Starting phenix.real_space_refine on Fri Jul 3 07:18:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tth_26115/07_2026/7tth_26115.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tth_26115/07_2026/7tth_26115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tth_26115/07_2026/7tth_26115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tth_26115/07_2026/7tth_26115.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tth_26115/07_2026/7tth_26115.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tth_26115/07_2026/7tth_26115.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tth_26115/07_2026/7tth_26115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tth_26115/07_2026/7tth_26115.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 82 5.16 5 C 8296 2.51 5 N 2114 2.21 5 O 2204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12698 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 875, 6292 Classifications: {'peptide': 875} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'CIS': 3, 'PTRANS': 38, 'TRANS': 833} Chain breaks: 1 Unresolved non-hydrogen bonds: 496 Unresolved non-hydrogen angles: 618 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 28, 'GLN:plan1': 9, 'PHE:plan': 5, 'ASN:plan1': 7, 'ARG:plan': 9, 'HIS:plan': 6, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 333 Chain: "B" Number of atoms: 6292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 875, 6292 Classifications: {'peptide': 875} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'CIS': 3, 'PTRANS': 38, 'TRANS': 833} Chain breaks: 1 Unresolved non-hydrogen bonds: 496 Unresolved non-hydrogen angles: 618 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 28, 'GLN:plan1': 9, 'PHE:plan': 5, 'ASN:plan1': 7, 'ARG:plan': 9, 'HIS:plan': 6, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 333 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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: 2.93, per 1000 atoms: 0.23 Number of scatterers: 12698 At special positions: 0 Unit cell: (114.66, 95.004, 149.604, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 82 16.00 O 2204 8.00 N 2114 7.00 C 8296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.04 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.04 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 361 " " NAG E 1 " - " ASN B 312 " " NAG F 1 " - " ASN B 361 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 732.3 milliseconds 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 6 sheets defined 58.9% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 141 through 177 removed outlier: 6.965A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 198 through 227 removed outlier: 3.726A pdb=" N ALA A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 269 removed outlier: 4.319A pdb=" N ALA A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 298 removed outlier: 4.067A pdb=" N SER A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.523A pdb=" N SER A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.800A pdb=" N MET A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 removed outlier: 3.568A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 446 through 477 removed outlier: 3.927A pdb=" N ILE A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Proline residue: A 452 - end of helix Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.542A pdb=" N GLY A 487 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 488' Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'A' and resid 503 through 537 removed outlier: 4.245A pdb=" N ILE A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 543 through 547 removed outlier: 3.976A pdb=" N HIS A 547 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 570 Processing helix chain 'A' and resid 573 through 602 Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.562A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 661 Processing helix chain 'A' and resid 666 through 680 removed outlier: 3.651A pdb=" N ALA A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 720 removed outlier: 3.756A pdb=" N LEU A 712 " --> pdb=" O TYR A 708 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 756 removed outlier: 3.796A pdb=" N ILE A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 756 " --> pdb=" O MET A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 781 removed outlier: 4.206A pdb=" N GLN A 779 " --> pdb=" O ALA A 775 