Starting phenix.real_space_refine on Wed Jun 11 13:00:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tth_26115/06_2025/7tth_26115.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tth_26115/06_2025/7tth_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tth_26115/06_2025/7tth_26115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tth_26115/06_2025/7tth_26115.map" model { file = "/net/cci-nas-00/data/ceres_data/7tth_26115/06_2025/7tth_26115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tth_26115/06_2025/7tth_26115.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 9, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 28, 'ARG:plan': 9} 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: {'GLN:plan1': 9, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 28, 'ARG:plan': 9} 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: 7.75, per 1000 atoms: 0.61 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: 3.26 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.27 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: 4.45 Time building geometry restraints manager: 3.85 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: 0.00 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.270 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.180 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (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 TRP 0.017 0.001 TRP B 556 HIS 0.003 0.001 HIS A 788 PHE 0.016 0.001 PHE A 591 TYR 0.013 0.001 TYR B 216 ARG 0.006 0.000 ARG B 528 Details of bonding type rmsd link_NAG-ASN : bond 0.01645 ( 4) link_NAG-ASN : angle 6.48773 ( 12) link_BETA1-4 : bond 0.01701 ( 4) link_BETA1-4 : angle 3.89388 ( 12) hydrogen bonds : bond 0.16076 ( 707) hydrogen bonds : angle 6.09337 ( 2052) SS BOND : bond 0.00683 ( 6) SS BOND : angle 1.85366 ( 12) covalent geometry : bond 0.00363 (12996) covalent geometry : angle 0.70486 (17792) *********************** 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 : 1.428 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: 0.2751 time to fit residues: 98.1678 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 : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 0.0070 chunk 73 optimal weight: 0.0030 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 overall best weight: 0.7010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 537 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.192774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.165285 restraints weight = 16523.504| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.44 r_work: 0.3910 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 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 = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13010 Z= 0.137 Angle : 0.658 11.898 17828 Z= 0.316 Chirality : 0.045 0.407 2182 Planarity : 0.004 0.034 2194 Dihedral : 7.703 97.282 2030 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.33 % Allowed : 7.32 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1742 helix: 1.76 (0.18), residues: 878 sheet: -0.53 (0.45), residues: 146 loop : -1.82 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 690 HIS 0.004 0.001 HIS A 344 PHE 0.016 0.001 PHE A1059 TYR 0.012 0.001 TYR A 292 ARG 0.005 0.000 ARG B 528 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 4) link_NAG-ASN : angle 5.73919 ( 12) link_BETA1-4 : bond 0.00907 ( 4) link_BETA1-4 : angle 3.24682 ( 12) hydrogen bonds : bond 0.04890 ( 707) hydrogen bonds : angle 4.45484 ( 2052) SS BOND : bond 0.00587 ( 6) SS BOND : angle 1.47859 ( 12) covalent geometry : bond 0.00297 (12996) covalent geometry : angle 0.63511 (17792) *********************** 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: 16 poor density : 178 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: A 231 PRO cc_start: 0.6919 (Cg_exo) cc_final: 0.6683 (Cg_endo) REVERT: A 556 TRP cc_start: 0.7071 (m-90) cc_final: 0.6692 (m100) REVERT: A 771 ARG cc_start: 0.7592 (ptp90) cc_final: 0.7358 (ptp90) REVERT: A 1042 ASN cc_start: 0.7650 (t0) cc_final: 0.7163 (m-40) REVERT: A 1059 PHE cc_start: 0.5217 (p90) cc_final: 0.4113 (m-80) REVERT: B 1059 PHE cc_start: 0.5168 (p90) cc_final: 0.4092 (m-80) outliers start: 16 outliers final: 8 residues processed: 188 average time/residue: 0.2087 time to