Starting phenix.real_space_refine on Sun Sep 13 07:14:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6cna_7529/09_2026/6cna_7529.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cna_7529/09_2026/6cna_7529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cna_7529/09_2026/6cna_7529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cna_7529/09_2026/6cna_7529.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6cna_7529/09_2026/6cna_7529.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6cna_7529/09_2026/6cna_7529.cif" model { file = "/net/cci-nas-00/data/ceres_data/6cna_7529/09_2026/6cna_7529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cna_7529/09_2026/6cna_7529.cif" } resolution = 4.6 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= 0.004 sd= 1.443 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: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 13514 2.51 5 N 3632 2.21 5 O 4176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21426 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5381 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 795, 5381 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 247} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 761} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1130 Unresolved non-hydrogen dihedrals: 774 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'ARG:plan': 26, 'GLU:plan': 26, 'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 8, 'ASP:plan': 12, 'ASN:plan1': 7, 'PHE:plan': 11} Unresolved non-hydrogen planarities: 481 Chain: "B" Number of atoms: 5178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5178 Classifications: {'peptide': 785} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 281} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 755} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1050 Unresolved non-hydrogen angles: 1297 Unresolved non-hydrogen dihedrals: 896 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 34, 'HIS:plan': 6, 'ARG:plan': 18, 'GLN:plan1': 13, 'PHE:plan': 17, 'TYR:plan': 7, 'TRP:plan': 3, 'ASN:plan1': 12} Unresolved non-hydrogen planarities: 567 Chain: "C" Number of atoms: 5381 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 795, 5381 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 247} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 761} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1130 Unresolved non-hydrogen dihedrals: 774 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'ARG:plan': 26, 'GLU:plan': 26, 'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 8, 'ASP:plan': 12, 'ASN:plan1': 7, 'PHE:plan': 11} Unresolved non-hydrogen planarities: 481 Chain: "D" Number of atoms: 5178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5178 Classifications: {'peptide': 785} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 281} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 755} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1050 Unresolved non-hydrogen angles: 1297 Unresolved non-hydrogen dihedrals: 896 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 34, 'HIS:plan': 6, 'ARG:plan': 18, 'GLN:plan1': 13, 'PHE:plan': 17, 'TYR:plan': 7, 'TRP:plan': 3, 'ASN:plan1': 12} Unresolved non-hydrogen planarities: 567 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: "G" 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: "H" 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: "I" 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: "J" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" 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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 Time building chain proxies: 4.84, per 1000 atoms: 0.23 Number of scatterers: 21426 At special positions: 0 Unit cell: (116.59, 142.79, 174.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 4176 8.00 N 3632 7.00 C 13514 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.02 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.04 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.02 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.04 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.02 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.04 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.02 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 904 " - " ASN A 297 " " NAG A 905 " - " ASN A 321 " " NAG B 903 " - " ASN B 74 " " NAG B 904 " - " ASN B 341 " " NAG C 904 " - " ASN C 297 " " NAG C 905 " - " ASN C 321 " " NAG D 903 " - " ASN D 74 " " NAG D 904 " - " ASN D 341 " " NAG E 1 " - " ASN A 389 " " NAG F 1 " - " ASN A 224 " " NAG G 1 " - " ASN B 688 " " NAG H 1 " - " ASN C 389 " " NAG I 1 " - " ASN C 224 " " NAG J 1 " - " ASN D 688 " Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 881.9 milliseconds 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5896 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 32 sheets defined 44.1% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.548A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.801A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 159 removed outlier: 3.693A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 225 through 235 removed outlier: 3.728A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.700A pdb=" N TYR A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.760A pdb=" N GLU A 318 " --> pdb=" O HIS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 543 through 546 Processing helix chain 'A' and resid 580 through 605 removed outlier: 4.387A pdb=" N SER A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.860A pdb=" N MET A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 677 Processing helix chain 'A' and resid 690 through 695 Processing helix chain 'A' and resid 708 through 716 removed outlier: 4.217A pdb=" N ARG A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 728 removed outlier: 3.763A pdb=" N GLU A 728 " --> pdb=" O TYR A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 744 Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 788 through 802 removed outlier: 3.998A pdb=" N GLN A 792 " --> pdb=" O PRO A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 813 Processing helix chain 'A' and resid 832 through 862 Processing helix chain 'B' and resid 46 through 57 removed outlier: 3.534A pdb=" N ILE B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.768A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 120 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 149 through 165 removed outlier: 4.109A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 4.028A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.667A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 4.251A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 322 through 326 removed outlier: 3.508A pdb=" N HIS B 325 " --> pdb=" O TYR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 341 removed outlier: 4.460A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 519 through 523 removed outlier: 3.612A pdb=" N VAL B 522 " --> pdb=" O ARG B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 556 Processing helix chain 'B' and resid 556 through 578 removed outlier: 4.041A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 613 Processing helix chain 'B' and resid 625 through 655 Processing helix chain 'B' and resid 673 through 677 removed outlier: 3.973A pdb=" N PHE B 677 " --> pdb=" O PRO B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 699 removed outlier: 4.410A pdb=" N ASN B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.715A pdb=" N HIS B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 713 through 724 removed outlier: 3.850A pdb=" N ALA B 717 " --> pdb=" O GLY B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 771 through 786 removed outlier: 4.036A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 796 removed outlier: 4.199A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 843 removed outlier: 3.774A pdb=" N ALA B 819 " --> pdb=" O ILE B 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 51 removed outlier: 3.549A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 80 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 105 through 114 Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.803A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 159 removed outlier: 3.693A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 225 through 235 removed outlier: 3.728A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 234 " --> pdb=" O MET C 230 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 235 " --> pdb=" O GLU C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 259 Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.701A pdb=" N TYR C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 318 removed outlier: 3.760A pdb=" N GLU C 318 " --> pdb=" O HIS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 349 Processing helix chain 'C' and resid 478 through 491 Processing helix chain 'C' and resid 521 through 528 Processing helix chain 'C' and resid 543 through 546 Processing helix chain 'C' and resid 580 through 605 removed outlier: 4.387A pdb=" N SER C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 removed outlier: 3.860A pdb=" N MET C 628 " --> pdb=" O LEU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 677 Processing helix chain 'C' and resid 690 through 695 Processing helix chain 'C' and resid 708 through 716 removed outlier: 4.217A pdb=" N ARG C 716 " --> pdb=" O ILE C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 728 removed outlier: 3.763A pdb=" N GLU C 728 " --> pdb=" O TYR C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 744 Processing helix chain 'C' and resid 754 through 764 Processing helix chain 'C' and resid 788 through 802 removed outlier: 3.997A pdb=" N GLN C 792 " --> pdb=" O PRO C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 813 Processing helix chain 'C' and resid 832 through 862 Processing helix chain 'D' and resid 46 through 57 removed outlier: 3.533A pdb=" N ILE D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.769A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 149 through 165 removed outlier: 4.110A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 removed outlier: 4.028A pdb=" N ASN D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 221 Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.667A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 removed outlier: 4.251A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 322 through 326 removed outlier: 3.508A pdb=" N HIS D 325 " --> pdb=" O TYR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 341 removed outlier: 4.460A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 