chirality : 0.045 0.393 2182 Planarity : 0.004 0.034 2194 Dihedral : 7.728 97.866 2030 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.41 % Allowed : 7.32 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.21), residues: 1742 helix: 1.77 (0.18), residues: 878 sheet: -0.53 (0.45), residues: 146 loop : -1.81 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 528 TYR 0.012 0.001 TYR A 292 PHE 0.015 0.001 PHE A1059 TRP 0.010 0.001 TRP B 690 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00300 (12996) covalent geometry : angle 0.63761 (17792) SS BOND : bond 0.00583 ( 6) SS BOND : angle 1.46277 ( 12) hydrogen bonds : bond 0.04872 ( 707) hydrogen bonds : angle 4.45572 ( 2052) link_BETA1-4 : bond 0.00870 ( 4) link_BETA1-4 : angle 3.38345 ( 12) link_NAG-ASN : bond 0.00715 ( 4) link_NAG-ASN : angle 5.73911 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 231 PRO cc_start: 0.6934 (Cg_exo) cc_final: 0.6694 (Cg_endo) REVERT: A 556 TRP cc_start: 0.7062 (m-90) cc_final: 0.6681 (m100) REVERT: A 771 ARG cc_start: 0.7588 (ptp90) cc_final: 0.7356 (ptp90) REVERT: A 1059 PHE cc_start: 0.5216 (p90) cc_final: 0.4124 (m-80) REVERT: B 1059 PHE cc_start: 0.5171 (p90) cc_final: 0.4106 (m-80) outliers start: 17 outliers final: 8 residues processed: 188 average time/residue: 0.0938 time to fit residues: 27.0038 Evaluate side-chains 165 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 121 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 537 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.189878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.162496 restraints weight = 16715.173| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.45 r_work: 0.3895 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13010 Z= 0.135 Angle : 0.643 14.024 17828 Z= 0.303 Chirality : 0.045 0.479 2182 Planarity : 0.004 0.035 2194 Dihedral : 6.727 92.299 2030 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.08 % Allowed : 10.07 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.21), residues: 1742 helix: 1.80 (0.18), residues: 878 sheet: -0.56 (0.43), residues: 146 loop : -1.74 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 528 TYR 0.013 0.001 TYR B 384 PHE 0.021 0.002 PHE B1059 TRP 0.011 0.001 TRP B 635 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00305 (12996) covalent geometry : angle 0.61596 (17792) SS BOND : bond 0.01021 ( 6) SS BOND : angle 1.79556 ( 12) hydrogen bonds : bond 0.04756 ( 707) hydrogen bonds : angle 4.18903 ( 2052) link_BETA1-4 : bond 0.00892 ( 4) link_BETA1-4 : angle 3.13619 ( 12) link_NAG-ASN : bond 0.00776 ( 4) link_NAG-ASN : angle 6.17685 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 478 GLU cc_start: 0.6976 (pm20) cc_final: 0.6715 (pm20) REVERT: A 521 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6898 (mp-120) REVERT: A 587 MET cc_start: 0.7965 (tpt) cc_final: 0.7587 (tpp) REVERT: A 1059 PHE cc_start: 0.5505 (p90) cc_final: 0.3745 (m-80) REVERT: B 536 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.6910 (t0) REVERT: B 587 MET cc_start: 0.7948 (tpt) cc_final: 0.7709 (tpt) REVERT: B 1059 PHE cc_start: 0.5595 (p90) cc_final: 0.3971 (m-80) outliers start: 25 outliers final: 14 residues processed: 189 average time/residue: 0.0992 time to fit residues: 28.5503 Evaluate side-chains 170 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 1062 VAL Chi-restraints excluded: chain B residue 1080 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 159 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 80 optimal weight: 0.0270 chunk 154 optimal weight: 2.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.189441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.161891 restraints weight = 16695.955| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.47 r_work: 0.3887 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13010 Z= 0.126 Angle : 0.623 12.508 17828 Z= 0.295 Chirality : 0.044 0.473 2182 Planarity : 0.004 0.032 2194 Dihedral : 6.399 88.254 2030 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.66 % Allowed : 12.40 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1742 helix: 1.91 (0.18), residues: 880 sheet: 0.50 (0.44), residues: 116 loop : -1.74 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 528 TYR 0.010 0.001 TYR A 292 PHE 0.022 0.001 PHE B1059 TRP 0.011 0.001 TRP B 635 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00282 (12996) covalent geometry : angle 0.59552 (17792) SS BOND : bond 0.00708 ( 6) SS BOND : angle 1.74711 ( 12) hydrogen bonds : bond 0.04422 ( 707) hydrogen bonds : angle 4.03172 ( 2052) link_BETA1-4 : bond 0.00887 ( 4) link_BETA1-4 : angle 3.17237 ( 12) link_NAG-ASN : bond 0.00694 ( 4) link_NAG-ASN : angle 6.19707 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 410 