fit residues: 60.1580 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 : 1.332 ------------------------------------------------------------------------------- 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 97 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 95 optimal weight: 0.2980 chunk 139 optimal weight: 0.9990 chunk 120 optimal weight: 0.0170 chunk 115 optimal weight: 0.2980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.195358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.168119 restraints weight = 16534.386| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.47 r_work: 0.3943 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3825 r_free = 0.3825 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3824 r_free = 0.3824 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13010 Z= 0.115 Angle : 0.616 13.505 17828 Z= 0.289 Chirality : 0.044 0.456 2182 Planarity : 0.004 0.032 2194 Dihedral : 6.726 92.221 2030 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.58 % Allowed : 9.98 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1742 helix: 2.02 (0.18), residues: 866 sheet: -0.50 (0.44), residues: 146 loop : -1.74 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 635 HIS 0.004 0.001 HIS A 344 PHE 0.020 0.001 PHE B1059 TYR 0.010 0.001 TYR B1056 ARG 0.005 0.000 ARG B 528 Details of bonding type rmsd link_NAG-ASN : bond 0.00806 ( 4) link_NAG-ASN : angle 5.96262 ( 12) link_BETA1-4 : bond 0.00925 ( 4) link_BETA1-4 : angle 3.25603 ( 12) hydrogen bonds : bond 0.04291 ( 707) hydrogen bonds : angle 4.12933 ( 2052) SS BOND : bond 0.00620 ( 6) SS BOND : angle 1.58791 ( 12) covalent geometry : bond 0.00237 (12996) covalent geometry : angle 0.58967 (17792) *********************** 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 198 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 478 GLU cc_start: 0.6845 (pm20) cc_final: 0.6563 (pm20) REVERT: A 521 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.6816 (mp-120) REVERT: A 556 TRP cc_start: 0.7094 (m-90) cc_final: 0.6629 (m100) REVERT: A 587 MET cc_start: 0.7950 (tpt) cc_final: 0.7619 (tpp) REVERT: A 1042 ASN cc_start: 0.7568 (t0) cc_final: 0.7125 (m-40) REVERT: A 1059 PHE cc_start: 0.5294 (p90) cc_final: 0.3823 (m-80) REVERT: B 536 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6961 (t0) REVERT: B 587 MET cc_start: 0.7908 (tpt) cc_final: 0.7640 (tpt) REVERT: B 1059 PHE cc_start: 0.5263 (p90) cc_final: 0.3954 (m-80) outliers start: 19 outliers final: 10 residues processed: 194 average time/residue: 0.2186 time to fit residues: 63.7532 Evaluate side-chains 174 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 448 GLN 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 B residue 188 MET Chi-restraints excluded: chain B residue 289 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 1062 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 149 optimal weight: 0.0870 chunk 72 optimal weight: 3.9990 chunk 167 optimal weight: 30.0000 chunk 104 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 161 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 = 0.4276 r_free = 0.4276 target = 0.192225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.164739 restraints weight = 16536.696| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.46 r_work: 0.3912 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2048 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= 0.119 Angle : 0.612 10.498 17828 Z= 0.288 Chirality : 0.043 0.469 2182 Planarity : 0.004 0.033 2194 Dihedral : 6.378 88.398 2030 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.58 % Allowed : 11.90 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1742 helix: 2.01 (0.18), residues: 880 sheet: 0.59 (0.45), residues: 116 loop : -1.73 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 635 HIS 0.004 0.001 HIS A 344 PHE 0.022 0.001 PHE B1059 TYR 0.009 0.001 TYR B 292 ARG 0.005 0.000 ARG B 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00771 ( 4) link_NAG-ASN : angle 5.15569 ( 12) link_BETA1-4 : bond 0.00799 ( 4) link_BETA1-4 : angle 3.14722 ( 12) hydrogen bonds : bond 0.04173 ( 707) hydrogen bonds : angle 3.98679 ( 2052) SS BOND : bond 0.00688 ( 6) SS BOND : angle 1.69717 ( 12) covalent geometry : bond 0.00263 (12996) covalent geometry : angle 