Processing helix chain 'D' and resid 496 through 503 Processing helix chain 'D' and resid 519 through 523 removed outlier: 3.611A pdb=" N VAL D 522 " --> pdb=" O ARG D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 556 Processing helix chain 'D' and resid 556 through 578 removed outlier: 4.042A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL D 574 " --> pdb=" O SER D 570 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 613 Processing helix chain 'D' and resid 625 through 655 Processing helix chain 'D' and resid 673 through 677 removed outlier: 3.972A pdb=" N PHE D 677 " --> pdb=" O PRO D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 699 removed outlier: 4.411A pdb=" N ASN D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 removed outlier: 3.714A pdb=" N HIS D 703 " --> pdb=" O TYR D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 710 No H-bonds generated for 'chain 'D' and resid 708 through 710' Processing helix chain 'D' and resid 713 through 724 removed outlier: 3.850A pdb=" N ALA D 717 " --> pdb=" O GLY D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 771 through 786 removed outlier: 4.037A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 796 removed outlier: 4.199A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 843 removed outlier: 3.775A pdb=" N ALA D 819 " --> pdb=" O ILE D 815 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29 removed outlier: 5.523A pdb=" N VAL A 27 " --> pdb=" O GLN A 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 216 removed outlier: 3.525A pdb=" N VAL A 167 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 166 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 292 removed outlier: 6.549A pdb=" N TYR A 372 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE A 387 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 374 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 494 through 499 removed outlier: 8.552A pdb=" N MET A 533 " --> pdb=" O ARG A 418 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS A 420 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET A 783 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 431 through 433 Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.533A pdb=" N GLU A 509 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 702 through 704 removed outlier: 6.742A pdb=" N ALA A 703 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ASP A 753 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP A 752 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 563 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 768 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 702 through 704 removed outlier: 6.742A pdb=" N ALA A 703 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ASP A 753 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP A 752 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS A 555 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY A 778 " --> pdb=" O LYS A 555 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLN A 557 " --> pdb=" O ARG A 776 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ARG A 776 " --> pdb=" O GLN A 557 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 774 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 73 removed outlier: 5.833A pdb=" N ILE B 35 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLU B 69 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE B 37 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL B 71 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY B 36 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL B 98 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA B 100 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE B 40 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE B 126 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N PHE B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 202 through 204 removed outlier: 6.411A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 257 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 230 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B 280 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 366 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU B 374 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 351 through 352 removed outlier: 3.832A pdb=" N TYR B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 377 through 380 removed outlier: 3.770A pdb=" N LYS B 378 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 385 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 408 through 409 removed outlier: 3.641A pdb=" N VAL B 409 " --> pdb=" O MET B 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 434 through 436 Processing sheet with id=AB6, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.239A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 749 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.239A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE B 530 " --> pdb=" O GLY B 761 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY B 761 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR B 532 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N SER B 759 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 26 through 29 removed outlier: 5.523A pdb=" N VAL C 27 " --> pdb=" O GLN C 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 215 through 216 removed outlier: 3.525A pdb=" N VAL C 167 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU C 166 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 288 through 292 removed outlier: 6.549A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE C 374 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 494 through 499 removed outlier: 8.551A pdb=" N MET C 533 " --> pdb=" O ARG C 418 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS C 420 " --> pdb=" O MET C 533 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET C 783 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 431 through 433 Processing sheet with id=AC4, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.532A pdb=" N GLU C 509 " --> pdb=" O GLU C 518 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 702 through 704 removed outlier: 6.743A pdb=" N ALA C 703 " --> pdb=" O ILE C 751 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ASP C 753 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP C 752 " --> pdb=" O THR C 560 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL C 563 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 768 " --> pdb=" O VAL C 563 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 702 through 704 removed outlier: 6.743A pdb=" N ALA C 703 " --> pdb=" O ILE C 751 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ASP C 753 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP C 752 " --> pdb=" O THR C 560 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS C 555 " --> pdb=" O GLY C 778 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY C 778 " --> pdb=" O LYS C 555 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN C 557 " --> pdb=" O ARG C 776 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ARG C 776 " --> pdb=" O GLN C 557 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 774 " --> pdb=" O LEU C 559 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 66 through 73 removed outlier: 5.834A pdb=" N ILE D 35 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLU D 69 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE D 37 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL D 71 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY D 36 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ALA D 100 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE D 126 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N PHE D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 202 through 204 removed outlier: 6.412A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 257 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU D 230 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL D 280 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 366 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU D 374 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 351 through 352 removed outlier: 3.831A pdb=" N TYR D 356 " --> pdb=" O SER D 352 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 377 through 380 removed outlier: 3.770A pdb=" N LYS D 378 " --> pdb=" O GLN D 385 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN D 385 " --> pdb=" O LYS D 378 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 408 through 409 removed outlier: 3.641A pdb=" N VAL D 409 " --> pdb=" O MET D 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 434 through 436 Processing sheet with id=AD4, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.240A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 749 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.240A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE D 530 " --> pdb=" O GLY D 761 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY D 761 " --> pdb=" O ILE D 530 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR D 532 " --> pdb=" O SER D 759 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N SER D 759 " --> pdb=" O THR D 532 " (cutoff:3.500A) 1022 hydrogen bonds defined for protein. 