Starting phenix.real_space_refine on Sun Aug 24 17:33:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cna_7529/08_2025/6cna_7529.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cna_7529/08_2025/6cna_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_7529/08_2025/6cna_7529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cna_7529/08_2025/6cna_7529.map" model { file = "/net/cci-nas-00/data/ceres_data/6cna_7529/08_2025/6cna_7529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cna_7529/08_2025/6cna_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-2.0-5787/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.73, per 1000 atoms: 0.22 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: 1.81 Conformation dependent library (CDL) restraints added in 850.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.93 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: 3.83 Time building geometry restraints manager: 2.47 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 - 24.74: 12722 24.74 - 49.47: 156 49.47 - 74.21: 46 74.21 - 98.95: 28 98.95 - 123.69: 32 Dihedral angle restraints: 12984 sinusoidal: 3862 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 12981 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: 0.03 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.480 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 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 : 13.747 123.685 7040 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 aren 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 covalent geometry : bond 0.00650 (21822) covalent geometry : angle 0.92749 (30008) SS BOND : bond 0.00646 ( 16) SS BOND : angle 1.67083 ( 32) hydrogen bonds : bond 0.15667 ( 1008) hydrogen bonds : angle 11.35714 ( 2946) link_BETA1-4 : bond 0.00650 ( 6) link_BETA1-4 : angle 1.92557 ( 18) link_NAG-ASN : bond 0.01294 ( 14) link_NAG-ASN : angle 5.94183 ( 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 : 0.134 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: 0.8354 (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: 0.8561 (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: 0.8407 (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: 0.0568 time to fit residues: 16.6412 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 : 0.126 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 : 0.182 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: 0.0455 time to fit residues: 12.7535 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 : 0.127 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: 0.0008 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 : 0.000 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 118 GLN D 483 ASN D 486 HIS Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.090871 restraints weight = 14128.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.094978 restraints weight = 8474.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.098070 restraints weight = 5691.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.100426 restraints weight = 4116.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.102141 restraints weight = 3137.017| |-----------------------------------------------------------------------------| r_work (final): 0.3329 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.144692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.116023 restraints weight = 10915.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.120335 restraints weight = 6709.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.123476 restraints weight = 4525.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.125863 restraints weight = 3271.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.127569 restraints weight = 2502.875| |-----------------------------------------------------------------------------| r_work (final): 0.3702 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2234 r_free = 0.2234 target = 0.046150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2232 r_free = 0.2232 target = 0.044556 restraints weight = 59.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2238 r_free = 0.2238 target = 0.045229 restraints weight = 12.