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N CYS A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 821 removed outlier: 3.922A pdb=" N THR A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 Processing helix chain 'A' and resid 854 through 859 removed outlier: 3.859A pdb=" N LEU A 858 " --> pdb=" O ASP A 854 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET A 859 " --> pdb=" O GLY A 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 854 through 859' Processing helix chain 'A' and resid 860 through 867 removed outlier: 4.115A pdb=" N GLN A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 902 removed outlier: 3.790A pdb=" N LYS A 893 " --> pdb=" O ILE A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1034 removed outlier: 3.947A pdb=" N VAL A1023 " --> pdb=" O MET A1019 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A1028 " --> pdb=" O LYS A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1064 removed outlier: 4.287A pdb=" N GLU A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL A1062 " --> pdb=" O GLU A1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 141 through 177 removed outlier: 6.999A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 198 through 227 removed outlier: 3.755A pdb=" N ALA B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 269 removed outlier: 4.130A pdb=" N ALA B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 298 removed outlier: 4.043A pdb=" N SER B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 removed outlier: 3.516A pdb=" N SER B 340 " --> pdb=" O THR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.697A pdb=" N MET B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.587A pdb=" N LEU B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 433 through 439 removed outlier: 3.518A pdb=" N SER B 438 " --> pdb=" O MET B 435 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 439 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 477 removed outlier: 3.934A pdb=" N ILE B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Proline residue: B 452 - end of helix Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.507A pdb=" N GLY B 487 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B 488 " --> pdb=" O LYS B 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 484 through 488' Processing helix chain 'B' and resid 495 through 499 Processing helix chain 'B' and resid 503 through 537 removed outlier: 4.317A pdb=" N ILE B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 543 through 547 removed outlier: 3.849A pdb=" N HIS B 547 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 570 Processing helix chain 'B' and resid 573 through 602 removed outlier: 3.530A pdb=" N ALA B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Proline residue: B 579 - end of helix Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.559A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 661 Processing helix chain 'B' and resid 666 through 680 removed outlier: 3.637A pdb=" N ALA B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 720 removed outlier: 3.778A pdb=" N LEU B 712 " --> pdb=" O TYR B 708 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 719 " --> pdb=" O ALA B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 756 removed outlier: 3.504A pdb=" N ALA B 742 " --> pdb=" O SER B 738 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 756 " --> pdb=" O MET B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 781 removed outlier: 4.201A pdb=" N GLN B 779 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N CYS B 781 " --> pdb=" O LEU B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 821 removed outlier: 3.774A pdb=" N THR B 810 " --> pdb=" O ARG B 806 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N PHE B 811 " --> pdb=" O ALA B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 834 Processing helix chain 'B' and resid 854 through 859 removed outlier: 3.839A pdb=" N LEU B 858 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET B 859 " --> pdb=" O GLY B 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 854 through 859' Processing helix chain 'B' and resid 860 through 867 removed outlier: 4.117A pdb=" N GLN B 867 " --> pdb=" O PHE B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 874 removed outlier: 4.323A pdb=" N LYS B 873 " --> pdb=" O VAL B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 902 removed outlier: 3.588A pdb=" N LYS B 893 " --> pdb=" O ILE B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1034 removed outlier: 3.905A pdb=" N VAL B1023 " --> pdb=" O MET B1019 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B1028 " --> pdb=" O LYS B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1064 removed outlier: 4.460A pdb=" N GLU B1061 " --> pdb=" O MET B1057 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL B1062 " --> pdb=" O GLU B1058 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AA3, first strand: chain 'A' and resid 761 through 767 removed outlier: 6.511A pdb=" N THR A 725 " --> pdb=" O PHE A 761 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN A 763 " --> pdb=" O THR A 725 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 727 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL A 765 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER A 729 " --> pdb=" O VAL A 765 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA A 767 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE A 731 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU A 694 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLY A 728 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 696 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N VAL A 730 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU A 695 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL A1070 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A1039 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL A1073 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU A1041 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP A 847 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ASN A1042 " --> pdb=" O ASP A 847 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N TRP A 849 " --> pdb=" O ASN A1042 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AA5, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AA6, first strand: chain 'B' and resid 761 through 767 removed outlier: 6.382A pdb=" N THR B 725 " --> pdb=" O PHE B 761 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLN B 763 " --> pdb=" O THR B 725 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL B 727 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL B 765 " --> pdb=" O VAL B 727 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER B 729 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ALA B 767 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE B 731 " --> pdb=" O ALA B 767 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU B 694 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLY B 728 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 696 " --> pdb=" O GLY B 728 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL B 730 " --> pdb=" O VAL B 696 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 695 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B1070 " --> pdb=" O LYS B 829 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B1039 " --> pdb=" O LEU B1071 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL B1073 " --> pdb=" O VAL B1039 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B1041 " --> pdb=" O VAL B1073 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASP B 847 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ASN B1042 " --> pdb=" O ASP B 847 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N TRP B 849 " --> pdb=" O ASN B1042 " (cutoff:3.500A) 707 hydrogen bonds defined for protein. 2052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.44 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 - 15.26: 6861 15.26 - 30.52: 492 30.52 - 45.77: 98 45.77 - 61.03: 23 61.03 - 76.29: 8 Dihedral angle restraints: 7482 sinusoidal: 2460 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 7479 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.540 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 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 : 11.663 76.291 4248 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.21), residues: 1742 helix: 1.66 (0.18), residues: 862 sheet: -0.66 (0.45), residues: 142 loop : -2.00 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 528 TYR 0.013 0.001 TYR B 216 PHE 0.016 0.001 PHE A 591 TRP 0.017 0.001 TRP B 556 HIS 0.003 0.001 HIS A 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (12996) covalent geometry : angle 0.70486 / 0.38 (17792) SS BOND : bond 0.00683 / 0.41 ( 6) SS BOND : angle 1.85366 / 1.00 ( 12) hydrogen bonds : bond 0.16076 / 10.95 ( 707) hydrogen bonds : angle 6.09337 / 4.51 ( 2052) link_BETA1-4 : bond 0.01701 / 1.17 ( 4) link_BETA1-4 : angle 3.89388 / 2.40 ( 12) link_NAG-ASN : bond 0.01645 / 1.16 ( 4) link_NAG-ASN : angle 6.48773 / 3.