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6410 (tt) REVERT: A 478 GLU cc_start: 0.6895 (pm20) cc_final: 0.6617 (pm20) REVERT: A 521 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6965 (mp-120) REVERT: A 587 MET cc_start: 0.7938 (tpt) cc_final: 0.7678 (tpp) REVERT: A 1059 PHE cc_start: 0.5930 (p90) cc_final: 0.3859 (m-80) REVERT: B 536 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6993 (t0) REVERT: B 587 MET cc_start: 0.7853 (tpt) cc_final: 0.7512 (tpp) REVERT: B 1059 PHE cc_start: 0.5855 (p90) cc_final: 0.4062 (m-80) outliers start: 20 outliers final: 10 residues processed: 176 average time/residue: 0.0910 time to fit residues: 24.9008 Evaluate side-chains 167 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 75 optimal weight: 0.0070 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 169 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.189666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.162104 restraints weight = 16742.018| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.48 r_work: 0.3891 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13010 Z= 0.120 Angle : 0.595 10.743 17828 Z= 0.284 Chirality : 0.043 0.476 2182 Planarity : 0.004 0.033 2194 Dihedral : 6.069 83.373 2030 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.08 % Allowed : 12.65 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.21), residues: 1742 helix: 2.00 (0.18), residues: 886 sheet: 0.58 (0.44), residues: 116 loop : -1.71 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 313 TYR 0.009 0.001 TYR A 292 PHE 0.020 0.001 PHE B1059 TRP 0.010 0.001 TRP A 635 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00267 (12996) covalent geometry : angle 0.56968 (17792) SS BOND : bond 0.00566 ( 6) SS BOND : angle 1.42333 ( 12) hydrogen bonds : bond 0.04258 ( 707) hydrogen bonds : angle 3.94534 ( 2052) link_BETA1-4 : bond 0.00881 ( 4) link_BETA1-4 : angle 3.11536 ( 12) link_NAG-ASN : bond 0.00700 ( 4) link_NAG-ASN : angle 5.76843 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7204 (mt0) REVERT: A 478 GLU cc_start: 0.6835 (pm20) cc_final: 0.6522 (pm20) REVERT: A 521 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6970 (mp-120) REVERT: A 587 MET cc_start: 0.7903 (tpt) cc_final: 0.7577 (tpp) REVERT: A 1059 PHE cc_start: 0.6123 (p90) cc_final: 0.3778 (m-80) REVERT: B 536 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6972 (t0) REVERT: B 587 MET cc_start: 0.7805 (tpt) cc_final: 0.7465 (tpp) REVERT: B 1059 PHE cc_start: 0.6005 (p90) cc_final: 0.4047 (m-80) outliers start: 25 outliers final: 12 residues processed: 180 average time/residue: 0.0972 time to fit residues: 27.0157 Evaluate side-chains 171 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 83 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.188250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.160659 restraints weight = 16649.795| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.47 r_work: 0.3875 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3751 r_free = 0.3751 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3751 r_free = 0.3751 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13010 Z= 0.129 Angle : 0.614 10.905 17828 Z= 0.292 Chirality : 0.044 0.478 2182 Planarity : 0.004 0.033 2194 Dihedral : 5.873 77.329 2030 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.41 % Allowed : 12.90 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.21), residues: 1742 helix: 2.00 (0.18), residues: 886 sheet: 0.62 (0.44), residues: 116 loop : -1.71 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 528 TYR 0.009 0.001 TYR A 292 PHE 0.019 0.001 PHE B1059 TRP 0.010 0.001 TRP B 635 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00296 (12996) covalent geometry : angle 0.58959 (17792) SS BOND : bond 0.00668 ( 6) SS BOND : angle 1.82975 ( 12) hydrogen bonds : bond 0.04437 ( 707) hydrogen bonds : angle 3.97894 ( 2052) link_BETA1-4 : bond 0.00809 ( 4) link_BETA1-4 : angle 3.22155 ( 12) link_NAG-ASN : bond 0.00679 ( 4) link_NAG-ASN : angle 5.59545 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7312 (mt0) REVERT: A 478 GLU cc_start: 0.6987 (pm20) cc_final: 0.6589 (pm20) REVERT: A 521 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.7003 (mp-120) REVERT: A 587 MET cc_start: 0.7961 (tpt) cc_final: 0.7633 (tpp) REVERT: A 1059 PHE cc_start: 0.6076 (p90) cc_final: 0.3652 (m-80) REVERT: B 251 MET cc_start: 0.6355 (mtt) cc_final: 0.6132 (mtt) REVERT: B 536 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6986 (t0) REVERT: B 587 MET cc_start: 0.7856 (tpt) cc_final: 0.7522 (tpp) REVERT: B 808 TRP cc_start: 0.5768 (p-90) cc_final: 0.5414 (p-90) REVERT: B 1059 PHE cc_start: 0.5866 (p90) cc_final: 0.3773 (m-80) outliers start: 29 outliers final: 19 residues