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2241 r_free = 0.2241 target = 0.045475 restraints weight = 3.432 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2242 r_free = 0.2242 target = 0.045511 restraints weight = 0.933 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2242 r_free = 0.2242 target = 0.045523 restraints weight = 0.260 | |-----------------------------------------------------------------------------| r_work (final): 0.2244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3327 r_start: 0.3702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 21858 Z= 0.190 Angle : 0.901 42.348 30100 Z= 0.437 Chirality : 0.058 0.880 3702 Planarity : 0.005 0.059 3930 Dihedral : 12.587 95.968 3738 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.23 % Favored : 92.65 % 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 : 0.00 % 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 aren not related in a simple way. whole: -2.98 (0.13), residues: 3128 helix: -1.64 (0.12), residues: 1248 sheet: -2.50 (0.23), residues: 270 loop : -2.13 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 124 TYR 0.020 0.002 TYR C 109 PHE 0.025 0.002 PHE A 361 TRP 0.017 0.002 TRP C 632 HIS 0.008 0.002 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00387 (21822) covalent geometry : angle 0.76029 (30008) SS BOND : bond 0.00604 ( 16) SS BOND : angle 3.81497 ( 32) hydrogen bonds : bond 0.05281 ( 1008) hydrogen bonds : angle 7.06643 ( 2946) link_BETA1-4 : bond 0.00209 ( 6) link_BETA1-4 : angle 1.88501 ( 18) link_NAG-ASN : bond 0.01405 ( 14) link_NAG-ASN : angle 12.47937 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 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 : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 MET cc_start: 0.8494 (tpt) cc_final: 0.8085 (mtm) REVERT: C 42 PHE cc_start: 0.9420 (t80) cc_final: 0.9087 (t80) REVERT: C 64 SER cc_start: 0.7918 (t) cc_final: 0.7688 (t) REVERT: C 76 LEU cc_start: 0.8892 (mt) cc_final: 0.8672 (mt) REVERT: C 127 ILE cc_start: 0.9358 (tp) cc_final: 0.9141 (tp) REVERT: C 147 GLN cc_start: 0.9369 (mt0) cc_final: 0.8969 (mt0) REVERT: C 148 SER cc_start: 0.9677 (t) cc_final: 0.9388 (t) REVERT: C 151 TRP cc_start: 0.8103 (m-10) cc_final: 0.7763 (m-10) REVERT: C 152 PHE cc_start: 0.9377 (t80) cc_final: 0.8660 (t80) REVERT: C 174 ARG cc_start: 0.8159 (mtt90) cc_final: 0.7714 (mtt90) REVERT: C 185 GLU cc_start: 0.9449 (tp30) cc_final: 0.9040 (tm-30) REVERT: C 228 LEU cc_start: 0.9396 (mp) cc_final: 0.9139 (mp) REVERT: C 266 TYR cc_start: 0.8150 (m-80) cc_final: 0.7922 (m-80) REVERT: C 301 HIS cc_start: 0.9024 (m90) cc_final: 0.8284 (m-70) REVERT: C 334 ASN cc_start: 0.9293 (m-40) cc_final: 0.9089 (p0) REVERT: C 343 LYS cc_start: 0.9034 (tttm) cc_final: 0.8403 (tmtt) REVERT: C 346 LEU cc_start: 0.9532 (mt) cc_final: 0.9331 (mt) REVERT: C 384 GLN cc_start: 0.8535 (pp30) cc_final: 0.8335 (pp30) REVERT: C 474 GLN cc_start: 0.8641 (mt0) cc_final: 0.8015 (mm110) REVERT: C 498 HIS cc_start: 0.8508 (p-80) cc_final: 0.8082 (p-80) REVERT: C 554 PHE cc_start: 0.7493 (p90) cc_final: 0.7049 (p90) REVERT: C 702 TYR cc_start: 0.8729 (p90) cc_final: 0.8248 (p90) REVERT: C 731 ASN cc_start: 0.9232 (m-40) cc_final: 0.8806 (m110) REVERT: C 732 TYR cc_start: 0.8702 (m-80) cc_final: 0.8438 (m-80) REVERT: C 757 LEU cc_start: 0.9233 (mm) cc_final: 0.8982 (mm) REVERT: C 799 LYS cc_start: 0.8486 (tptm) cc_final: 0.8102 (ttpp) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.0517 time to fit residues: 14.1346 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 : 0.204 Evaluate side-chains 192 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.132 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: 0.8882 (mm-30) cc_final: 0.8391 (tt0) REVERT: D 106 GLU cc_start: 0.9472 (pm20) cc_final: 0.9086 (pm20) REVERT: D 121 THR cc_start: 0.9075 (m) cc_final: 0.8768 (p) REVERT: D 132 MET cc_start: 0.8070 (mtm) cc_final: 0.7824 (mtm) REVERT: D 144 PHE cc_start: 0.9071 (m-80) cc_final: 0.8615 (m-80) REVERT: D 152 GLN cc_start: 0.7940 (mp10) cc_final: 0.7674 (mp10) REVERT: D 159 ASN cc_start: 0.8340 (m110) cc_final: 0.7645 (m-40) REVERT: D 220 LEU cc_start: 0.9183 (mt) cc_final: 0.8872 (mt) REVERT: D 224 GLN cc_start: 0.8746 (tp40) cc_final: 0.8221 (tm-30) REVERT: D 227 ILE