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.415 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: 0.1013 time to fit residues: 36.6030 Evaluate side-chains 167 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 537 ASN B 537 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.192778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.165226 restraints weight = 16674.970| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.46 r_work: 0.3908 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1391 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= 0.140 Angle : 0.652 11.731 17828 Z= 0.314 Chirality : 0.045 0.364 2182 Planarity : 0.004 0.034 2194 Dihedral : 4.195 26.554 1862 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.25 % Allowed : 7.32 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.21), residues: 1742 helix: 1.77 (0.18), residues: 878 sheet: -0.53 (0.45), residues: 146 loop : -1.81 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 528 TYR 0.012 0.001 TYR A 292 PHE 0.015 0.001 PHE A1059 TRP 0.010 0.001 TRP B 690 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (12996) covalent geometry : angle 0.63052 / 0.31 (17792) SS BOND : bond 0.00610 / 0.36 ( 6) SS BOND : angle 1.50974 / 0.82 ( 12) hydrogen bonds : bond 0.04985 / 3.28 ( 707) hydrogen bonds : angle 4.47620 / 3.32 ( 2052) link_BETA1-4 : bond 0.01333 / 0.85 ( 4) link_BETA1-4 : angle 2.73649 / 1.79 ( 12) link_NAG-ASN : bond 0.00887 / 0.63 ( 4) link_NAG-ASN : angle 5.60852 / 3.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 231 PRO cc_start: 0.6908 (Cg_exo) cc_final: 0.6669 (Cg_endo) REVERT: A 556 TRP cc_start: 0.7073 (m-90) cc_final: 0.6692 (m100) REVERT: A 771 ARG cc_start: 0.7598 (ptp90) cc_final: 0.7371 (ptp90) REVERT: A 1059 PHE cc_start: 0.5007 (p90) cc_final: 0.3952 (m-80) REVERT: B 312 ASN cc_start: 0.8290 (t0) cc_final: 0.8089 (t0) REVERT: B 1059 PHE cc_start: 0.5160 (p90) cc_final: 0.4069 (m-80) outliers start: 15 outliers final: 7 residues processed: 185 average time/residue: 0.0909 time to fit residues: 25.9075 Evaluate side-chains 164 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 B residue 465 VAL Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 121 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 537 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.190760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.163182 restraints weight = 16666.865| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.50 r_work: 0.3891 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1752 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= 0.135 Angle : 0.627 14.167 17828 Z= 0.299 Chirality : 0.044 0.335 2182 Planarity : 0.004 0.034 2194 Dihedral : 4.120 25.433 1862 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.66 % Allowed : 10.32 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.21), residues: 1742 helix: 1.82 (0.18), residues: 878 sheet: -0.53 (0.44), residues: 146 loop : -1.75 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 528 TYR 0.010 0.001 TYR B 292 PHE 0.020 0.001 PHE B1059 TRP 0.011 0.001 TRP B 635 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (12996) covalent geometry : angle 0.60760 / 0.29 (17792) SS BOND : bond 0.00365 / 0.22 ( 6) SS BOND : angle 1.43302 / 0.80 ( 12) hydrogen bonds : bond 0.04743 / 3.12 ( 707) hydrogen bonds : angle 4.23315 / 3.13 ( 2052) link_BETA1-4 : bond 0.01046 / 0.64 ( 4) link_BETA1-4 : angle 2.73486 / 1.79 ( 12) link_NAG-ASN : bond 0.00903 / 0.64 ( 4) link_NAG-ASN : angle 5.15520 / 2.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 231 PRO cc_start: 0.6968 (Cg_exo) cc_final: 0.6763 (Cg_endo) REVERT: A 262 MET cc_start: 0.6571 (mtp) cc_final: 0.6355 (mtp) REVERT: A 478 GLU cc_start: 0.6972 (pm20) cc_final: 0.6610 (pm20) REVERT: A 521 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6890 (mp-120) REVERT: A 556 TRP cc_start: 0.7254 (m-90) cc_final: 0.6777 (m100) REVERT: A 587 MET cc_start: 0.8022 (tpt) cc_final: 0.7669 (tpp) REVERT: A 1059 PHE cc_start: 0.5395 (p90) cc_final: 0.3858 (m-80) REVERT: B 312 ASN cc_start: 0.8399 (t0) cc_final: 0.8183 (t0) REVERT: B 536 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6938 (t0) REVERT: B 587 MET cc_start: 0.7994 (tpt) cc_final: 0.7595 (tpp) REVERT: B 1059 PHE cc_start: 0.5419 (p90) cc_final: 0.3958 (m-80) outliers start: 20 outliers final: 10 residues processed: 186 average time/residue: 0.0861 time to fit residues: 24.6830 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 : 0.344 ------------------------------------------------------------------------------- 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 469 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 159 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 80 optimal weight: 0.0470 chunk 154 optimal weight: 4.