0.59091 (17792) *********************** 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 178 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 410 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6179 (tt) REVERT: A 448 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: A 478 GLU cc_start: 0.6892 (pm20) cc_final: 0.6548 (pm20) REVERT: A 521 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6897 (mp-120) REVERT: A 587 MET cc_start: 0.7920 (tpt) cc_final: 0.7645 (tpp) REVERT: A 1042 ASN cc_start: 0.7676 (t0) cc_final: 0.7195 (m-40) REVERT: A 1059 PHE cc_start: 0.5567 (p90) cc_final: 0.3740 (m-80) REVERT: B 536 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6984 (t0) REVERT: B 587 MET cc_start: 0.7830 (tpt) cc_final: 0.7465 (tpp) REVERT: B 1059 PHE cc_start: 0.5683 (p90) cc_final: 0.4041 (m-80) outliers start: 19 outliers final: 10 residues processed: 175 average time/residue: 0.2077 time to fit residues: 55.9182 Evaluate side-chains 171 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 448 GLN 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 188 MET 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 56 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 0.0000 chunk 23 optimal weight: 0.2980 chunk 85 optimal weight: 0.5980 chunk 167 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 = 0.4281 r_free = 0.4281 target = 0.192670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.165113 restraints weight = 16596.408| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.48 r_work: 0.3921 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13010 Z= 0.110 Angle : 0.582 10.837 17828 Z= 0.274 Chirality : 0.043 0.476 2182 Planarity : 0.004 0.033 2194 Dihedral : 5.915 81.291 2030 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.33 % Allowed : 12.15 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1742 helix: 2.21 (0.18), residues: 874 sheet: 0.73 (0.45), residues: 116 loop : -1.72 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 635 HIS 0.003 0.000 HIS A 344 PHE 0.023 0.001 PHE B1059 TYR 0.010 0.001 TYR B1056 ARG 0.007 0.000 ARG B 528 Details of bonding type rmsd link_NAG-ASN : bond 0.00745 ( 4) link_NAG-ASN : angle 5.10185 ( 12) link_BETA1-4 : bond 0.00849 ( 4) link_BETA1-4 : angle 3.32547 ( 12) hydrogen bonds : bond 0.03898 ( 707) hydrogen bonds : angle 3.85935 ( 2052) SS BOND : bond 0.00569 ( 6) SS BOND : angle 1.39889 ( 12) covalent geometry : bond 0.00235 (12996) covalent geometry : angle 0.55986 (17792) *********************** 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 189 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7251 (mt0) REVERT: A 478 GLU cc_start: 0.6874 (pm20) cc_final: 0.6525 (pm20) REVERT: A 521 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6899 (mp-120) REVERT: A 553 GLU cc_start: 0.7504 (tt0) cc_final: 0.7264 (tt0) REVERT: A 587 MET cc_start: 0.7878 (tpt) cc_final: 0.7569 (tpp) REVERT: A 1059 PHE cc_start: 0.6026 (p90) cc_final: 0.3764 (m-80) REVERT: B 536 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.7039 (t0) REVERT: B 587 MET cc_start: 0.7770 (tpt) cc_final: 0.7414 (tpp) REVERT: B 1059 PHE cc_start: 0.5792 (p90) cc_final: 0.4012 (m-80) outliers start: 28 outliers final: 11 residues processed: 184 average time/residue: 0.2059 time to fit residues: 58.6647 Evaluate side-chains 167 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 344 HIS 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 B residue 188 MET 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 5 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 87 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4265 r_free = 0.4265 target = 0.191165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.163374 restraints weight = 16841.357| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.50 r_work: 0.3902 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13010 Z= 0.116 Angle : 0.597 10.985 17828 Z= 0.281 Chirality : 0.043 0.474 2182 Planarity : 0.004 0.033 2194 Dihedral : 5.694 73.958 2030 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.16 % Allowed : 13.31 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1742 helix: 2.12 (0.18), residues: 886 sheet: 0.79 (0.46), residues: 116 loop : -1.65 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 635 HIS 