2946 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.77 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7266 1.34 - 1.46: 5171 1.46 - 1.58: 9218 1.58 - 1.70: 1 1.70 - 1.82: 166 Bond restraints: 21822 Sorted by residual: bond pdb=" C VAL C 472 " pdb=" N PRO C 473 " ideal model delta sigma weight residual 1.334 1.588 -0.254 2.34e-02 1.83e+03 1.18e+02 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C VAL A 472 " pdb=" N PRO A 473 " ideal model delta sigma weight residual 1.334 1.395 -0.062 2.34e-02 1.83e+03 6.93e+00 bond pdb=" CB PHE A 550 " pdb=" CG PHE A 550 " ideal model delta sigma weight residual 1.502 1.457 0.045 2.30e-02 1.89e+03 3.85e+00 ... (remaining 21817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.01: 29961 6.01 - 12.02: 39 12.02 - 18.03: 2 18.03 - 24.04: 4 24.04 - 30.05: 2 Bond angle restraints: 30008 Sorted by residual: angle pdb=" O PRO A 473 " pdb=" C PRO A 473 " pdb=" N GLN A 474 " ideal model delta sigma weight residual 122.73 105.59 17.14 7.10e-01 1.98e+00 5.83e+02 angle pdb=" C VAL A 472 " pdb=" N PRO A 473 " pdb=" CA PRO A 473 " ideal model delta sigma weight residual 120.79 91.74 29.05 1.30e+00 5.92e-01 4.99e+02 angle pdb=" O VAL A 472 " pdb=" C VAL A 472 " pdb=" N PRO A 473 " ideal model delta sigma weight residual 121.10 139.13 -18.03 1.14e+00 7.69e-01 2.50e+02 angle pdb=" C VAL C 472 " pdb=" N PRO C 473 " pdb=" CA PRO C 473 " ideal model delta sigma weight residual 120.79 101.64 19.15 1.30e+00 5.92e-01 2.17e+02 angle pdb=" CA PRO A 473 " pdb=" C PRO A 473 " pdb=" N GLN A 474 " ideal model delta sigma weight residual 116.09 128.04 -11.95 9.20e-01 1.18e+00 1.69e+02 ... (remaining 30003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 12179 16.26 - 32.52: 287 32.52 - 48.79: 48 48.79 - 65.05: 6 65.05 - 81.31: 2 Dihedral angle restraints: 12522 sinusoidal: 3400 harmonic: 9122 Sorted by residual: dihedral pdb=" CA PRO D 415 " pdb=" C PRO D 415 " pdb=" N PHE D 416 " pdb=" CA PHE D 416 " ideal model delta harmonic sigma weight residual -180.00 -144.20 -35.80 0 5.00e+00 4.00e-02 5.13e+01 dihedral pdb=" CA PRO B 415 " pdb=" C PRO B 415 " pdb=" N PHE B 416 " pdb=" CA PHE B 416 " ideal model delta harmonic sigma weight residual -180.00 -144.21 -35.79 0 5.00e+00 4.00e-02 5.12e+01 dihedral pdb=" CA GLU D 449 " pdb=" C GLU D 449 " pdb=" N PRO D 450 " pdb=" CA PRO D 450 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 ... (remaining 12519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3634 0.120 - 0.241: 62 0.241 - 0.361: 4 0.361 - 0.482: 0 0.482 - 0.602: 2 Chirality restraints: 3702 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.37e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.12e+01 chirality pdb=" C1 NAG B 904 " pdb=" ND2 ASN B 341 " pdb=" C2 NAG B 904 " pdb=" O5 NAG B 904 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.06e+00 ... (remaining 3699 not shown) Planarity restraints: 3944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 473 " 0.045 2.00e-02 2.50e+03 8.99e-02 8.09e+01 pdb=" C PRO C 473 " -0.155 2.00e-02 2.50e+03 pdb=" O PRO C 473 " 0.060 2.00e-02 2.50e+03 pdb=" N GLN C 474 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 473 " -0.039 2.00e-02 2.50e+03 6.74e-02 4.55e+01 pdb=" C PRO A 473 " 0.117 2.00e-02 2.50e+03 pdb=" O PRO A 473 " -0.039 2.00e-02 2.50e+03 pdb=" N GLN A 474 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 269 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO B 270 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " -0.039 5.00e-02 4.00e+02 ... (remaining 3941 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 433 2.60 - 3.17: 22753 3.17 - 3.75: 32598 3.75 - 4.32: 43694 4.32 - 4.90: 63974 Nonbonded interactions: 163452 Sorted by model distance: nonbonded pdb=" O HIS D 127 " pdb=" OG SER D 130 " model vdw 2.021 3.040 nonbonded pdb=" O HIS B 127 " pdb=" OG SER B 130 " model vdw 2.021 3.040 nonbonded pdb=" O GLU C 758 " pdb=" OG SER C 762 " model vdw 2.047 3.040 nonbonded pdb=" O GLU A 758 " pdb=" OG SER A 762 " model vdw 2.048 3.040 nonbonded pdb=" OD2 ASP D 138 " pdb=" OG SER D 140 " model vdw 2.060 3.040 ... (remaining 163447 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.620 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 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 : 0.007 0.254 21858 Z= 0.330 Angle : 0.955 30.052 30100 Z= 0.556 Chirality : 0.052 0.602 3702 Planarity : 0.006 0.090 3930 Dihedral : 8.640 81.310 6578 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.65 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.80 (0.11), residues: 3128 helix: -3.86 (0.09), residues: 1220 sheet: -2.67 (0.21), residues: 336 loop : -2.67 (0.12), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 544 TYR 0.030 0.003 TYR B 179 PHE 0.027 0.003 PHE A 554 TRP 0.029 0.003 TRP B 796 HIS 0.008 0.003 HIS D 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.33 (21822) covalent geometry : angle 0.92749 / 0.55 (30008) SS BOND : bond 0.00646 / 0.50 ( 16) SS BOND : angle 1.67083 / 1.16 ( 32) hydrogen bonds : bond 0.15667 / 10.32 ( 1008) hydrogen bonds : angle 11.35714 / 8.17 ( 2946) link_BETA1-4 : bond 0.00650 / 0.31 ( 6) link_BETA1-4 : angle 1.92557 / 1.23 ( 18) link_NAG-ASN : bond 0.01294 / 0.83 ( 14) link_NAG-ASN : angle 5.94183 / 4.66 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9229 (mt) cc_final: 0.8559 (mt) REVERT: A 41 MET cc_start: 0.8292 (tpt) cc_final: 0.7912 (mtm) REVERT: A 42 PHE cc_start: 0.9295 (t80) cc_final: 0.8999 (t80) REVERT: A 65 VAL cc_start: 0.9096 (m) cc_final: 0.8849 (m) REVERT: A 76 LEU cc_start: 0.9321 (mt) cc_final: 0.9098 (mt) REVERT: A 127 ILE cc_start: 0.9615 (tp) cc_final: 0.9391 (tp) REVERT: A 147 GLN cc_start: 0.9194 (mt0) cc_final: 0.8913 (mt0) REVERT: A 151 TRP cc_start: 0.8355 (m-10) cc_final: 0.7958 (m-10) REVERT: A 152 PHE cc_start: 0.9460 (t80) cc_final: 0.8233 (t80) REVERT: A 155 MET cc_start: 0.8232 (mtp) cc_final: 0.7536 (ttm) REVERT: A 156 ARG cc_start: 0.8081 (mtp-110) cc_final: 0.7836 (ttp-110) REVERT: A 161 ASN cc_start: 0.8546 (m-40) cc_final: 0.8279 (m-40) REVERT: A 228 LEU cc_start: 0.9512 (mp) cc_final: 0.9280 (mp) REVERT: A 301 HIS cc_start: 0.8768 (m90) cc_final: 0.8097 (m90) REVERT: A 334 ASN cc_start: 0.9504 (m-40) cc_final: 0.9277 (p0) REVERT: A 343 LYS cc_start: 0.9153 (tttm) cc_final: 0.8575 (tmtt) REVERT: A 400 ILE cc_start: 0.7994 (mt) cc_final: 0.7777 (pt) REVERT: A 474 GLN cc_start: 0.8562 (mt0) cc_final: 0.8107 (mm110) REVERT: A 482 ASP cc_start: 0.9200 (m-30) cc_final: 0.8998 (m-30) REVERT: A 498 HIS cc_start: 0.8323 (p-80) cc_final: 0.7954 (p-80) REVERT: A 554 PHE cc_start: 0.7912 (p90) cc_final: 0.7705 (p90) REVERT: A 688 ILE cc_start: 0.8406 (tt) cc_final: 0.8055 (mm) REVERT: A 689 ASN cc_start: 0.8840 (m-40) cc_final: 0.8560 (m-40) REVERT: A 799 LYS cc_start: 0.8086 (tptm) cc_final: 0.7848 (ttpp) REVERT: A 806 MET cc_start: 0.8711 (mmt) cc_final: 0.8378 (mmt) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.0583 time to fit residues: 17.0398 Evaluate side-chains 146 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.142 Evaluate side-chains 200 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8386 (tt0) REVERT: B 103 THR cc_start: 0.8712 (p) cc_final: 0.8490 (p) REVERT: B 106 GLU cc_start: 0.9423 (pm20) cc_final: 0.9092 (pm20) REVERT: B 121 THR cc_start: 0.8979 (m) cc_final: 0.8659 (m) REVERT: B 126 ILE cc_start: 0.8547 (pt) cc_final: 0.8303 (pt) REVERT: B 136 ASP cc_start: 0.9384 (m-30) cc_final: 0.9125 (m-30) REVERT: B 159 ASN cc_start: 0.8937 (m110) cc_final: 0.8482 (m-40) REVERT: B 203 LEU cc_start: 0.8803 (mt) cc_final: 0.8173 (mt) REVERT: B 272 GLU cc_start: 0.9093 (mp0) cc_final: 0.8878 (pm20) REVERT: B 326 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8110 (pp20) REVERT: B 351 PHE cc_start: 0.8797 (m-80) cc_final: 0.8238 (m-80) REVERT: B 407 SER cc_start: 0.8165 (t) cc_final: 0.7779 (t) REVERT: B 426 SER cc_start: 0.8391 (t) cc_final: 0.7997 (t) REVERT: B 500 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9101 (mm-30) REVERT: B 515 ILE cc_start: 0.7454 (mt) cc_final: 0.6942 (mt) REVERT: B 726 LEU cc_start: 0.8442 (tp) cc_final: 0.8164 (tp) REVERT: B 730 ILE cc_start: 0.8920 (mm) cc_final: 0.8582 (mm) REVERT: B 781 LEU cc_start: 0.9016 (mt) cc_final: 0.8781 (mt) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.0464 time to fit residues: 13.1638 Evaluate side-chains 157 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.199 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0050 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 483 ASN B 486 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.091265 restraints weight = 14113.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.095371 restraints weight = 8444.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.098450 restraints weight = 5675.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.100718 restraints weight = 4105.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.102555 restraints weight = 3148.276| |-----------------------------------------------------------------------------| r_work (final): 0.3334 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.143686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114744 restraints weight = 10913.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.119085 restraints weight = 6693.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.122198 restraints weight = 4512.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.124595 restraints weight = 3272.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.126174 restraints weight = 2502.153| |-----------------------------------------------------------------------------| r_work (final): 0.3701 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2193 r_free = 0.2193 target = 0.045089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2184 r_free = 0.2184 target = 0.043967 restraints weight = 64.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2192 r_free = 0.2192 target = 0.044169 restraints weight = 5.947 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2193 r_free = 0.2193 target = 0.044206 restraints weight = 0.832 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2194 r_free = 0.2194 target = 0.044218 restraints weight = 0.123 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2194 r_free = 0.2194 target = 0.044218 restraints weight = 0.018 | |-----------------------------------------------------------------------------| r_work (final): 0.2142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3329 r_start: 0.3696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21858 Z= 0.188 Angle : 0.889 36.082 30100 Z= 0.430 Chirality : 0.066 1.347 3702 Planarity : 0.005 0.059 3930 Dihedral : 6.351 31.536 3276 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.03 % Favored : 92.77 % Rotamer: Outliers : 0.24 % Allowed : 3.57 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % Twisted Proline : 1.67 % Twisted General : 0.07 % 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: -2.95 (0.13), residues: 3128 helix: -1.63 (0.12), residues: 1248 sheet: -2.41 (0.23), residues: 280 loop : -2.12 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 124 TYR 0.014 0.002 TYR C 109 PHE 0.023 0.002 PHE A 361 TRP 0.016 0.002 TRP C 632 HIS 0.008 0.002 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (21822) covalent geometry : angle 0.75124 / 0.40 (30008) SS BOND : bond 0.00416 / 0.28 ( 16) SS BOND : angle 3.27353 / 2.23 ( 32) hydrogen bonds : bond 0.05201 / 3.64 ( 1008) hydrogen bonds : angle 7.07425 / 5.10 ( 2946) link_BETA1-4 : bond 0.00442 / 0.25 ( 6) link_BETA1-4 : angle 2.12133 / 1.35 ( 18) link_NAG-ASN : bond 0.02499 / 1.60 ( 14) link_NAG-ASN : angle 12.38704 / 9.18 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 MET cc_start: 0.8483 (tpt) cc_final: 0.8087 (mtm) REVERT: C 42 PHE cc_start: 0.9411 (t80) cc_final: 0.9084 (t80) REVERT: C 64 SER cc_start: 0.7938 (t) cc_final: 0.7711 (t) REVERT: C 76 LEU cc_start: 0.8883 (mt) cc_final: 0.8655 (mt) REVERT: C 127 ILE cc_start: 0.9357 (tp) cc_final: 0.9125 (tp) REVERT: C 147 GLN cc_start: 0.9370 (mt0) cc_final: 0.8964 (mt0) REVERT: C 148 SER cc_start: 0.9678 (t) cc_final: 0.9389 (t) REVERT: C 151 TRP cc_start: 0.8096 (m-10) cc_final: 0.7758 (m-10) REVERT: C 152 PHE cc_start: 0.9375 (t80) cc_final: 0.8654 (t80) REVERT: C 174 ARG cc_start: 0.8145 (mtt90) cc_final: 0.7778 (mtt90) REVERT: C 185 GLU cc_start: 0.9450 (tp30) cc_final: 0.9041 (tm-30) REVERT: C 228 LEU cc_start: 0.9392 (mp) cc_final: 0.9133 (mp) REVERT: C 266 TYR cc_start: 0.8164 (m-80) cc_final: 0.7937 (m-80) REVERT: C 301 HIS cc_start: 0.9019 (m90) cc_final: 0.8179 (m-70) REVERT: C 343 LYS cc_start: 0.9034 (tttm) cc_final: 0.8403 (tmtt) REVERT: C 346 LEU cc_start: 0.9534 (mt) cc_final: 0.9330 (mt) REVERT: C 474 GLN cc_start: 0.8655 (mt0) cc_final: 0.8036 (mm110) REVERT: C 498 HIS cc_start: 0.8506 (p-80) cc_final: 0.8088 (p-80) REVERT: C 554 PHE cc_start: 0.7551 (p90) cc_final: 0.7089 (p90) REVERT: C 702 TYR cc_start: 0.8721 (p90) cc_final: 0.8255 (p90) REVERT: C 731 ASN cc_start: 0.9237 (m-40) cc_final: 0.8826 (m110) REVERT: C 732 TYR cc_start: 0.8713 (m-80) cc_final: 0.8441 (m-80) REVERT: C 757 LEU cc_start: 0.9237 (mm) cc_final: 0.8981 (mm) REVERT: C 799 LYS cc_start: 0.8483 (tptm) cc_final: 0.8099 (ttpp) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.0600 time to fit residues: 16.4169 Evaluate side-chains 137 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.213 Evaluate side-chains 190 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 75 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8375 (tt0) REVERT: D 106 GLU cc_start: 0.9530 (pm20) cc_final: 0.9082 (pm20) REVERT: D 121 THR cc_start: 0.9099 (m) cc_final: 0.8791 (p) REVERT: D 132 MET cc_start: 0.8103 (mtm) cc_final: 0.7762 (mtm) REVERT: D 144 PHE cc_start: 0.9072 (m-80) cc_final: 0.8617 (m-80) REVERT: D 152 GLN cc_start: 0.8032 (mp10) cc_final: 0.7759 (mp10) REVERT: D 159 ASN cc_start: 0.8337 (m110) cc_final: 0.7643 (m-40) REVERT: D 220 LEU cc_start: 0.9183 (mt) cc_final: 0.8863 (mt) REVERT: D 224 GLN cc_start: 0.8726 (tp40) cc_final: 0.8197 (tm-30) REVERT: D 227 ILE cc_start: 0.8081 (mt) cc_final: 0.7711 (mt) REVERT: D 236 GLU cc_start: 0.9403 (mt-10) cc_final: 0.8921 (mt-10) REVERT: D 326 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8020 (pp20) REVERT: D 351 PHE cc_start: 0.8785 (m-80) cc_final: 0.8059 (m-80) REVERT: D 795 LEU cc_start: 0.8617 (tp) cc_final: 0.8386 (tp) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.0542 time to fit residues: 14.2000 Evaluate side-chains 156 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.192 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 284 optimal weight: 6.9990 chunk 79 optimal weight: 0.0980 chunk 80 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 202 optimal weight: 0.5980 chunk 302 optimal weight: 8.9990 chunk 125 optimal weight: 0.0870 chunk 54 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 102 optimal weight: 0.0470 chunk 154 optimal weight: 6.9990 overall best weight: 0.9658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 301 HIS C 332 ASN D 486 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.151329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.113234 restraints weight = 10961.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.118468 restraints weight = 6059.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122397 restraints weight = 3878.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.125307 restraints weight = 2685.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.127368 restraints weight = 1961.734| |-----------------------------------------------------------------------------| r_work (final): 0.3402 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.146999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.117543 restraints weight = 10850.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.122054 restraints weight = 6533.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.125380 restraints weight = 4381.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.127834 restraints weight = 3149.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.129677 restraints weight = 2399.379| |-----------------------------------------------------------------------------| r_work (final): 0.3753 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.057464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.057354 restraints weight = 104.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.057440 restraints weight = 11.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.057442 restraints weight = 0.447 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.057437 restraints weight = 0.024 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 4)-----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.057436 restraints weight = 0.006 | |-----------------------------------------------------------------------------| r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21858 Z= 0.156 Angle : 0.765 27.198 30100 Z= 0.376 Chirality : 0.058 0.938 3702 Planarity : 0.005 0.052 3930 Dihedral : 5.756 31.891 3276 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.48 % Favored : 92.39 % Rotamer: Outliers : 0.24 % Allowed : 3.21 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % Twisted Proline : 1.67 % 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: -2.03 (0.14), residues: 3128 helix: -0.59 (0.13), residues: 1254 sheet: -2.31 (0.24), residues: 332 loop : -1.72 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 139 TYR 0.033 0.002 TYR A 253 PHE 0.020 0.002 PHE A 342 TRP 0.037 0.002 TRP B 610 HIS 0.007 0.001 HIS A 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (21822) covalent geometry : angle 0.66269 / 0.35 (30008) SS BOND : bond 0.00756 / 0.39 ( 16) SS BOND : angle 2.35844 / 1.61 ( 32) hydrogen bonds : bond 0.04660 / 3.23 ( 1008) hydrogen bonds : angle 6.28112 / 4.52 ( 2946) link_BETA1-4 : bond 0.00590 / 0.34 ( 6) link_BETA1-4 : angle 1.81497 / 1.15 ( 18) link_NAG-ASN : bond 0.01702 / 1.07 ( 14) link_NAG-ASN : angle 9.97267 / 7.44 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8455 (tpt) cc_final: 0.8033 (mtm) REVERT: A 42 PHE cc_start: 0.9357 (t80) cc_final: 0.9075 (t80) REVERT: A 64 SER cc_start: 0.7672 (t) cc_final: 0.7256 (t) REVERT: A 76 LEU cc_start: 0.8856 (mt) cc_final: 0.8625 (mt) REVERT: A 127 ILE cc_start: 0.9423 (tp) cc_final: 0.9114 (tp) REVERT: A 139 ARG cc_start: 0.8388 (mtm110) cc_final: 0.7905 (mtm110) REVERT: A 147 GLN cc_start: 0.9348 (mt0) cc_final: 0.8882 (mt0) REVERT: A 152 PHE cc_start: 0.9416 (t80) cc_final: 0.8799 (t80) REVERT: A 185 GLU cc_start: 0.9462 (tp30) cc_final: 0.9039 (tm-30) REVERT: A 228 LEU cc_start: 0.9390 (mp) cc_final: 0.9171 (mp) REVERT: A 238 ARG cc_start: 0.7034 (mmt-90) cc_final: 0.6532 (mmt-90) REVERT: A 261 MET cc_start: 0.8365 (mtt) cc_final: 0.8073 (mmt) REVERT: A 301 HIS cc_start: 0.9005 (m90) cc_final: 0.8251 (m-70) REVERT: A 343 LYS cc_start: 0.8906 (tttm) cc_final: 0.8302 (tmtt) REVERT: A 371 GLN cc_start: 0.9003 (mp10) cc_final: 0.8272 (mm-40) REVERT: A 402 TRP cc_start: 0.7520 (m100) cc_final: 0.6263 (m-10) REVERT: A 474 GLN cc_start: 0.8511 (mt0) cc_final: 0.8057 (mm110) REVERT: A 482 ASP cc_start: 0.8848 (m-30) cc_final: 0.8612 (m-30) REVERT: A 554 PHE cc_start: 0.7512 (p90) cc_final: 0.7082 (p90) REVERT: A 702 TYR cc_start: 0.8667 (p90) cc_final: 0.8261 (p90) REVERT: A 723 MET cc_start: 0.9143 (mtt) cc_final: 0.8697 (ptt) REVERT: A 731 ASN cc_start: 0.9186 (m-40) cc_final: 0.8717 (m110) REVERT: A 757 LEU cc_start: 0.9245 (mm) cc_final: 0.9011 (mm) REVERT: A 799 LYS cc_start: 0.8480 (tptm) cc_final: 0.8279 (ttpp) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.0556 time to fit residues: 14.4164 Evaluate side-chains 152 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.206 Evaluate side-chains 181 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 75 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8434 (tt0) REVERT: D 121 THR cc_start: 0.9140 (m) cc_final: 0.8767 (p) REVERT: D 132 MET cc_start: 0.8024 (mtm) cc_final: 0.7778 (mtm) REVERT: D 136 ASP cc_start: 0.9313 (m-30) cc_final: 0.8952 (m-30) REVERT: D 152 GLN cc_start: 0.8120 (mp10) cc_final: 0.7665 (mp10) REVERT: D 157 MET cc_start: 0.8074 (mtp) cc_final: 0.7808 (mtp) REVERT: D 163 GLU cc_start: 0.6937 (tt0) cc_final: 0.6243 (tt0) REVERT: D 220 LEU cc_start: 0.9131 (mt) cc_final: 0.8873 (mt) REVERT: D 224 GLN cc_start: 0.8599 (tp40) cc_final: 0.8098 (tm-30) REVERT: D 326 GLU cc_start: 0.8774 (mm-30) cc_final: 0.7986 (pp20) REVERT: D 338 TYR cc_start: 0.7487 (m-80) cc_final: 0.6957 (m-80) REVERT: D 795 LEU cc_start: 0.8446 (tp) cc_final: 0.8204 (tp) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.0553 time to fit residues: 13.9252 Evaluate side-chains 155 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.192 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 271 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 197 optimal weight: 0.0170 chunk 146 optimal weight: 0.7980 chunk 190 optimal weight: 0.5980 chunk 237 optimal weight: 0.0770 chunk 58 optimal weight: 10.0000 chunk 270 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 overall best weight: 0.8978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 HIS A 332 ASN D 110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.158128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117436 restraints weight = 11123.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122977 restraints weight = 5955.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.127002 restraints weight = 3721.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.129940 restraints weight = 2544.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.132082 restraints weight = 1850.520| |-----------------------------------------------------------------------------| r_work (final): 0.3430 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.150072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.120782 restraints weight = 10728.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.125367 restraints weight = 6463.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.128711 restraints weight = 4318.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.131078 restraints weight = 3100.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.132904 restraints weight = 2373.874| |-----------------------------------------------------------------------------| r_work (final): 0.3775 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.058400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.058200 restraints weight = 179.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.058353 restraints weight = 34.