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 ASN A 717 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.185085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157479 restraints weight = 16806.520| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.47 r_work: 0.3847 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13010 Z= 0.165 Angle : 0.650 9.743 17828 Z= 0.316 Chirality : 0.046 0.325 2182 Planarity : 0.004 0.034 2194 Dihedral : 4.276 29.893 1862 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.83 % Allowed : 11.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.20), residues: 1742 helix: 1.70 (0.17), residues: 880 sheet: 0.45 (0.43), residues: 120 loop : -1.79 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 771 TYR 0.012 0.001 TYR B 466 PHE 0.024 0.002 PHE B1059 TRP 0.011 0.001 TRP B 635 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 (12996) covalent geometry : angle 0.63224 / 0.31 (17792) SS BOND : bond 0.00833 / 0.49 ( 6) SS BOND : angle 2.19019 / 1.23 ( 12) hydrogen bonds : bond 0.05075 / 3.34 ( 707) hydrogen bonds : angle 4.16252 / 3.08 ( 2052) link_BETA1-4 : bond 0.00960 / 0.58 ( 4) link_BETA1-4 : angle 2.44970 / 1.59 ( 12) link_NAG-ASN : bond 0.00758 / 0.54 ( 4) link_NAG-ASN : angle 4.95732 / 2.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 410 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6508 (tt) REVERT: A 478 GLU cc_start: 0.7340 (pm20) cc_final: 0.7133 (pm20) REVERT: A 521 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.7088 (mp-120) REVERT: A 587 MET cc_start: 0.8043 (tpt) cc_final: 0.7707 (tpp) REVERT: A 1059 PHE cc_start: 0.6128 (p90) cc_final: 0.3828 (m-80) REVERT: B 410 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6518 (tt) REVERT: B 536 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6942 (t0) REVERT: B 587 MET cc_start: 0.7992 (tpt) cc_final: 0.7680 (tpp) REVERT: B 1059 PHE cc_start: 0.5950 (p90) cc_final: 0.3959 (m-80) outliers start: 34 outliers final: 18 residues processed: 185 average time/residue: 0.0843 time to fit residues: 24.4027 Evaluate side-chains 178 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 524 THR 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 850 TRP Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 75 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.187087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.159372 restraints weight = 16863.880| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.49 r_work: 0.3867 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13010 Z= 0.130 Angle : 0.601 9.561 17828 Z= 0.291 Chirality : 0.044 0.317 2182 Planarity : 0.004 0.032 2194 Dihedral : 4.100 25.708 1862 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.83 % Allowed : 13.48 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.21), residues: 1742 helix: 1.87 (0.18), residues: 882 sheet: -0.45 (0.42), residues: 146 loop : -1.72 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 528 TYR 0.011 0.001 TYR A 292 PHE 0.021 0.001 PHE B1059 TRP 0.011 0.001 TRP A 635 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (12996) covalent geometry : angle 0.58335 / 0.29 (17792) SS BOND : bond 0.00821 / 0.48 ( 6) SS BOND : angle 1.94462 / 1.09 ( 12) hydrogen bonds : bond 0.04614 / 3.03 ( 707) hydrogen bonds : angle 4.06882 / 3.00 ( 2052) link_BETA1-4 : bond 0.00968 / 0.59 ( 4) link_BETA1-4 : angle 2.51169 / 1.63 ( 12) link_NAG-ASN : bond 0.00766 / 0.53 ( 4) link_NAG-ASN : angle 4.65674 / 2.57 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7212 (mt0) REVERT: A 410 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6224 (tt) REVERT: A 478 GLU cc_start: 0.7175 (pm20) cc_final: 0.6947 (pm20) REVERT: A 521 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.7038 (mp-120) REVERT: A 587 MET cc_start: 0.7979 (tpt) cc_final: 0.7657 (tpp) REVERT: A 1059 PHE cc_start: 0.5994 (p90) cc_final: 0.3663 (m-80) REVERT: B 536 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6884 (t0) REVERT: B 587 MET cc_start: 0.7914 (tpt) cc_final: 0.7599 (tpp) REVERT: B 1059 PHE cc_start: 0.6044 (p90) cc_final: 0.4026 (m-80) outliers start: 22 outliers final: 10 residues processed: 180 average time/residue: 0.0971 time to fit residues: 27.2181 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 : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 83 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.187319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.159690 restraints weight = 16668.798| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.48 r_work: 0.3861 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13010 Z= 0.128 Angle : 0.592 9.368 17828 Z= 0.287 Chirality : 0.043 0.309 2182 Planarity : 0.004 0.033 2194 Dihedral : 4.007 23.819 1862 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.00 % Allowed : 13.64 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.21), residues: 1742 helix: 1.92 (0.18), residues: 888 sheet: -0.45 (0.42), residues: 146 loop : -1.69 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 528 TYR 0.009 0.001 TYR A 292 PHE 0.020 0.001 PHE B1059 TRP 0.010 0.001 TRP A 635 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (12996) covalent geometry : angle 0.57584 / 0.28 (17792) SS BOND : bond 0.00805 / 0.47 ( 6) SS BOND : angle 1.83599 / 1.03 ( 12) hydrogen bonds : bond 0.04464 / 2.93 ( 707) hydrogen bonds : angle 3.96847 / 2.93 ( 2052) link_BETA1-4 : bond 0.00918 / 0.55 ( 4) link_BETA1-4 : angle 2.45045 / 1.59 ( 12) link_NAG-ASN : bond 0.00741 / 0.52 ( 4) link_NAG-ASN : angle 4.49250 / 2.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7408 (mt0) REVERT: A 410 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6355 (tt) REVERT: A 478 GLU cc_start: 0.7177 (pm20) cc_final: 0.6859 (pm20) REVERT: A 484 ASP cc_start: 0.8218 (t0) cc_final: 0.7982 (t0) REVERT: A 521 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.7009 (mp-120) REVERT: A 587 MET cc_start: 0.7990 (tpt) cc_final: 0.7673 (tpp) REVERT: A 1059 PHE cc_start: 0.6178 (p90) cc_final: 0.3634 (m-80) REVERT: B 251 MET cc_start: 0.6324 (mtt) cc_final: 0.6115 (mtt) REVERT: B 319 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7258 (mt0) REVERT: B 536 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6853 (t0) REVERT: B 587 MET cc_start: 0.7913 (tpt) cc_final: 0.7602 (tpp) REVERT: B 808 TRP cc_start: 0.5813 (p-90) cc_final: 0.5487 (p-90) REVERT: B 1059 PHE cc_start: 0.6088 (p90) cc_final: 0.3845 (m-80) outliers start: 36 outliers final: 24 residues processed: 190 average time/residue: 0.0885 time to fit residues: 26.3146 Evaluate side-chains 186 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 850 TRP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 465 VAL 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 591 PHE Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 850 TRP Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.186576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.158926 restraints weight = 16676.489| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.48 r_work: 0.3851 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13010 Z= 0.131 Angle : 0.600 9.230 17828 Z= 0.290 Chirality : 0.044 0.301 2182 Planarity : 0.004 0.035 2194 Dihedral : 3.984 23.136 1862 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.75 % Allowed : 15.72 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.21), residues: 1742 helix: 1.88 (0.18), residues: 900 sheet: -0.44 (0.42), residues: 150 loop : -1.72 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 528 TYR 0.010 0.001 TYR B 292 PHE 0.020 0.001 PHE B 545 TRP 0.011 0.001 TRP A 635 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (12996) covalent geometry : angle 0.58529 / 0.29 (17792) SS BOND : bond 0.00707 / 0.41 ( 6) SS BOND : angle 1.64324 / 0.87 ( 12) hydrogen bonds : bond 0.04464 / 2.94 ( 707) hydrogen bonds : angle 3.95862 / 2.93 ( 2052) link_BETA1-4 : bond 0.00907 / 0.54 ( 4) link_BETA1-4 : angle 2.34878 / 1.53 ( 12) link_NAG-ASN : bond 0.00711 / 0.50 ( 4) link_NAG-ASN : angle 4.39418 / 2.