0.003 0.001 HIS A 344 PHE 0.021 0.001 PHE B1059 TYR 0.008 0.001 TYR A 292 ARG 0.006 0.000 ARG B 528 Details of bonding type rmsd link_NAG-ASN : bond 0.00690 ( 4) link_NAG-ASN : angle 5.06398 ( 12) link_BETA1-4 : bond 0.00771 ( 4) link_BETA1-4 : angle 3.35844 ( 12) hydrogen bonds : bond 0.04073 ( 707) hydrogen bonds : angle 3.88530 ( 2052) SS BOND : bond 0.00555 ( 6) SS BOND : angle 2.03036 ( 12) covalent geometry : bond 0.00259 (12996) covalent geometry : angle 0.57352 (17792) *********************** 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 184 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7300 (mt0) REVERT: A 478 GLU cc_start: 0.6876 (pm20) cc_final: 0.6470 (pm20) REVERT: A 484 ASP cc_start: 0.8155 (t0) cc_final: 0.7910 (t0) REVERT: A 521 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6880 (mp-120) REVERT: A 587 MET cc_start: 0.7919 (tpt) cc_final: 0.7582 (tpp) REVERT: A 1059 PHE cc_start: 0.6044 (p90) cc_final: 0.3634 (m-80) REVERT: B 536 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7056 (t0) REVERT: B 587 MET cc_start: 0.7819 (tpt) cc_final: 0.7450 (tpp) REVERT: B 1059 PHE cc_start: 0.6042 (p90) cc_final: 0.3982 (m-80) outliers start: 26 outliers final: 17 residues processed: 176 average time/residue: 0.2044 time to fit residues: 55.3568 Evaluate side-chains 173 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 529 LEU Chi-restraints excluded: chain A residue 591 PHE 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 188 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 524 THR 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 131 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 57 optimal weight: 0.0010 chunk 142 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.190357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.162641 restraints weight = 16622.128| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.48 r_work: 0.3896 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.3776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2514 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= 0.118 Angle : 0.596 10.689 17828 Z= 0.282 Chirality : 0.043 0.471 2182 Planarity : 0.004 0.034 2194 Dihedral : 5.435 62.694 2030 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.33 % Allowed : 13.73 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1742 helix: 2.17 (0.18), residues: 886 sheet: 0.85 (0.46), residues: 116 loop : -1.66 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 635 HIS 0.003 0.001 HIS A 344 PHE 0.020 0.001 PHE B1059 TYR 0.008 0.001 TYR B 292 ARG 0.006 0.000 ARG B 528 Details of bonding type rmsd link_NAG-ASN : bond 0.00680 ( 4) link_NAG-ASN : angle 5.03788 ( 12) link_BETA1-4 : bond 0.00732 ( 4) link_BETA1-4 : angle 3.58755 ( 12) hydrogen bonds : bond 0.04069 ( 707) hydrogen bonds : angle 3.85601 ( 2052) SS BOND : bond 0.00781 ( 6) SS BOND : angle 1.92314 ( 12) covalent geometry : bond 0.00266 (12996) covalent geometry : angle 0.57265 (17792) *********************** 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 185 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.6630 (mmm) cc_final: 0.6419 (mtt) REVERT: A 478 GLU cc_start: 0.6868 (pm20) cc_final: 0.6464 (pm20) REVERT: A 521 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6895 (mp-120) REVERT: A 587 MET cc_start: 0.7890 (tpt) cc_final: 0.7580 (tpp) REVERT: A 1059 PHE cc_start: 0.6174 (p90) cc_final: 0.3636 (m-80) REVERT: B 536 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7044 (t0) REVERT: B 587 MET cc_start: 0.7824 (tpt) cc_final: 0.7498 (tpp) REVERT: B 808 TRP cc_start: 0.5898 (p-90) cc_final: 0.5518 (p-90) REVERT: B 1059 PHE cc_start: 0.5951 (p90) cc_final: 0.3841 (m-80) outliers start: 28 outliers final: 22 residues processed: 176 average time/residue: 0.2189 time to fit residues: 58.9639 Evaluate side-chains 175 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 521 GLN 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 188 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 524 THR 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 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 107 optimal weight: 6.9990 chunk 171 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 158 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.189169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.161346 