cc_start: 0.8114 (mt) cc_final: 0.7759 (mt) REVERT: D 236 GLU cc_start: 0.9398 (mt-10) cc_final: 0.8646 (mt-10) REVERT: D 326 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8022 (pp20) REVERT: D 351 PHE cc_start: 0.8784 (m-80) cc_final: 0.8066 (m-80) REVERT: D 795 LEU cc_start: 0.8584 (tp) cc_final: 0.8338 (tp) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.0454 time to fit residues: 12.2132 Evaluate side-chains 161 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.160 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: 10.0000 chunk 79 optimal weight: 1.9990 chunk 80 optimal weight: 40.0000 chunk 9 optimal weight: 0.0470 chunk 202 optimal weight: 40.0000 chunk 302 optimal weight: 0.0000 chunk 125 optimal weight: 6.9990 chunk 54 optimal weight: 0.1980 chunk 71 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 154 optimal weight: 20.0000 overall best weight: 0.6484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 301 HIS A 332 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.090934 restraints weight = 14110.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.095107 restraints weight = 8403.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.098236 restraints weight = 5657.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.100537 restraints weight = 4118.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.102408 restraints weight = 3187.166| |-----------------------------------------------------------------------------| r_work (final): 0.3346 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.144784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115462 restraints weight = 11116.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119852 restraints weight = 6793.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.123040 restraints weight = 4583.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.125420 restraints weight = 3326.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.127210 restraints weight = 2556.064| |-----------------------------------------------------------------------------| r_work (final): 0.3715 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.053055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.053046 restraints weight = 106.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.053045 restraints weight = 0.406 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.053045 restraints weight = 119.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.053045 restraints weight = 104.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.053045 restraints weight = 127.844| |-----------------------------------------------------------------------------| r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 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 = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2842 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= 0.301 Angle : 1.130 42.858 30100 Z= 0.568 Chirality : 0.070 0.922 3702 Planarity : 0.012 0.297 3930 Dihedral : 12.218 94.068 3738 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.57 % Favored : 91.11 % Rotamer: Outliers : 0.83 % Allowed : 3.45 % Favored : 95.72 % 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 aren not related in a simple way. whole: -3.07 (0.13), residues: 3128 helix: -1.74 (0.12), residues: 1246 sheet: -2.46 (0.25), residues: 288 loop : -2.18 (0.14), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.091 0.003 ARG A 715 TYR 0.107 0.005 TYR C 495 PHE 0.085 0.007 PHE A 493 TRP 0.063 0.008 TRP C 632 HIS 0.069 0.006 HIS C 314 Details of bonding type rmsd covalent geometry : bond 0.00650 (21822) covalent geometry : angle 1.02462 (30008) SS BOND : bond 0.03222 ( 16) SS BOND : angle 3.83151 ( 32) hydrogen bonds : bond 0.05738 ( 1008) hydrogen bonds : angle 7.18499 ( 2946) link_BETA1-4 : bond 0.01321 ( 6) link_BETA1-4 : angle 1.38507 ( 18) link_NAG-ASN : bond 0.01363 ( 14) link_NAG-ASN : angle 12.37317 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 185 time to evaluate : 0.209 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 42 PHE cc_start: 0.9375 (t80) cc_final: 0.9012 (t80) REVERT: A 47 ASN cc_start: 0.9349 (m-40) cc_final: 0.8993 (m-40) REVERT: A 76 LEU cc_start: 0.8987 (mt) cc_final: 