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.058336 restraints weight = 4.946 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.058338 restraints weight = 0.672 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.058338 restraints weight = 0.518 | |-----------------------------------------------------------------------------| r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21858 Z= 0.136 Angle : 0.701 23.513 30100 Z= 0.343 Chirality : 0.054 0.799 3702 Planarity : 0.004 0.049 3930 Dihedral : 5.231 31.546 3276 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.52 % Favored : 93.29 % Rotamer: Outliers : 0.24 % Allowed : 2.97 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3128 helix: 0.20 (0.14), residues: 1254 sheet: -2.15 (0.23), residues: 348 loop : -1.52 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 124 TYR 0.026 0.002 TYR C 253 PHE 0.029 0.002 PHE B 351 TRP 0.058 0.002 TRP A 151 HIS 0.006 0.001 HIS D 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (21822) covalent geometry : angle 0.61133 / 0.32 (30008) SS BOND : bond 0.00977 / 0.66 ( 16) SS BOND : angle 1.95584 / 1.36 ( 32) hydrogen bonds : bond 0.04153 / 2.89 ( 1008) hydrogen bonds : angle 5.51756 / 4.00 ( 2946) link_BETA1-4 : bond 0.00243 / 0.14 ( 6) link_BETA1-4 : angle 0.82474 / 0.53 ( 18) link_NAG-ASN : bond 0.02120 / 1.39 ( 14) link_NAG-ASN : angle 9.03681 / 6.76 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8451 (tpt) cc_final: 0.8160 (mtm) REVERT: A 42 PHE cc_start: 0.9348 (t80) cc_final: 0.9064 (t80) REVERT: A 76 LEU cc_start: 0.8895 (mt) cc_final: 0.8669 (mt) REVERT: A 127 ILE cc_start: 0.9432 (tp) cc_final: 0.9183 (tp) REVERT: A 139 ARG cc_start: 0.8357 (mtm110) cc_final: 0.7958 (mtm110) REVERT: A 151 TRP cc_start: 0.8763 (m-10) cc_final: 0.8524 (m-10) REVERT: A 152 PHE cc_start: 0.9406 (t80) cc_final: 0.8934 (t80) REVERT: A 155 MET cc_start: 0.7730 (mmm) cc_final: 0.7467 (tpt) REVERT: A 185 GLU cc_start: 0.9437 (tp30) cc_final: 0.9011 (tm-30) REVERT: A 228 LEU cc_start: 0.9388 (mp) cc_final: 0.9167 (mp) REVERT: A 238 ARG cc_start: 0.7019 (mmt-90) cc_final: 0.6791 (mpt180) REVERT: A 243 SER cc_start: 0.9533 (t) cc_final: 0.9196 (p) REVERT: A 269 LEU cc_start: 0.8342 (tp) cc_final: 0.7817 (tp) REVERT: A 301 HIS cc_start: 0.8912 (m-70) cc_final: 0.8129 (m-70) REVERT: A 371 GLN cc_start: 0.8992 (mp10) cc_final: 0.8181 (mm-40) REVERT: A 402 TRP cc_start: 0.7447 (m100) cc_final: 0.6203 (m-10) REVERT: A 482 ASP cc_start: 0.8821 (m-30) cc_final: 0.8577 (m-30) REVERT: A 533 MET cc_start: 0.8801 (ttm) cc_final: 0.8491 (ttp) REVERT: A 694 ARG cc_start: 0.8390 (mmt180) cc_final: 0.7864 (mmm160) REVERT: A 723 MET cc_start: 0.9167 (mtt) cc_final: 0.8680 (ptt) REVERT: A 731 ASN cc_start: 0.9165 (m-40) cc_final: 0.8736 (m110) REVERT: A 737 GLU cc_start: 0.9273 (mp0) cc_final: 0.8998 (pm20) REVERT: A 757 LEU cc_start: 0.9245 (mm) cc_final: 0.9037 (mm) REVERT: A 799 LYS cc_start: 0.8528 (tptm) cc_final: 0.8306 (ttpp) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.0549 time to fit residues: 14.2577 Evaluate side-chains 153 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.201 Evaluate side-chains 185 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 MET cc_start: 0.8764 (tpt) cc_final: 0.8542 (tpp) REVERT: D 75 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8394 (tt0) REVERT: D 103 THR cc_start: 0.8818 (p) cc_final: 0.8600 (p) REVERT: D 113 ASP cc_start: 0.8749 (t0) cc_final: 0.8532 (t0) REVERT: D 121 THR cc_start: 0.9244 (m) cc_final: 0.8906 (p) REVERT: D 132 MET cc_start: 0.8031 (mtm) cc_final: 0.7734 (mtm) REVERT: D 143 PHE cc_start: 0.8634 (t80) cc_final: 0.8157 (t80) REVERT: D 152 GLN cc_start: 0.8246 (mp10) cc_final: 0.7919 (mp10) REVERT: D 159 ASN cc_start: 0.8728 (m-40) cc_final: 0.8458 (m-40) REVERT: D 164 TYR cc_start: 0.6918 (m-80) cc_final: 0.6552 (m-80) REVERT: D 209 LEU cc_start: 0.8288 (mt) cc_final: 0.8078 (tp) REVERT: D 220 LEU cc_start: 0.9195 (mt) cc_final: 0.8865 (mt) REVERT: D 224 GLN cc_start: 0.8707 (tp40) cc_final: 0.8132 (tm-30) REVERT: D 236 GLU cc_start: 0.9422 (mt-10) cc_final: 0.8994 (mt-10) REVERT: D 326 GLU cc_start: 0.8758 (mm-30) cc_final: 0.7675 (pp20) REVERT: D 330 TYR cc_start: 0.7899 (m-10) cc_final: 0.7406 (m-10) REVERT: D 519 ARG cc_start: 0.8898 (mtm110) cc_final: 0.8540 (mtm110) REVERT: D 726 LEU cc_start: 0.8612 (tp) cc_final: 0.8310 (tp) REVERT: D 795 LEU cc_start: 0.8442 (tp) cc_final: 0.8215 (tp) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.0532 time to fit residues: 13.8156 Evaluate side-chains 159 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.196 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 68 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 226 optimal weight: 0.9990 chunk 304 optimal weight: 0.5980 chunk 119 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 305 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 232 optimal weight: 8.9990 chunk 230 optimal weight: 0.0020 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 HIS A 332 ASN D 110 GLN D 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.158064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117192 restraints weight = 11132.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122707 restraints weight = 5913.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126698 restraints weight = 3684.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129571 restraints weight = 2521.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.131697 restraints weight = 1846.531| |-----------------------------------------------------------------------------| r_work (final): 0.3416 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.151090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.121367 restraints weight = 10582.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.126015 restraints weight = 6407.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.129403 restraints weight = 4291.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.131921 restraints weight = 3092.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.133647 restraints weight = 2353.968| |-----------------------------------------------------------------------------| r_work (final): 0.3781 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.059462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.059325 restraints weight = 156.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.059411 restraints weight = 10.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 6)-----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.059423 restraints weight = 0.769 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 5)-----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.059421 restraints weight = 0.062 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 5)-----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.059419 restraints weight = 0.005 | |-----------------------------------------------------------------------------| r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21858 Z= 0.126 Angle : 0.683 24.487 30100 Z= 0.333 Chirality : 0.054 0.806 3702 Planarity : 0.004 0.049 3930 Dihedral : 5.012 30.241 3276 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.01 % Favored : 93.80 % Rotamer: Outliers : 0.12 % Allowed : 1.66 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3128 helix: 0.50 (0.14), residues: 1264 sheet: -1.81 (0.23), residues: 418 loop : -1.42 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 124 TYR 0.031 0.002 TYR A 253 PHE 0.024 0.002 PHE D 474 TRP 0.026 0.001 TRP C 151 HIS 0.011 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (21822) covalent geometry : angle 0.58852 / 0.31 (30008) SS BOND : bond 0.00420 / 0.33 ( 16) SS BOND : angle 2.05183 / 1.51 ( 32) hydrogen bonds : bond 0.03998 / 2.80 ( 1008) hydrogen bonds : angle 5.22628 / 3.79 ( 2946) link_BETA1-4 : bond 0.00266 / 0.15 ( 6) link_BETA1-4 : angle 1.16987 / 0.76 ( 18) link_NAG-ASN : bond 0.01621 / 1.03 ( 14) link_NAG-ASN : angle 9.08820 / 6.75 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 MET cc_start: 0.8501 (tpt) cc_final: 0.8163 (mtp) REVERT: C 42 PHE cc_start: 0.9403 (t80) cc_final: 0.9090 (t80) REVERT: C 123 THR cc_start: 0.9039 (t) cc_final: 0.8830 (t) REVERT: C 139 ARG cc_start: 0.8228 (mtm110) cc_final: 0.7882 (mtm110) REVERT: C 147 GLN cc_start: 0.9453 (mt0) cc_final: 0.9247 (mt0) REVERT: C 151 TRP cc_start: 0.8785 (m-10) cc_final: 0.8514 (m-10) REVERT: C 152 PHE cc_start: 0.9440 (t80) cc_final: 0.9021 (t80) REVERT: C 155 MET cc_start: 0.7499 (mmm) cc_final: 0.7196 (tpt) REVERT: C 185 GLU cc_start: 0.9474 (tp30) cc_final: 0.8995 (tm-30) REVERT: C 228 LEU cc_start: 0.9438 (mp) cc_final: 0.9180 (tp) REVERT: C 269 LEU cc_start: 0.8390 (tp) cc_final: 0.7964 (tp) REVERT: C 301 HIS cc_start: 0.8908 (m-70) cc_final: 0.8331 (m-70) REVERT: C 343 LYS cc_start: 0.8900 (tttm) cc_final: 0.8362 (tmtt) REVERT: C 371 GLN cc_start: 0.9044 (mp10) cc_final: 0.8322 (mm-40) REVERT: C 402 TRP cc_start: 0.7270 (m100) cc_final: 0.6021 (m-10) REVERT: C 533 MET cc_start: 0.8831 (ttm) cc_final: 0.8595 (ttp) REVERT: C 694 ARG cc_start: 0.8127 (mmt180) cc_final: 0.7860 (mmm160) REVERT: C 702 TYR cc_start: 0.8557 (p90) cc_final: 0.8164 (p90) REVERT: C 723 MET cc_start: 0.9183 (mtt) cc_final: 0.8776 (ptt) REVERT: C 731 ASN cc_start: 0.9082 (m-40) cc_final: 0.8837 (m110) REVERT: C 737 GLU cc_start: 0.9240 (mp0) cc_final: 0.8911 (pm20) REVERT: C 757 LEU cc_start: 0.9137 (mm) cc_final: 0.8934 (mm) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.0567 time to fit residues: 14.4993 Evaluate side-chains 153 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.206 Evaluate side-chains 175 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 MET cc_start: 0.8829 (tpt) cc_final: 0.8582 (tpp) REVERT: D 103 THR cc_start: 0.8861 (p) cc_final: 0.8629 (p) REVERT: D 121 THR cc_start: 0.9246 (m) cc_final: 0.9015 (p) REVERT: D 132 MET cc_start: 0.8041 (mtm) cc_final: 0.7621 (mtm) REVERT: D 143 PHE cc_start: 0.8651 (t80) cc_final: 0.8192 (t80) REVERT: D 146 PHE cc_start: 0.6329 (m-10) cc_final: 0.4790 (m-80) REVERT: D 152 GLN cc_start: 0.8262 (mp10) cc_final: 0.7858 (mp10) REVERT: D 159 ASN cc_start: 0.8693 (m-40) cc_final: 0.8416 (m-40) REVERT: D 220 LEU cc_start: 0.9067 (mt) cc_final: 0.8853 (mt) REVERT: D 224 GLN cc_start: 0.8725 (tp40) cc_final: 0.8183 (tm-30) REVERT: D 236 GLU cc_start: 0.9379 (mt-10) cc_final: 0.9001 (mt-10) REVERT: D 272 GLU cc_start: 0.8927 (mp0) cc_final: 0.8545 (pm20) REVERT: D 519 ARG cc_start: 0.8870 (mtm110) cc_final: 0.7657 (mtm180) REVERT: D 726 LEU cc_start: 0.8601 (tp) cc_final: 0.8281 (tp) REVERT: D 795 LEU cc_start: 0.8448 (tp) cc_final: 0.8195 (tp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0542 time to fit residues: 13.3411 Evaluate side-chains 160 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.239 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 286 optimal weight: 0.7980 chunk 214 optimal weight: 30.0000 chunk 162 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 280 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 251 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 134 HIS C 332 ASN D 110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.121225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.091980 restraints weight = 14098.