restraints weight = 16727.309| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.50 r_work: 0.3879 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.3764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2627 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= 0.123 Angle : 0.607 10.517 17828 Z= 0.288 Chirality : 0.043 0.469 2182 Planarity : 0.004 0.033 2194 Dihedral : 5.210 56.763 2030 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.25 % Allowed : 14.14 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1742 helix: 2.16 (0.18), residues: 886 sheet: 0.80 (0.45), residues: 120 loop : -1.64 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 635 HIS 0.003 0.000 HIS A 344 PHE 0.020 0.001 PHE B1059 TYR 0.008 0.001 TYR A 292 ARG 0.006 0.000 ARG A 528 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 4) link_NAG-ASN : angle 5.02266 ( 12) link_BETA1-4 : bond 0.00657 ( 4) link_BETA1-4 : angle 3.80603 ( 12) hydrogen bonds : bond 0.04181 ( 707) hydrogen bonds : angle 3.85361 ( 2052) SS BOND : bond 0.00679 ( 6) SS BOND : angle 1.82227 ( 12) covalent geometry : bond 0.00281 (12996) covalent geometry : angle 0.58287 (17792) *********************** 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 179 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.6739 (mmm) cc_final: 0.6515 (mtt) REVERT: A 478 GLU cc_start: 0.6922 (pm20) cc_final: 0.6481 (pm20) REVERT: A 521 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6917 (mp-120) REVERT: A 587 MET cc_start: 0.7885 (tpt) cc_final: 0.7588 (tpp) REVERT: B 536 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6872 (t0) REVERT: B 587 MET cc_start: 0.7866 (tpt) cc_final: 0.7545 (tpp) REVERT: B 808 TRP cc_start: 0.5865 (p-90) cc_final: 0.5480 (p-90) REVERT: B 1059 PHE cc_start: 0.6159 (p90) cc_final: 0.3829 (m-80) outliers start: 27 outliers final: 20 residues processed: 170 average time/residue: 0.2096 time to fit residues: 55.3862 Evaluate side-chains 172 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 289 LEU 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 529 LEU Chi-restraints excluded: chain A residue 591 PHE 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 188 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 524 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 79 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.190365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.162692 restraints weight = 16661.575| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.48 r_work: 0.3889 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2703 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= 0.114 Angle : 0.594 10.468 17828 Z= 0.281 Chirality : 0.043 0.461 2182 Planarity : 0.004 0.034 2194 Dihedral : 5.027 56.496 2030 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.25 % Allowed : 14.23 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1742 helix: 2.17 (0.18), residues: 890 sheet: 0.85 (0.46), residues: 120 loop : -1.60 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 635 HIS 0.003 0.000 HIS A 344 PHE 0.018 0.001 PHE B1059 TYR 0.009 0.001 TYR A 292 ARG 0.006 0.000 ARG B 528 Details of bonding type rmsd link_NAG-ASN : bond 0.00670 ( 4) link_NAG-ASN : angle 4.94641 ( 12) link_BETA1-4 : bond 0.00705 ( 4) link_BETA1-4 : angle 3.93252 ( 12) hydrogen bonds : bond 0.04025 ( 707) hydrogen bonds : angle 3.82216 ( 2052) SS BOND : bond 0.00640 ( 6) SS BOND : angle 1.63535 ( 12) covalent geometry : bond 0.00255 (12996) covalent geometry : angle 0.57037 (17792) *********************** 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 173 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 GLU cc_start: 0.6918 (pm20) cc_final: 0.6490 (pm20) REVERT: A 521 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6888 (mp-120) REVERT: A 587 MET cc_start: 0.7840 (tpt) cc_final: 0.7539 (tpp) REVERT: B 536 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6973 (t0) REVERT: B 587 MET cc_start: 0.7813 (tpt) cc_final: 0.7504 (tpp) REVERT: B 808 TRP cc_start: 0.5859 (p-90) cc_final: 0.5485 (p-90) REVERT: B 1059 PHE cc_start: 0.6282 (p90) cc_final: 0.3941 (m-80) outliers start: 27 outliers final: 21 residues processed: 165 average time/residue: 0.1964 time to fit residues: 52.1425 Evaluate