0.8783 (mt) REVERT: A 127 ILE cc_start: 0.9419 (tp) cc_final: 0.9100 (tp) REVERT: A 152 PHE cc_start: 0.9366 (t80) cc_final: 0.8673 (t80) REVERT: A 174 ARG cc_start: 0.8251 (mtt90) cc_final: 0.7989 (mtt90) REVERT: A 185 GLU cc_start: 0.9465 (tp30) cc_final: 0.9018 (tm-30) REVERT: A 228 LEU cc_start: 0.9364 (mp) cc_final: 0.9096 (mp) REVERT: A 261 MET cc_start: 0.8636 (mtt) cc_final: 0.8169 (mmt) REVERT: A 282 TYR cc_start: 0.7868 (m-10) cc_final: 0.7657 (m-80) REVERT: A 301 HIS cc_start: 0.8894 (m-70) cc_final: 0.7932 (m90) REVERT: A 334 ASN cc_start: 0.9320 (m-40) cc_final: 0.9029 (p0) REVERT: A 343 LYS cc_start: 0.8901 (tttm) cc_final: 0.8357 (tmtt) REVERT: A 474 GLN cc_start: 0.8558 (mt0) cc_final: 0.7963 (mm110) REVERT: A 482 ASP cc_start: 0.8953 (m-30) cc_final: 0.8712 (m-30) REVERT: A 493 PHE cc_start: 0.8399 (p90) cc_final: 0.8153 (p90) REVERT: A 688 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8178 (mm) REVERT: A 757 LEU cc_start: 0.9351 (mm) cc_final: 0.9060 (mm) REVERT: A 799 LYS cc_start: 0.8486 (tptm) cc_final: 0.8050 (ttpp) outliers start: 7 outliers final: 1 residues processed: 188 average time/residue: 0.0477 time to fit residues: 12.3650 Evaluate side-chains 153 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 0.165 Evaluate side-chains 179 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.145 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: D 73 MET cc_start: 0.8633 (tpt) cc_final: 0.8396 (tpp) REVERT: D 106 GLU cc_start: 0.9419 (pm20) cc_final: 0.8939 (pm20) REVERT: D 121 THR cc_start: 0.9123 (m) cc_final: 0.8821 (p) REVERT: D 126 ILE cc_start: 0.8658 (pt) cc_final: 0.8350 (pt) REVERT: D 132 MET cc_start: 0.8157 (mtm) cc_final: 0.7713 (mtm) REVERT: D 136 ASP cc_start: 0.9370 (m-30) cc_final: 0.8998 (m-30) REVERT: D 152 GLN cc_start: 0.7981 (mp10) cc_final: 0.7609 (mp10) REVERT: D 162 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8316 (tp30) REVERT: D 220 LEU cc_start: 0.9161 (mt) cc_final: 0.8823 (mt) REVERT: D 224 GLN cc_start: 0.8586 (tp40) cc_final: 0.8038 (tm-30) REVERT: D 272 GLU cc_start: 0.8885 (mp0) cc_final: 0.8659 (pm20) REVERT: D 278 ILE cc_start: 0.9005 (mm) cc_final: 0.8732 (mm) REVERT: D 302 THR cc_start: 0.9544 (t) cc_final: 0.9342 (t) REVERT: D 338 TYR cc_start: 0.7663 (m-80) cc_final: 0.7290 (m-80) REVERT: D 351 PHE cc_start: 0.8732 (m-80) cc_final: 0.8007 (m-80) REVERT: D 726 LEU cc_start: 0.8585 (tp) cc_final: 0.8310 (tp) REVERT: D 795 LEU cc_start: 0.8531 (tp) cc_final: 0.8320 (tp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0543 time to fit residues: 13.3957 Evaluate side-chains 150 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.113 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: 0.0008 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 163 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 286 optimal weight: 4.9990 chunk 90 optimal weight: 0.0270 chunk 141 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 0.2980 chunk 239 optimal weight: 30.0000 chunk 294 optimal weight: 30.0000 chunk 174 optimal weight: 5.9990 overall best weight: 3.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 161 ASN C 332 ASN ** C 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.110221 restraints weight = 11151.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114551 restraints weight = 6332.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117816 restraints weight = 4106.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.120227 restraints weight = 2865.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121646 restraints weight = 2135.186| |-----------------------------------------------------------------------------| r_work (final): 0.3388 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.144497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115800 restraints weight = 11138.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.120205 restraints weight = 6777.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.123349 restraints weight = 4538.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.125674 restraints weight = 3282.