processed: 177 average time/residue: 0.0929 time to fit residues: 25.5646 Evaluate side-chains 177 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 850 TRP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 865 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.188094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.161045 restraints weight = 16641.241| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.36 r_work: 0.3877 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13010 Z= 0.127 Angle : 0.604 10.916 17828 Z= 0.288 Chirality : 0.043 0.475 2182 Planarity : 0.004 0.033 2194 Dihedral : 5.612 67.218 2030 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.41 % Allowed : 14.14 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1742 helix: 2.03 (0.18), residues: 888 sheet: 0.67 (0.44), residues: 116 loop : -1.70 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 528 TYR 0.009 0.001 TYR B 292 PHE 0.019 0.001 PHE B1059 TRP 0.010 0.001 TRP A 635 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00293 (12996) covalent geometry : angle 0.57862 (17792) SS BOND : bond 0.00801 ( 6) SS BOND : angle 1.97638 ( 12) hydrogen bonds : bond 0.04367 ( 707) hydrogen bonds : angle 3.94586 ( 2052) link_BETA1-4 : bond 0.00756 ( 4) link_BETA1-4 : angle 3.43398 ( 12) link_NAG-ASN : bond 0.00665 ( 4) link_NAG-ASN : angle 5.44314 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 478 GLU cc_start: 0.6993 (pm20) cc_final: 0.6620 (pm20) REVERT: A 521 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6920 (mp-120) REVERT: A 587 MET cc_start: 0.7952 (tpt) cc_final: 0.7669 (tpp) REVERT: A 1059 PHE cc_start: 0.6372 (p90) cc_final: 0.3729 (m-80) REVERT: B 251 MET cc_start: 0.6336 (mtt) cc_final: 0.6118 (mtt) REVERT: B 536 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6850 (t0) REVERT: B 587 MET cc_start: 0.7832 (tpt) cc_final: 0.7516 (tpp) REVERT: B 808 TRP cc_start: 0.5732 (p-90) cc_final: 0.5358 (p-90) REVERT: B 1059 PHE cc_start: 0.6156 (p90) cc_final: 0.3891 (m-80) outliers start: 29 outliers final: 22 residues processed: 182 average time/residue: 0.0976 time to fit residues: 27.7242 Evaluate side-chains 176 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 0.0980 chunk 101 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.188456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.161502 restraints weight = 16515.634| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.35 r_work: 0.3876 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13010 Z= 0.122 Angle : 0.606 10.470 17828 Z= 0.287 Chirality : 0.043 0.468 2182 Planarity : 0.004 0.033 2194 Dihedral : 5.405 56.761 2030 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.33 % Allowed : 15.22 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.21), residues: 1742 helix: 2.08 (0.18), residues: 888 sheet: -0.30 (0.43), residues: 146 loop : -1.58 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 528 TYR 0.009 0.001 TYR A 292 PHE 0.017 0.001 PHE B 545 TRP 0.010 0.001 TRP A 635 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00276 (12996) covalent geometry : angle 0.58320 (17792) SS BOND : bond 0.00647 ( 6) SS BOND : angle 1.74240 ( 12) hydrogen bonds : bond 0.04258 ( 707) hydrogen bonds : angle 3.90171 ( 2052) link_BETA1-4 : bond 0.00715 ( 4) link_BETA1-4 : angle 3.66212 ( 12) link_NAG-ASN : bond 0.00660 ( 4) link_NAG-ASN : angle 4.95137 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 GLU cc_start: 0.6927 (pm20) cc_final: 0.6567 (pm20) REVERT: A 521 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6955 (mp-120) REVERT: A 587 MET cc_start: 0.7908 (tpt) cc_final: 0.7606 (tpp) REVERT: B 536 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6867 (t0) REVERT: B 587 MET cc_start: 0.7823 (tpt) cc_final: 0.7521 (tpp) REVERT: B 808 TRP cc_start: 0.5793 (p-90) cc_final: 0.5420 (p-90) REVERT: B 1059 PHE cc_start: 0.6314 (p90) cc_final: 0.3891 (m-80) outliers start: 28 outliers final: 23 residues processed: 171 average time/residue: 0.0974 time to fit residues: 25.7340 Evaluate side-chains 178 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 139 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 30 optimal weight: 0.0370 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.187864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.159948 restraints weight = 16729.984| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.49 r_work: 0.3875 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3751 r_free = 0.3751 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3751 r_free = 0.3751 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13010 Z= 0.122 Angle : 0.599 10.392 17828 Z= 0.286 Chirality : 0.043 0.462 2182 Planarity : 0.004 0.034 2194 Dihedral : 5.103 56.576 2030 