side-chains 168 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 289 LEU 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 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 A residue 1078 ARG Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 524 THR 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 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 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 164 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4264 r_free = 0.4264 target = 0.190645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.163025 restraints weight = 16611.120| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.48 r_work: 0.3888 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2769 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= 0.113 Angle : 0.591 10.351 17828 Z= 0.279 Chirality : 0.043 0.455 2182 Planarity : 0.004 0.035 2194 Dihedral : 4.925 56.279 2030 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.75 % Allowed : 14.73 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1742 helix: 2.17 (0.18), residues: 890 sheet: -0.08 (0.44), residues: 150 loop : -1.54 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 635 HIS 0.003 0.000 HIS A 344 PHE 0.018 0.001 PHE B1059 TYR 0.009 0.001 TYR A 292 ARG 0.006 0.000 ARG B 528 Details of bonding type rmsd link_NAG-ASN : bond 0.00672 ( 4) link_NAG-ASN : angle 4.88833 ( 12) link_BETA1-4 : bond 0.00784 ( 4) link_BETA1-4 : angle 3.93002 ( 12) hydrogen bonds : bond 0.03961 ( 707) hydrogen bonds : angle 3.79575 ( 2052) SS BOND : bond 0.00645 ( 6) SS BOND : angle 1.62598 ( 12) covalent geometry : bond 0.00250 (12996) covalent geometry : angle 0.56682 (17792) ********************** 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 170 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 GLU cc_start: 0.6910 (pm20) cc_final: 0.6460 (pm20) REVERT: A 521 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6883 (mp-120) REVERT: A 587 MET cc_start: 0.7848 (tpt) cc_final: 0.7558 (tpp) REVERT: A 1078 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6819 (mmt90) REVERT: B 536 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6979 (t0) REVERT: B 587 MET cc_start: 0.7824 (tpt) cc_final: 0.7516 (tpp) REVERT: B 808 TRP cc_start: 0.5862 (p-90) cc_final: 0.5485 (p-90) REVERT: B 1059 PHE cc_start: 0.6325 (p90) cc_final: 0.4008 (m-80) outliers start: 21 outliers final: 18 residues processed: 163 average time/residue: 0.1855 time to fit residues: 48.2893 Evaluate side-chains 168 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 289 LEU 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 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 A residue 1078 ARG Chi-restraints excluded: chain B residue 188 MET 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 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 865 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 5 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 166 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.187821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.160665 restraints weight = 16570.928| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.38 r_work: 0.3874 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13010 Z= 0.132 Angle : 0.611 10.261 17828 Z= 0.292 Chirality : 0.044 0.460 2182 Planarity : 0.004 0.034 2194 Dihedral : 4.976 56.501 2030 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.91 % Allowed : 14.81 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.21), residues: 1742 helix: 2.08 (0.18), residues: 890 sheet: 0.98 (0.46), residues: 120 loop : -1.63 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 635 HIS 0.003 0.001 HIS A 344 PHE 0.018 0.001 PHE B1059 TYR 0.010 0.001 TYR B 292 ARG 0.005 0.000 ARG B 528 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 4) link_NAG-ASN : angle 4.92856 ( 12) link_BETA1-4 : bond 0.00747 ( 4) link_BETA1-4 : angle 3.77464 ( 12) hydrogen bonds : bond 0.04364 ( 707) hydrogen bonds : angle 3.86019 ( 2052) SS BOND : bond 0.00735 ( 6) SS BOND : angle 1.79449 ( 12) covalent geometry : bond 0.00309 (12996) covalent geometry : angle 0.58809 (17792) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6495.50 seconds wall clock time: 111 minutes 58.80 seconds (6718.80 seconds total)