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.127404 restraints weight = 2512.770| |-----------------------------------------------------------------------------| r_work (final): 0.3657 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.053979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.053926 restraints weight = 142.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.053981 restraints weight = 9.535 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.053993 restraints weight = 0.592 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.053989 restraints weight = 0.035 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.053932 restraints weight = 100.017| |-----------------------------------------------------------------------------| r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 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 = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.205 21858 Z= 0.360 Angle : 1.293 43.428 30100 Z= 0.650 Chirality : 0.082 1.740 3702 Planarity : 0.011 0.294 3930 Dihedral : 12.025 92.481 3738 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.70 % Favored : 90.98 % Rotamer: Outliers : 0.24 % Allowed : 2.85 % Favored : 96.91 % 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 aren not related in a simple way. whole: -3.26 (0.13), residues: 3128 helix: -1.88 (0.12), residues: 1248 sheet: -2.74 (0.24), residues: 300 loop : -2.25 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.074 0.004 ARG A 715 TYR 0.261 0.005 TYR A 109 PHE 0.167 0.008 PHE C 554 TRP 0.056 0.008 TRP A 632 HIS 0.032 0.004 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00829 (21822) covalent geometry : angle 1.19363 (30008) SS BOND : bond 0.01013 ( 16) SS BOND : angle 3.66790 ( 32) hydrogen bonds : bond 0.05667 ( 1008) hydrogen bonds : angle 7.28032 ( 2946) link_BETA1-4 : bond 0.00547 ( 6) link_BETA1-4 : angle 2.48167 ( 18) link_NAG-ASN : bond 0.02107 ( 14) link_NAG-ASN : angle 12.90955 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 MET cc_start: 0.8525 (tpt) cc_final: 0.8228 (mtp) REVERT: C 42 PHE cc_start: 0.9397 (t80) cc_final: 0.9013 (t80) REVERT: C 47 ASN cc_start: 0.9349 (m-40) cc_final: 0.9002 (m-40) REVERT: C 76 LEU cc_start: 0.8890 (mt) cc_final: 0.8668 (mt) REVERT: C 127 ILE cc_start: 0.9340 (tp) cc_final: 0.8965 (tp) REVERT: C 147 GLN cc_start: 0.9434 (mt0) cc_final: 0.9045 (mt0) REVERT: C 174 ARG cc_start: 0.8292 (mtt90) cc_final: 0.8076 (mtt90) REVERT: C 185 GLU cc_start: 0.9459 (tp30) cc_final: 0.9037 (tm-30) REVERT: C 228 LEU cc_start: 0.9356 (mp) cc_final: 0.9143 (mp) REVERT: C 282 TYR cc_start: 0.7890 (m-10) cc_final: 0.7679 (m-80) REVERT: C 334 ASN cc_start: 0.9311 (m-40) cc_final: 0.9058 (p0) REVERT: C 343 LYS cc_start: 0.8887 (tttm) cc_final: 0.8318 (tmtt) REVERT: C 371 GLN cc_start: 0.9019 (mp10) cc_final: 0.8403 (mm-40) REVERT: C 422 VAL cc_start: 0.9241 (p) cc_final: 0.8678 (p) REVERT: C 474 GLN cc_start: 0.8527 (mt0) cc_final: 0.7951 (mm110) REVERT: C 482 ASP cc_start: 0.8915 (m-30) cc_final: 0.8699 (m-30) REVERT: C 498 HIS cc_start: 0.8149 (p-80) cc_final: 0.7944 (p-80) REVERT: C 695 ASN cc_start: 0.9404 (t0) cc_final: 0.9158 (t0) REVERT: C 731 ASN cc_start: 0.9248 (m-40) cc_final: 0.8776 (m110) REVERT: C 757 LEU cc_start: 0.9317 (mm) cc_final: 0.9059 (mm) REVERT: C 799 LYS cc_start: 0.8199 (tptm) cc_final: 0.7989 (ttpp) outliers start: 2 outliers final: 1 residues processed: 177 average time/residue: 0.0591 time to fit residues: 14.3545 Evaluate side-chains 144 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.204 Evaluate side-chains 182 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.209 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: D 75 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8429 (tt0) REVERT: D 103 THR cc_start: 0.8970 (p) cc_final: 0.8764 (p) REVERT: D 106 GLU cc_start: 0.9524 (pm20) cc_final: 0.8983 (pm20) REVERT: D 126 ILE cc_start: 0.8697 (pt) cc_final: 0.8396 (pt) REVERT: D 132 MET cc_start: 0.8102 (mtm) cc_final: 0.7756 (mtm) REVERT: D 134 MET cc_start: 0.8509 (ttt) cc_final: 0.8240 (ttp) REVERT: D 136 ASP cc_start: 0.9342 (m-30) cc_final: 0.8975 (m-30) REVERT: D 152 GLN cc_start: 0.8107 (mp10) cc_final: 0.7674 (mp10) REVERT: D 162 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8424 (tp30) REVERT: D 220 LEU cc_start: 0.9139 (mt) cc_final: 0.8862 (mt) REVERT: D 224 GLN