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.41 % Allowed : 15.22 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.21), residues: 1742 helix: 2.00 (0.18), residues: 902 sheet: 0.91 (0.46), residues: 116 loop : -1.68 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 528 TYR 0.009 0.001 TYR A 292 PHE 0.019 0.001 PHE B 545 TRP 0.010 0.001 TRP B 635 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00276 (12996) covalent geometry : angle 0.57485 (17792) SS BOND : bond 0.00643 ( 6) SS BOND : angle 1.72580 ( 12) hydrogen bonds : bond 0.04210 ( 707) hydrogen bonds : angle 3.86493 ( 2052) link_BETA1-4 : bond 0.00678 ( 4) link_BETA1-4 : angle 3.90988 ( 12) link_NAG-ASN : bond 0.00644 ( 4) link_NAG-ASN : angle 4.94775 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 521 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6940 (mp-120) REVERT: A 587 MET cc_start: 0.7863 (tpt) cc_final: 0.7489 (tpp) REVERT: A 591 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7762 (t80) REVERT: B 536 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6892 (t0) REVERT: B 587 MET cc_start: 0.7835 (tpt) cc_final: 0.7541 (tpp) REVERT: B 808 TRP cc_start: 0.5848 (p-90) cc_final: 0.5480 (p-90) outliers start: 29 outliers final: 20 residues processed: 171 average time/residue: 0.0888 time to fit residues: 24.2825 Evaluate side-chains 172 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 114 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 717 GLN B 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.181927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.154791 restraints weight = 16937.552| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.39 r_work: 0.3813 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13010 Z= 0.188 Angle : 0.676 10.250 17828 Z= 0.329 Chirality : 0.047 0.480 2182 Planarity : 0.004 0.038 2194 Dihedral : 5.357 57.008 2030 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.33 % Allowed : 15.31 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.20), residues: 1742 helix: 1.64 (0.17), residues: 898 sheet: 0.62 (0.43), residues: 120 loop : -1.83 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 528 TYR 0.013 0.001 TYR B 466 PHE 0.027 0.002 PHE B 545 TRP 0.013 0.001 TRP B 850 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00460 (12996) covalent geometry : angle 0.65498 (17792) SS BOND : bond 0.00884 ( 6) SS BOND : angle 2.14456 ( 12) hydrogen bonds : bond 0.05345 ( 707) hydrogen bonds : angle 4.12071 ( 2052) link_BETA1-4 : bond 0.00577 ( 4) link_BETA1-4 : angle 3.68570 ( 12) link_NAG-ASN : bond 0.00554 ( 4) link_NAG-ASN : angle 5.03769 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 521 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.7152 (mp-120) REVERT: A 808 TRP cc_start: 0.6095 (p-90) cc_final: 0.5815 (p-90) REVERT: B 379 ASN cc_start: 0.9011 (OUTLIER) cc_final: 0.8783 (p0) REVERT: B 536 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6978 (t0) REVERT: B 539 ILE cc_start: 0.8239 (mm) cc_final: 0.8036 (mt) REVERT: B 587 MET cc_start: 0.7996 (tpt) cc_final: 0.7719 (tpp) outliers start: 28 outliers final: 21 residues processed: 165 average time/residue: 0.0894 time to fit residues: 23.5551 Evaluate side-chains 165 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1059 PHE Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 64 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 0.0570 chunk 164 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 137 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.182077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.154625 restraints weight = 16815.270| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.46 r_work: 0.3807 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 13010 Z= 0.189 Angle : 0.888 59.199 17828 Z= 0.489 Chirality : 0.050 0.939 2182 Planarity : 0.004 0.054 2194 Dihedral : 5.371 56.779 2030 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.08 % Allowed : 16.22 % Favored : 81.70 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1742 helix: 1.62 (0.17), residues: 898 sheet: 0.60 (0.43), residues: 120 loop : -1.85 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 528 TYR 0.013 0.001 TYR B 292 PHE 0.025 0.002 PHE B 545 TRP 0.012 0.001 TRP B 850 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00428 (12996) covalent geometry : angle 0.87230 (17792) SS BOND : bond 0.00802 ( 6) SS BOND : angle 2.03989 ( 12) hydrogen bonds : bond 0.05234 ( 707) hydrogen bonds : angle 4.11856 ( 2052) link_BETA1-4 : bond 0.00682 ( 4) link_BETA1-4 : angle 3.73203 ( 12) link_NAG-ASN : bond 0.00561 ( 4) link_NAG-ASN : angle 5.04847 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3261.86 seconds wall clock time: 56 minutes 30.89 seconds (3390.89 seconds total)