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.096159 restraints weight = 8385.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.099315 restraints weight = 5636.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.101750 restraints weight = 4086.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.103593 restraints weight = 3130.161| |-----------------------------------------------------------------------------| r_work (final): 0.3376 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.153981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.124538 restraints weight = 10502.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.129045 restraints weight = 6392.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132271 restraints weight = 4286.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.134708 restraints weight = 3090.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.136371 restraints weight = 2340.736| |-----------------------------------------------------------------------------| r_work (final): 0.3741 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.059656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.059651 restraints weight = 131.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.059653 restraints weight = 0.383 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.059652 restraints weight = 0.022 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.059652 restraints weight = 0.012 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.059652 restraints weight = 0.012 | |-----------------------------------------------------------------------------| r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21858 Z= 0.157 Angle : 0.696 26.214 30100 Z= 0.339 Chirality : 0.054 0.859 3702 Planarity : 0.004 0.051 3930 Dihedral : 4.947 29.488 3276 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.78 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % 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: -0.94 (0.15), residues: 3128 helix: 0.67 (0.14), residues: 1264 sheet: -2.05 (0.23), residues: 386 loop : -1.33 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 505 TYR 0.034 0.002 TYR C 253 PHE 0.025 0.002 PHE D 474 TRP 0.019 0.001 TRP A 151 HIS 0.008 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (21822) covalent geometry : angle 0.59892 / 0.32 (30008) SS BOND : bond 0.00415 / 0.24 ( 16) SS BOND : angle 1.85559 / 1.33 ( 32) hydrogen bonds : bond 0.03955 / 2.75 ( 1008) hydrogen bonds : angle 5.15448 / 3.73 ( 2946) link_BETA1-4 : bond 0.00167 / 0.09 ( 6) link_BETA1-4 : angle 1.17718 / 0.76 ( 18) link_NAG-ASN : bond 0.01513 / 0.96 ( 14) link_NAG-ASN : angle 9.37949 / 6.98 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8534 (tpt) cc_final: 0.8199 (mtp) REVERT: A 42 PHE cc_start: 0.9388 (t80) cc_final: 0.9100 (t80) REVERT: A 127 ILE cc_start: 0.9483 (tp) cc_final: 0.9263 (tp) REVERT: A 139 ARG cc_start: 0.8273 (mtm110) cc_final: 0.7997 (mtm110) REVERT: A 147 GLN cc_start: 0.9465 (mt0) cc_final: 0.9201 (mt0) REVERT: A 151 TRP cc_start: 0.8871 (m-10) cc_final: 0.8473 (m-10) REVERT: A 152 PHE cc_start: 0.9420 (t80) cc_final: 0.9016 (t80) REVERT: A 185 GLU cc_start: 0.9472 (tp30) cc_final: 0.8976 (tm-30) REVERT: A 228 LEU cc_start: 0.9495 (mp) cc_final: 0.9184 (tp) REVERT: A 243 SER cc_start: 0.9603 (t) cc_final: 0.9222 (p) REVERT: A 301 HIS cc_start: 0.8941 (m-70) cc_final: 0.8314 (m-70) REVERT: A 343 LYS cc_start: 0.8967 (tttm) cc_final: 0.8511 (tmtt) REVERT: A 371 GLN cc_start: 0.9107 (mp10) cc_final: 0.8433 (mm-40) REVERT: A 474 GLN cc_start: 0.8405 (mt0) cc_final: 0.7949 (mm110) REVERT: A 482 ASP cc_start: 0.8810 (m-30) cc_final: 0.8521 (m-30) REVERT: A 533 MET cc_start: 0.8817 (ttm) cc_final: 0.8506 (ttp) REVERT: A 694 ARG cc_start: 0.8380 (mmt180) cc_final: 0.7942 (mmm160) REVERT: A 723 MET cc_start: 0.9139 (mtt) cc_final: 0.8739 (ptm) REVERT: A 731 ASN cc_start: 0.9256 (m-40) cc_final: 0.8825 (m110) REVERT: A 737 GLU cc_start: 0.9379 (mp0) cc_final: 0.9060 (pm20) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.0517 time to fit residues: 12.7390 Evaluate side-chains 138 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.222 Evaluate side-chains 176 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 74 ASN cc_start: 0.8479 (m-40) cc_final: 0.8172 (m-40) REVERT: D 75 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8435 (tt0) REVERT: D 103 THR cc_start: 0.8811 (p) cc_final: 0.8610 (p) REVERT: D 121 THR cc_start: 0.9206 (m) cc_final: 0.8967 (p) REVERT: D 132 MET cc_start: 0.8044 (mtm) cc_final: 0.7710 (mtm) REVERT: D 134 MET cc_start: 0.7049 (ttt) cc_final: 0.6798 (ttp) REVERT: D 143 PHE cc_start: 0.8715 (t80) cc_final: 0.8248 (t80) REVERT: D 152 GLN cc_start: 0.8343 (mp10) cc_final: 0.7744 (mp10) REVERT: D 159 ASN cc_start: 0.8682 (m-40) cc_final: 0.8453 (m-40) REVERT: D 164 TYR cc_start: 0.6725 (m-10) cc_final: 0.6505 (m-10) REVERT: D 220 LEU cc_start: 0.9104 (mt) cc_final: 0.8781 (mt) REVERT: D 224 GLN cc_start: 0.8732 (tp40) cc_final: 0.8165 (tm-30) REVERT: D 238 THR cc_start: 0.8861 (t) cc_final: 0.8347 (t) REVERT: D 272 GLU cc_start: 0.8874 (mp0) cc_final: 0.8501 (pm20) REVERT: D 326 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8219 (tm-30) REVERT: D 339 LEU cc_start: 0.9192 (mt) cc_final: 0.8902 (mt) REVERT: D 367 LEU cc_start: 0.8696 (tp) cc_final: 0.8462 (tp) REVERT: D 519 ARG cc_start: 0.8894 (mtm110) cc_final: 0.8676 (mtm110) REVERT: D 726 LEU cc_start: 0.8497 (tp) cc_final: 0.8149 (tp) REVERT: D 795 LEU cc_start: 0.8664 (tp) cc_final: 0.8423 (tp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0535 time to fit residues: 13.1939 Evaluate side-chains 149 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.198 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 250 optimal weight: 5.9990 chunk 216 optimal weight: 0.0970 chunk 39 optimal weight: 0.0060 chunk 59 optimal weight: 0.0030 chunk 65 optimal weight: 1.9990 chunk 278 optimal weight: 0.9980 chunk 252 optimal weight: 0.0770 chunk 146 optimal weight: 0.0670 chunk 214 optimal weight: 40.0000 chunk 276 optimal weight: 20.0000 chunk 98 optimal weight: 0.0370 overall best weight: 0.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 HIS D 153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.094800 restraints weight = 13787.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099193 restraints weight = 8127.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102566 restraints weight = 5420.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104956 restraints weight = 3889.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.106921 restraints weight = 2988.671| |-----------------------------------------------------------------------------| r_work (final): 0.3415 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.163831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.133191 restraints weight = 10112.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.138084 restraints weight = 5937.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.141634 restraints weight = 3888.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.144188 restraints weight = 2740.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.146199 restraints weight = 2046.016| |-----------------------------------------------------------------------------| r_work (final): 0.3850 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.057952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.057933 restraints weight = 130.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.057930 restraints weight = 7.117 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.057936 restraints weight = 0.288 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.057936 restraints weight = 0.013 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.057936 restraints weight = 0.013 | |-----------------------------------------------------------------------------| r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21858 Z= 0.130 Angle : 0.696 25.986 30100 Z= 0.334 Chirality : 0.055 0.863 3702 Planarity : 0.004 0.057 3930 Dihedral : 4.792 29.600 3276 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.88 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % 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: -0.86 (0.15), residues: 3128 helix: 0.76 (0.14), residues: 1280 sheet: -1.81 (0.22), residues: 448 loop : -1.36 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 124 TYR 0.067 0.002 TYR B 646 PHE 0.022 0.002 PHE B 474 TRP 0.017 0.001 TRP B 610 HIS 0.010 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (21822) covalent geometry : angle 0.59908 / 0.31 (30008) SS BOND : bond 0.00431 / 0.24 ( 16) SS BOND : angle 1.70066 / 1.17 ( 32) hydrogen bonds : bond 0.03955 / 2.74 ( 1008) hydrogen bonds : angle 4.94607 / 3.58 ( 2946) link_BETA1-4 : bond 0.00692 / 0.39 ( 6) link_BETA1-4 : angle 1.20420 / 0.78 ( 18) link_NAG-ASN : bond 0.01531 / 0.99 ( 14) link_NAG-ASN : angle 9.38053 / 6.97 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 MET cc_start: 0.8548 (tpt) cc_final: 0.8218 (mtp) REVERT: C 42 PHE cc_start: 0.9418 (t80) cc_final: 0.9144 (t80) REVERT: C 127 ILE cc_start: 0.9492 (tp) cc_final: 0.9219 (tp) REVERT: C 147 GLN cc_start: 0.9443 (mt0) cc_final: 0.9236 (mt0) REVERT: C 152 PHE cc_start: 0.9379 (t80) cc_final: 0.8994 (t80) REVERT: C 155 MET cc_start: 0.7200 (tpt) cc_final: 0.6799 (tpt) REVERT: C 181 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8870 (mt-10) REVERT: C 185 GLU cc_start: 0.9463 (tp30) cc_final: 0.8950 (tm-30) REVERT: C 228 LEU cc_start: 0.9462 (mp) cc_final: 0.9099 (mt) REVERT: C 261 MET cc_start: 0.8506 (tpp) cc_final: 0.8177 (tpp) REVERT: C 301 HIS cc_start: 0.8961 (m-70) cc_final: 0.8341 (m-70) REVERT: C 343 LYS cc_start: 0.8987 (tttm) cc_final: 0.8503 (tmtt) REVERT: C 371 GLN cc_start: 0.9115 (mp10) cc_final: 0.8425 (mm-40) REVERT: C 474 GLN cc_start: 0.8356 (mt0) cc_final: 0.7918 (mm110) REVERT: C 533 MET cc_start: 0.8640 (ttm) cc_final: 0.8346 (ttp) REVERT: C 694 ARG cc_start: 0.8211 (mmt180) cc_final: 0.7755 (mmm160) REVERT: C 723 MET cc_start: 0.9057 (mtt) cc_final: 0.8796 (ptm) REVERT: C 731 ASN cc_start: 0.9085 (m-40) cc_final: 0.8782 (m110) REVERT: C 737 GLU cc_start: 0.9275 (mp0) cc_final: 0.8965 (pm20) REVERT: C 757 LEU cc_start: 0.9153 (mm) cc_final: 0.8927 (mm) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.0500 time to fit residues: 12.9476 Evaluate side-chains 152 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.210 Evaluate side-chains 176 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.7788 (tpp) cc_final: 0.7577 (tpp) REVERT: B 75 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8440 (tt0) REVERT: B 132 MET cc_start: 0.7980 (mtm) cc_final: 0.7637 (mtm) REVERT: B 144 PHE cc_start: 0.8916 (m-80) cc_final: 0.8652 (m-80) REVERT: B 146 PHE cc_start: 0.5934 (m-10) cc_final: 0.5334 (m-80) REVERT: B 152 GLN cc_start: 0.8393 (mp10) cc_final: 0.7822 (mp10) REVERT: B 159 ASN cc_start: 0.8561 (m-40) cc_final: 0.8343 (m-40) REVERT: B 164 TYR cc_start: 0.6995 (m-10) cc_final: 0.6589 (m-10) REVERT: B 220 LEU cc_start: 0.8994 (mt) cc_final: 0.8714 (mt) REVERT: B 224 GLN cc_start: 0.8813 (tp40) cc_final: 0.8266 (tm-30) REVERT: B 272 GLU cc_start: 0.8928 (mp0) cc_final: 0.8425 (pm20) REVERT: B 326 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8219 (tm-30) REVERT: B 416 PHE cc_start: 0.8055 (m-10) cc_final: 0.7568 (m-80) REVERT: B 519 ARG cc_start: 0.8853 (mtm110) cc_final: 0.7626 (mtm180) REVERT: B 726 LEU cc_start: 0.8468 (tp) cc_final: 0.8142 (tp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0550 time to fit residues: 13.5598 Evaluate side-chains 158 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.192 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 292 optimal weight: 0.0000 chunk 159 optimal weight: 10.0000 chunk 275 optimal weight: 2.9990 chunk 280 optimal weight: 0.0050 chunk 246 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 259 optimal weight: 0.0370 chunk 107 optimal weight: 0.8980 chunk 299 optimal weight: 0.9980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 GLN B 153 GLN C 332 ASN C 745 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.151446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114511 restraints weight = 10876.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.120145 restraints weight = 5662.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.124207 restraints weight = 3475.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127138 restraints weight = 2354.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.129261 restraints weight = 1709.101| |-----------------------------------------------------------------------------| r_work (final): 0.3445 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.161710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.131766 restraints weight = 10248.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.136516 restraints weight = 6228.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.139961 restraints weight = 4145.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.142491 restraints weight = 2952.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.144130 restraints weight = 2222.400| |-----------------------------------------------------------------------------| r_work (final): 0.3879 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.058020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.058019 restraints weight = 141.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.058006 restraints weight = 164.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.058009 restraints weight = 6.905 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.057997 restraints weight = 0.417 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.057993 restraints weight = 0.044 | |-----------------------------------------------------------------------------| r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21858 Z= 0.121 Angle : 0.704 27.155 30100 Z= 0.336 Chirality : 0.054 0.877 3702 Planarity : 0.004 0.054 3930 Dihedral : 4.628 28.427 3276 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.14 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 3128 helix: 0.97 (0.14), residues: 1276 sheet: -1.69 (0.22), residues: 448 loop : -1.32 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 179 TYR 0.047 0.002 TYR D 646 PHE 0.023 0.002 PHE D 474 TRP 0.021 0.001 TRP D 610 HIS 0.013 0.002 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (21822) covalent geometry : angle 0.59506 / 0.31 (30008) SS BOND : bond 0.00423 / 0.24 ( 16) SS BOND : angle 1.63241 / 1.13 ( 32) hydrogen bonds : bond 0.03789 / 2.61 ( 1008) hydrogen bonds : angle 4.80305 / 3.48 ( 2946) link_BETA1-4 : bond 0.00374 / 0.21 ( 6) link_BETA1-4 : angle 1.04607 / 0.68 ( 18) link_NAG-ASN : bond 0.01402 / 0.91 ( 14) link_NAG-ASN : angle 9.99012 / 7.51 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 MET cc_start: 0.8517 (tpt) cc_final: 0.8214 (mtp) REVERT: C 42 PHE cc_start: 0.9375 (t80) cc_final: 0.9145 (t80) REVERT: C 127 ILE cc_start: 0.9459 (tp) cc_final: 0.9155 (tp) REVERT: C 130 ASP cc_start: 0.8415 (t0) cc_final: 0.7563 (p0) REVERT: C 133 ILE cc_start: 0.7526 (tt) cc_final: 0.7226 (tp) REVERT: C 147 GLN cc_start: 0.9410 (mt0) cc_final: 0.9154 (mt0) REVERT: C 152 PHE cc_start: 0.9399 (t80) cc_final: 0.9045 (t80) REVERT: C 155 MET cc_start: 0.7102 (tpt) cc_final: 0.6681 (tpt) REVERT: C 185 GLU cc_start: 0.9450 (tp30) cc_final: 0.8942 (tm-30) REVERT: C 228 LEU cc_start: 0.9469 (mp) cc_final: 0.9124 (mt) REVERT: C 243 SER cc_start: 0.9633 (t) cc_final: 0.9243 (p) REVERT: C 261 MET cc_start: 0.8569 (tpp) cc_final: 0.8255 (tpp) REVERT: C 301 HIS cc_start: 0.8964 (m-70) cc_final: 0.8384 (m-70) REVERT: C 343 LYS cc_start: 0.8990 (tttm) cc_final: 0.8497 (tmtt) REVERT: C 371 GLN cc_start: 0.9148 (mp10) cc_final: 0.8483 (mm-40) REVERT: C 474 GLN cc_start: 0.8365 (mt0) cc_final: 0.7974 (mm110) REVERT: C 533 MET cc_start: 0.8915 (ttm) cc_final: 0.8587 (ttp) REVERT: C 657 TRP cc_start: 0.9470 (t60) cc_final: 0.9256 (t60) REVERT: C 694 ARG cc_start: 0.8214 (mmt180) cc_final: 0.7813 (mmm160) REVERT: C 723 MET cc_start: 0.9116 (mtt) cc_final: 0.8796 (ptm) REVERT: C 737 GLU cc_start: 0.9064 (mp0) cc_final: 0.8740 (pm20) REVERT: C 757 LEU cc_start: 0.9073 (mm) cc_final: 0.8810 (mm) REVERT: C 783 MET cc_start: 0.9304 (mmp) cc_final: 0.8967 (mmm) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0486 time to fit residues: 12.3596 Evaluate side-chains 145 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.214 Evaluate side-chains 169 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 THR cc_start: 0.8789 (p) cc_final: 0.8580 (p) REVERT: B 146 PHE cc_start: 0.6186 (m-10) cc_final: 0.5639 (m-80) REVERT: B 159 ASN cc_start: 0.8617 (m-40) cc_final: 0.8360 (m-40) REVERT: B 220 LEU cc_start: 0.8996 (mt) cc_final: 0.8714 (mt) REVERT: B 224 GLN cc_start: 0.8718 (tp40) cc_final: 0.8200 (tm-30) REVERT: B 238 THR cc_start: 0.8819 (t) cc_final: 0.8263 (t) REVERT: B 272 GLU cc_start: 0.8880 (mp0) cc_final: 0.8527 (pm20) REVERT: B 416 PHE cc_start: 0.7916 (m-10) cc_final: 0.7518 (m-80) REVERT: B 519 ARG cc_start: 0.8773 (mtm110) cc_final: 0.7744 (mtm180) REVERT: B 726 LEU cc_start: 0.8523 (tp) cc_final: 0.8224 (tp) REVERT: B 795 LEU cc_start: 0.8603 (tp) cc_final: 0.8330 (tp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.0533 time to fit residues: 12.6449 Evaluate side-chains 160 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.195 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 237 optimal weight: 0.0370 chunk 150 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 243 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 chunk 212 optimal weight: 30.0000 chunk 157 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.094296 restraints weight = 14885.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.098132 restraints weight = 9041.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.101068 restraints weight = 6203.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.103273 restraints weight = 4563.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.104849 restraints weight = 3548.943| |-----------------------------------------------------------------------------| r_work (final): 0.3392 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.146401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.117006 restraints weight = 10934.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.121617 restraints weight = 6657.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.124907 restraints weight = 4453.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.127507 restraints weight = 3202.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129271 restraints weight = 2419.652| |-----------------------------------------------------------------------------| r_work (final): 0.3760 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.061593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.061579 restraints weight = 118.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 11)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.061588 restraints weight = 2.083 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.061588 restraints weight = 0.042 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.061588 restraints weight = 0.040 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.061588 restraints weight = 0.040 | |-----------------------------------------------------------------------------| r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 21858 Z= 0.234 Angle : 0.791 29.534 30100 Z= 0.394 Chirality : 0.055 0.918 3702 Planarity : 0.005 0.105 3930 Dihedral : 4.945 27.349 3276 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.23 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % 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: -0.83 (0.15), residues: 3128 helix: 0.84 (0.14), residues: 1266 sheet: -1.99 (0.23), residues: 364 loop : -1.38 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 139 TYR 0.052 0.003 TYR B 646 PHE 0.027 0.002 PHE B 474 TRP 0.026 0.002 TRP B 610 HIS 0.015 0.002 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.23 (21822) covalent geometry : angle 0.68691 / 0.37 (30008) SS BOND : bond 0.00411 / 0.21 ( 16) SS BOND : angle 1.77865 / 1.23 ( 32) hydrogen bonds : bond 0.04225 / 2.87 ( 1008) hydrogen bonds : angle 5.17786 / 3.73 ( 2946) link_BETA1-4 : bond 0.00371 / 0.21 ( 6) link_BETA1-4 : angle 1.18854 / 0.75 ( 18) link_NAG-ASN : bond 0.01336 / 0.84 ( 14) link_NAG-ASN : angle 10.42122 / 7.81 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8534 (tpt) cc_final: 0.8261 (mtp) REVERT: A 42 PHE cc_start: 0.9381 (t80) cc_final: 0.9178 (t80) REVERT: A 127 ILE cc_start: 0.9507 (tp) cc_final: 0.9304 (tp) REVERT: A 152 PHE cc_start: 0.9272 (t80) cc_final: 0.8872 (t80) REVERT: A 228 LEU cc_start: 0.9500 (mp) cc_final: 0.9263 (mp) REVERT: A 301 HIS cc_start: 0.9010 (m-70) cc_final: 0.8404 (m-70) REVERT: A 343 LYS cc_start: 0.9029 (tttm) cc_final: 0.8602 (tmtt) REVERT: A 371 GLN cc_start: 0.9234 (mp10) cc_final: 0.8600 (mm-40) REVERT: A 474 GLN cc_start: 0.8482 (mt0) cc_final: 0.7838 (mm110) REVERT: A 479 PHE cc_start: 0.8645 (t80) cc_final: 0.8409 (t80) REVERT: A 482 ASP cc_start: 0.8818 (m-30) cc_final: 0.8487 (m-30) REVERT: A 523 MET cc_start: 0.8211 (mtp) cc_final: 0.7984 (mtp) REVERT: A 533 MET cc_start: 0.8821 (ttm) cc_final: 0.8436 (ttp) REVERT: A 694 ARG cc_start: 0.8632 (mmt180) cc_final: 0.8000 (mmm160) REVERT: A 723 MET cc_start: 0.9045 (mtt) cc_final: 0.8649 (ttt) REVERT: A 737 GLU cc_start: 0.9267 (mp0) cc_final: 0.8951 (pm20) REVERT: A 789 TRP cc_start: 0.8365 (m100) cc_final: 0.8050 (m100) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.0436 time to fit residues: 10.1543 Evaluate side-chains 131 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.242 Evaluate side-chains 169 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.8899 (tpt) cc_final: 0.8692 (tpp) REVERT: B 103 THR cc_start: 0.8766 (p) cc_final: 0.8550 (p) REVERT: B 146 PHE cc_start: 0.6515 (m-10) cc_final: 0.5923 (m-80) REVERT: B 159 ASN cc_start: 0.8627 (m-40) cc_final: 0.8399 (m-40) REVERT: B 220 LEU cc_start: 0.9181 (mt) cc_final: 0.8888 (mt) REVERT: B 224 GLN cc_start: 0.8797 (tp40) cc_final: 0.8087 (tm-30) REVERT: B 236 GLU cc_start: 0.9324 (mt-10) cc_final: 0.9118 (mm-30) REVERT: B 500 GLU cc_start: 0.9302 (mp0) cc_final: 0.9015 (mp0) REVERT: B 508 MET cc_start: 0.7865 (mtp) cc_final: 0.7642 (mtp) REVERT: B 706 MET cc_start: 0.8973 (mmt) cc_final: 0.8545 (mmm) REVERT: B 726 LEU cc_start: 0.8555 (tp) cc_final: 0.8182 (tp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.0520 time to fit residues: 12.4842 Evaluate side-chains 146 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.197 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 261 optimal weight: 0.0030 chunk 49 optimal weight: 0.0050 chunk 121 optimal weight: 0.7980 chunk 264 optimal weight: 0.0020 chunk 9 optimal weight: 0.4980 chunk 253 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 296 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 overall best weight: 0.2612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.127930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.098936 restraints weight = 13988.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.103133 restraints weight = 8446.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.106169 restraints weight = 5708.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.108485 restraints weight = 4164.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.110134 restraints weight = 3201.056| |-----------------------------------------------------------------------------| r_work (final): 0.3466 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.161443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.131856 restraints weight = 10131.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.136512 restraints weight = 6160.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.139743 restraints weight = 4119.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.142361 restraints weight = 2989.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.144010 restraints weight = 2255.126| |-----------------------------------------------------------------------------| r_work (final): 0.3848 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.059666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.059579 restraints weight = 137.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.059630 restraints weight = 10.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.059640 restraints weight = 0.954 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.059640 restraints weight = 0.428 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.059640 restraints weight = 0.428 | |-----------------------------------------------------------------------------| r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 21858 Z= 0.131 Angle : 0.746 27.835 30100 Z= 0.357 Chirality : 0.056 0.914 3702 Planarity : 0.005 0.112 3930 Dihedral : 4.737 27.779 3276 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.01 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % 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: -0.53 (0.15), residues: 3128 helix: 1.13 (0.14), residues: 1276 sheet: -1.58 (0.25), residues: 372 loop : -1.34 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 139 TYR 0.044 0.002 TYR D 646 PHE 0.061 0.002 PHE D 182 TRP 0.129 0.003 TRP A 151 HIS 0.010 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (21822) covalent geometry : angle 0.64424 / 0.33 (30008) SS BOND : bond 0.00915 / 0.70 ( 16) SS BOND : angle 1.61500 / 1.14 ( 32) hydrogen bonds : bond 0.03811 / 2.63 ( 1008) hydrogen bonds : angle 4.81924 / 3.49 ( 2946) link_BETA1-4 : bond 0.00461 / 0.26 ( 6) link_BETA1-4 : angle 1.18286 / 0.77 ( 18) link_NAG-ASN : bond 0.01441 / 0.92 ( 14) link_NAG-ASN : angle 10.00853 / 7.50 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 MET cc_start: 0.8557 (tpt) cc_final: 0.8255 (mtp) REVERT: C 42 PHE cc_start: 0.9390 (t80) cc_final: 0.9173 (t80) REVERT: C 130 ASP cc_start: 0.8461 (t0) cc_final: 0.7707 (p0) REVERT: C 146 HIS cc_start: 0.8577 (m90) cc_final: 0.8301 (m90) REVERT: C 152 PHE cc_start: 0.9399 (t80) cc_final: 0.8941 (t80) REVERT: C 155 MET cc_start: 0.7217 (tpt) cc_final: 0.6842 (tpt) REVERT: C 185 GLU cc_start: 0.9445 (tp30) cc_final: 0.8906 (tm-30) REVERT: C 228 LEU cc_start: 0.9440 (mp) cc_final: 0.9072 (mt) REVERT: C 301 HIS cc_start: 0.8982 (m-70) cc_final: 0.8414 (m-70) REVERT: C 343 LYS cc_start: 0.9070 (tttm) cc_final: 0.8539 (tmtt) REVERT: C 371 GLN cc_start: 0.9221 (mp10) cc_final: 0.8565 (mm-40) REVERT: C 377 LEU cc_start: 0.8063 (tp) cc_final: 0.7860 (tp) REVERT: C 422 VAL cc_start: 0.8757 (p) cc_final: 0.8255 (p) REVERT: C 474 GLN cc_start: 0.8365 (mt0) cc_final: 0.7866 (mm110) REVERT: C 694 ARG cc_start: 0.8457 (mmt180) cc_final: 0.7879 (mmm160) REVERT: C 702 TYR cc_start: 0.8758 (p90) cc_final: 0.8421 (p90) REVERT: C 737 GLU cc_start: 0.9110 (mp0) cc_final: 0.8800 (pm20) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.0494 time to fit residues: 11.9188 Evaluate side-chains 146 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.213 Evaluate side-chains 168 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 99 PHE cc_start: 0.7328 (t80) cc_final: 0.7053 (t80) REVERT: D 103 THR cc_start: 0.8722 (p) cc_final: 0.8516 (p) REVERT: D 159 ASN cc_start: 0.8630 (m-40) cc_final: 0.8333 (m-40) REVERT: D 220 LEU cc_start: 0.8980 (mt) cc_final: 0.8705 (mt) REVERT: D 224 GLN cc_start: 0.8632 (tp40) cc_final: 0.8011 (tm-30) REVERT: D 272 GLU cc_start: 0.8845 (mp0) cc_final: 0.8499 (pm20) REVERT: D 500 GLU cc_start: 0.9077 (mp0) cc_final: 0.8873 (mp0) REVERT: D 519 ARG cc_start: 0.8739 (mtm110) cc_final: 0.7650 (mtm180) REVERT: D 706 MET cc_start: 0.8894 (mmt) cc_final: 0.8473 (mmm) REVERT: D 726 LEU cc_start: 0.8485 (tp) cc_final: 0.8174 (tp) REVERT: D 795 LEU cc_start: 0.8625 (tp) cc_final: 0.8396 (tp) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0552 time to fit residues: 13.0334 Evaluate side-chains 163 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.189 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 66 optimal weight: 0.2980 chunk 248 optimal weight: 6.9990 chunk 229 optimal weight: 0.6980 chunk 139 optimal weight: 20.0000 chunk 73 optimal weight: 0.0070 chunk 274 optimal weight: 0.0000 chunk 202 optimal weight: 0.0970 chunk 224 optimal weight: 0.9990 chunk 14 optimal weight: 0.0370 chunk 279 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 overall best weight: 0.0878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN D 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.097619 restraints weight = 13430.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.102741 restraints weight = 7551.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106499 restraints weight = 4870.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.109340 restraints weight = 3419.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111356 restraints weight = 2540.163| |-----------------------------------------------------------------------------| r_work (final): 0.3405 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.158370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.128351 restraints weight = 10260.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.133110 restraints weight = 6298.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.136547 restraints weight = 4233.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139147 restraints weight = 3050.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.141015 restraints weight = 2309.051| |-----------------------------------------------------------------------------| r_work (final): 0.3896 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2348 r_free = 0.2348 target = 0.053164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.053105 restraints weight = 154.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2341 r_free = 0.2341 target = 0.053160 restraints weight = 11.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2341 r_free = 0.2341 target = 0.053150 restraints weight = 0.329 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2341 r_free = 0.2341 target = 0.053150 restraints weight = 0.013 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2341 r_free = 0.2341 target = 0.053150 restraints weight = 0.012 | |-----------------------------------------------------------------------------| r_work (final): 0.2348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 21858 Z= 0.127 Angle : 0.719 27.585 30100 Z= 0.344 Chirality : 0.055 0.898 3702 Planarity : 0.005 0.099 3930 Dihedral : 4.623 26.854 3276 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.07 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.15), residues: 3128 helix: 1.13 (0.14), residues: 1278 sheet: -1.49 (0.25), residues: 374 loop : -1.34 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 139 TYR 0.042 0.002 TYR D 646 PHE 0.044 0.002 PHE B 182 TRP 0.021 0.001 TRP D 610 HIS 0.013 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (21822) covalent geometry : angle 0.61759 / 0.32 (30008) SS BOND : bond 0.00312 / 0.16 ( 16) SS BOND : angle 1.55108 / 1.11 ( 32) hydrogen bonds : bond 0.03758 / 2.59 ( 1008) hydrogen bonds : angle 4.80216 / 3.48 ( 2946) link_BETA1-4 : bond 0.00394 / 0.22 ( 6) link_BETA1-4 : angle 1.00231 / 0.65 ( 18) link_NAG-ASN : bond 0.01491 / 0.95 ( 14) link_NAG-ASN : angle 9.77358 / 7.32 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2553.24 seconds wall clock time: 45 minutes 7.90 seconds (2707.90 seconds total)