cc_start: 0.8564 (tp40) cc_final: 0.8062 (tm-30) REVERT: D 326 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8048 (pp20) REVERT: D 351 PHE cc_start: 0.8577 (m-80) cc_final: 0.7947 (m-80) REVERT: D 367 LEU cc_start: 0.8635 (tp) cc_final: 0.8405 (tp) REVERT: D 726 LEU cc_start: 0.8590 (tp) cc_final: 0.8288 (tp) REVERT: D 795 LEU cc_start: 0.8664 (tp) cc_final: 0.8455 (tp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0493 time to fit residues: 12.6219 Evaluate side-chains 151 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.181 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: 0.0008 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 137 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 25 optimal weight: 0.0570 chunk 277 optimal weight: 9.9990 chunk 204 optimal weight: 0.0370 chunk 176 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 191 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN ** A 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.091027 restraints weight = 14401.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095235 restraints weight = 8591.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.098313 restraints weight = 5762.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.100661 restraints weight = 4182.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.102339 restraints weight = 3203.362| |-----------------------------------------------------------------------------| r_work (final): 0.3342 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.142279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115066 restraints weight = 11261.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.119007 restraints weight = 6927.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.121889 restraints weight = 4712.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.123981 restraints weight = 3423.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.125407 restraints weight = 2634.412| |-----------------------------------------------------------------------------| r_work (final): 0.3668 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.053979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 18)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.053923 restraints weight = 128.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.053980 restraints weight = 9.055 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.053991 restraints weight = 0.574 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.053988 restraints weight = 0.034 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.053940 restraints weight = 111.496| |-----------------------------------------------------------------------------| r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 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 = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 1.079 21858 Z= 0.955 Angle : 1.436 43.428 30100 Z= 0.715 Chirality : 0.082 1.740 3702 Planarity : 0.011 0.294 3930 Dihedral : 12.025 92.481 3738 Min Nonbonded Distance : 1.294 Molprobity Statistics. All-atom Clashscore : 31.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.70 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: -3.26 (0.13), residues: 3128 helix: -1.88 (0.12), residues: 1248 sheet: -2.74 (0.24), residues: 300 loop : -2.25 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.074 0.004 ARG A 715 TYR 0.261 0.005 TYR A 109 PHE 0.167 0.008 PHE C 554 TRP 0.056 0.008 TRP C 632 HIS 0.032 0.004 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00830 (21822) covalent geometry : angle 1.19397 (30008) SS BOND : bond 0.65337 ( 16) SS BOND : angle 19.49570 ( 32) hydrogen bonds : bond 0.05667 ( 1008) hydrogen bonds : angle 7.28032 ( 2946) link_BETA1-4 : bond 0.00547 ( 6) link_BETA1-4 : angle 2.48167 ( 18) link_NAG-ASN : bond 0.02107 ( 14) link_NAG-ASN : angle 12.90955 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8517 (tpt) cc_final: 0.8224 (mtp) REVERT: A 42 PHE cc_start: 0.9361 (t80) cc_final: 0.8988 (t80) REVERT: A 47 ASN cc_start: 0.9333 (m-40) cc_final: 0.8978 (m-40) REVERT: A 76 LEU cc_start: 0.9020 (mt) cc_final: 0.8808 (mt) REVERT: A 127 ILE cc_start: 0.9351 (tp) cc_final: 0.9012 (tp) REVERT: A 144 TYR cc_start: 