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6890 (pm20) REVERT: A 521 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6981 (mp-120) REVERT: A 587 MET cc_start: 0.7987 (tpt) cc_final: 0.7653 (tpp) REVERT: A 1059 PHE cc_start: 0.6260 (p90) cc_final: 0.3492 (m-80) REVERT: B 536 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6875 (t0) REVERT: B 587 MET cc_start: 0.7934 (tpt) cc_final: 0.7626 (tpp) REVERT: B 808 TRP cc_start: 0.5816 (p-90) cc_final: 0.5485 (p-90) REVERT: B 1059 PHE cc_start: 0.6232 (p90) cc_final: 0.3823 (m-80) outliers start: 33 outliers final: 23 residues processed: 179 average time/residue: 0.0982 time to fit residues: 27.2649 Evaluate side-chains 180 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 850 TRP Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 39 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 28 optimal weight: 0.0020 chunk 127 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.188459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.161528 restraints weight = 16504.579| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.35 r_work: 0.3879 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 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 = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13010 Z= 0.119 Angle : 0.590 9.166 17828 Z= 0.283 Chirality : 0.043 0.293 2182 Planarity : 0.004 0.035 2194 Dihedral : 3.905 26.920 1862 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.66 % Allowed : 15.89 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1742 helix: 1.97 (0.18), residues: 900 sheet: -0.28 (0.43), residues: 146 loop : -1.69 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 528 TYR 0.009 0.001 TYR A 292 PHE 0.017 0.001 PHE B 545 TRP 0.011 0.001 TRP A 635 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (12996) covalent geometry : angle 0.57475 / 0.28 (17792) SS BOND : bond 0.00562 / 0.33 ( 6) SS BOND : angle 1.68113 / 0.88 ( 12) hydrogen bonds : bond 0.04222 / 2.77 ( 707) hydrogen bonds : angle 3.90499 / 2.89 ( 2052) link_BETA1-4 : bond 0.00880 / 0.51 ( 4) link_BETA1-4 : angle 2.36619 / 1.54 ( 12) link_NAG-ASN : bond 0.00751 / 0.52 ( 4) link_NAG-ASN : angle 4.32911 / 2.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6689 (pm20) REVERT: A 521 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7039 (mp-120) REVERT: A 587 MET cc_start: 0.7824 (tpt) cc_final: 0.7536 (tpp) REVERT: B 536 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6851 (t0) REVERT: B 587 MET cc_start: 0.7797 (tpt) cc_final: 0.7559 (tpp) REVERT: B 808 TRP cc_start: 0.5846 (p-90) cc_final: 0.5474 (p-90) REVERT: B 1059 PHE cc_start: 0.6500 (p90) cc_final: 0.4074 (m-80) outliers start: 32 outliers final: 26 residues processed: 178 average time/residue: 0.0881 time to fit residues: 24.8149 Evaluate side-chains 180 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 850 TRP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 465 VAL 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 591 PHE 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 139 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 ASN B 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.182893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.154934 restraints weight = 16903.073| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.49 r_work: 0.3814 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13010 Z= 0.174 Angle : 0.649 9.105 17828 Z= 0.317 Chirality : 0.046 0.293 2182 Planarity : 0.004 0.033 2194 Dihedral : 4.165 26.789 1862 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.83 % Allowed : 16.22 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.21), residues: 1742 helix: 1.69 (0.17), residues: 904 sheet: 0.62 (0.44), residues: 120 loop : -1.81 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 528 TYR 0.012 0.001 TYR B 466 PHE 0.022 0.002 PHE A 545 TRP 0.010 0.001 TRP A 690 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.17 (12996) covalent geometry : angle 0.63328 / 0.31 (17792) SS BOND : bond 0.00955 / 0.55 ( 6) SS BOND : angle 2.41929 / 1.30 ( 12) hydrogen bonds : bond 0.05065 / 3.34 ( 707) hydrogen bonds : angle 4.08504 / 3.02 ( 2052) link_BETA1-4 : bond 0.00854 / 0.50 ( 4) link_BETA1-4 : angle 2.19284 / 1.41 ( 12) link_NAG-ASN : bond 0.00638 / 0.45 ( 4) link_NAG-ASN : angle 4.46637 / 2.