0.8611 (m-80) cc_final: 0.8207 (m-80) REVERT: A 147 GLN cc_start: 0.9406 (mt0) cc_final: 0.9011 (mt0) REVERT: A 174 ARG cc_start: 0.8285 (mtt90) cc_final: 0.7635 (ttm110) REVERT: A 185 GLU cc_start: 0.9466 (tp30) cc_final: 0.9021 (tm-30) REVERT: A 228 LEU cc_start: 0.9357 (mp) cc_final: 0.9126 (mp) REVERT: A 282 TYR cc_start: 0.7972 (m-10) cc_final: 0.7759 (m-80) REVERT: A 334 ASN cc_start: 0.9332 (m-40) cc_final: 0.9102 (p0) REVERT: A 343 LYS cc_start: 0.8938 (tttm) cc_final: 0.8401 (tmtt) REVERT: A 371 GLN cc_start: 0.8993 (mp10) cc_final: 0.8393 (mm-40) REVERT: A 422 VAL cc_start: 0.9131 (p) cc_final: 0.8668 (p) REVERT: A 474 GLN cc_start: 0.8490 (mt0) cc_final: 0.7947 (mm110) REVERT: A 482 ASP cc_start: 0.8954 (m-30) cc_final: 0.8723 (m-30) REVERT: A 498 HIS cc_start: 0.8181 (p-80) cc_final: 0.7848 (p-80) REVERT: A 695 ASN cc_start: 0.9469 (t0) cc_final: 0.9200 (t0) REVERT: A 702 TYR cc_start: 0.8845 (p90) cc_final: 0.8198 (p90) REVERT: A 723 MET cc_start: 0.8995 (mtt) cc_final: 0.8658 (ptt) REVERT: A 757 LEU cc_start: 0.9324 (mm) cc_final: 0.9079 (mm) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.0476 time to fit residues: 11.6141 Evaluate side-chains 140 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.127 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 : 0.156 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: D 103 THR cc_start: 0.8969 (p) cc_final: 0.8762 (p) REVERT: D 106 GLU cc_start: 0.9529 (pm20) cc_final: 0.9065 (pm20) REVERT: D 126 ILE cc_start: 0.8729 (pt) cc_final: 0.8402 (pt) REVERT: D 132 MET cc_start: 0.8096 (mtm) cc_final: 0.7786 (mtm) REVERT: D 136 ASP cc_start: 0.9329 (m-30) cc_final: 0.8986 (m-30) REVERT: D 152 GLN cc_start: 0.8092 (mp10) cc_final: 0.7673 (mp10) REVERT: D 162 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8277 (tp30) REVERT: D 220 LEU cc_start: 0.9145 (mt) cc_final: 0.8864 (mt) REVERT: D 224 GLN cc_start: 0.8580 (tp40) cc_final: 0.8064 (tm-30) REVERT: D 351 PHE cc_start: 0.8572 (m-80) cc_final: 0.7961 (m-80) REVERT: D 462 ILE cc_start: 0.8715 (mp) cc_final: 0.8502 (mp) REVERT: D 726 LEU cc_start: 0.8614 (tp) cc_final: 0.8293 (tp) REVERT: D 795 LEU cc_start: 0.8662 (tp) cc_final: 0.8445 (tp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0454 time to fit residues: 11.3872 Evaluate side-chains 154 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.208 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: 0.0007 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.1365 > 50: distance: 0 - 1: 7.074 distance: 0 - 6: 9.893 distance: 1 - 2: 4.250 distance: 1 - 4: 4.314 distance: 2 - 3: 6.264 distance: 2 - 7: 7.299 distance: 4 - 5: 10.074 distance: 5 - 6: 3.812 distance: 7 - 8: 5.854 distance: 8 - 9: 11.199 distance: 8 - 11: 8.195 distance: 9 - 10: 20.723 distance: 9 - 15: 12.398 distance: 11 - 12: 14.931 distance: 12 - 13: 12.767 distance: 12 - 14: 17.313 distance: 15 - 16: 13.464 distance: 16 - 17: 9.928 distance: 16 - 19: 34.472 distance: 17 - 18: 45.731 distance: 17 - 20: 14.209 distance: 20 - 21: 17.154 distance: 21 - 22: 22.761 distance: 21 - 24: 22.202 distance: 22 - 23: 13.880 distance: 22 - 27: 15.443 distance: 24 - 25: 15.488 distance: 24 - 26: 10.515 distance: 27 - 28: 6.865 distance: 28 - 29: 25.897 distance: 28 - 31: 24.593 distance: 29 - 30: 36.946 distance: 29 - 33: 17.553 distance: 31 - 32: 19.594 distance: 33 - 34: 14.609 distance: 33 - 39: 30.888 distance: 34 - 35: 30.979 distance: 34 - 37: 22.413 distance: 35 - 36: 21.142 distance: 35 - 40: 23.003 distance: 37 - 38: 29.565 distance: 38 - 39: 43.221 distance: 40 - 41: 53.014 distance: 41 - 42: 8.082 distance: 42 - 43: 14.468 distance: 42 - 44: 48.345 distance: 44 - 45: 16.292 distance: 45 - 46: 6.950 distance: 45 - 48: 6.692 distance: 46 - 47: 7.635 distance: 46 - 50: 13.146 distance: 48 - 49: 14.398 distance: 50 - 51: 12.795 distance: 50 - 56: 7.304 distance: 51 - 52: 17.285 distance: 51 - 54: 18.929 distance: 52 - 53: 27.056 distance: 52 - 57: 14.035 distance: 54 - 55: 3.824 distance: 55 - 56: 20.102 distance: 57 - 60: 9.026 distance: 58 - 59: 5.393 distance: 58 - 60: 31.134 distance: 61 - 62: 42.242 distance: 62 - 63: 15.107 distance: 63 - 64: 27.041 distance: 64 - 65: 11.047 distance: 65 - 66: 41.563 distance: 65 - 67: 31.875