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 379 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8678 (p0) REVERT: A 478 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7032 (pm20) REVERT: A 521 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7083 (mp-120) REVERT: A 587 MET cc_start: 0.8013 (tpt) cc_final: 0.7706 (tpp) REVERT: A 808 TRP cc_start: 0.6037 (p-90) cc_final: 0.5735 (p-90) REVERT: B 379 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8753 (p0) REVERT: B 536 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6945 (t0) REVERT: B 587 MET cc_start: 0.8019 (tpt) cc_final: 0.7742 (tpp) REVERT: B 808 TRP cc_start: 0.5829 (p-90) cc_final: 0.5516 (p-90) outliers start: 34 outliers final: 23 residues processed: 169 average time/residue: 0.0938 time to fit residues: 24.6436 Evaluate side-chains 169 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 850 TRP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 465 VAL 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 827 VAL Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 1062 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 114 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 31 optimal weight: 0.0000 chunk 78 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 ASN B 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.182460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.155123 restraints weight = 16759.599| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.42 r_work: 0.3809 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 13010 Z= 0.197 Angle : 1.023 59.127 17828 Z= 0.588 Chirality : 0.047 0.440 2182 Planarity : 0.004 0.043 2194 Dihedral : 4.198 26.714 1862 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.66 % Allowed : 16.64 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.21), residues: 1742 helix: 1.68 (0.17), residues: 904 sheet: 0.61 (0.44), residues: 120 loop : -1.81 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 528 TYR 0.012 0.001 TYR B 292 PHE 0.019 0.002 PHE A 545 TRP 0.010 0.001 TRP A 690 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (12996) covalent geometry : angle 1.01446 / 0.59 (17792) SS BOND : bond 0.00895 / 0.51 ( 6) SS BOND : angle 2.24029 / 1.19 ( 12) hydrogen bonds : bond 0.05001 / 3.29 ( 707) hydrogen bonds : angle 4.08334 / 3.02 ( 2052) link_BETA1-4 : bond 0.00654 / 0.40 ( 4) link_BETA1-4 : angle 2.20204 / 1.44 ( 12) link_NAG-ASN : bond 0.00661 / 0.47 ( 4) link_NAG-ASN : angle 4.46966 / 2.45 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6999 (pm20) REVERT: A 521 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7099 (mp-120) REVERT: A 587 MET cc_start: 0.7981 (tpt) cc_final: 0.7666 (tpp) REVERT: A 808 TRP cc_start: 0.6029 (p-90) cc_final: 0.5724 (p-90) REVERT: B 536 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6950 (t0) REVERT: B 587 MET cc_start: 0.7988 (tpt) cc_final: 0.7724 (tpp) REVERT: B 808 TRP cc_start: 0.5811 (p-90) cc_final: 0.5501 (p-90) outliers start: 32 outliers final: 25 residues processed: 168 average time/residue: 0.0918 time to fit residues: 24.5151 Evaluate side-chains 169 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 850 TRP 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 465 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 64 optimal weight: 0.5980 chunk 156 optimal weight: 0.0870 chunk 171 optimal weight: 4.9990 chunk 68 optimal weight: 0.0970 chunk 71 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.185133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.157318 restraints weight = 16744.399| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.48 r_work: 0.3836 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13010 Z= 0.134 Angle : 0.633 9.193 17828 Z= 0.310 Chirality : 0.044 0.291 2182 Planarity : 0.004 0.034 2194 Dihedral : 4.108 27.011 1862 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.41 % Allowed : 16.81 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.21), residues: 1742 helix: 1.77 (0.17), residues: 902 sheet: 0.63 (0.44), residues: 120 loop : -1.80 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 528 TYR 0.012 0.001 TYR B 292 PHE 0.024 0.001 PHE B 545 TRP 0.018 0.001 TRP B 850 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (12996) covalent geometry : angle 0.61812 / 0.31 (17792) SS BOND : bond 0.00823 / 0.48 ( 6) SS BOND : angle 2.02566 / 1.10 ( 12) hydrogen bonds : bond 0.04751 / 3.12 ( 707) hydrogen bonds : angle 4.01886 / 2.97 ( 2052) link_BETA1-4 : bond 0.00648 / 0.39 ( 4) link_BETA1-4 : angle 2.28827 / 1.47 ( 12) link_NAG-ASN : bond 0.00752 / 0.52 ( 4) link_NAG-ASN : angle 4.45266 / 2.44 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3003.98 seconds wall clock time: 52 minutes 10.96 seconds (3130.96 seconds total)