Starting phenix.real_space_refine on Fri Jun 5 19:29:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iyp_61000/06_2026/9iyp_61000_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iyp_61000/06_2026/9iyp_61000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iyp_61000/06_2026/9iyp_61000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iyp_61000/06_2026/9iyp_61000.map" model { file = "/net/cci-nas-00/data/ceres_data/9iyp_61000/06_2026/9iyp_61000_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iyp_61000/06_2026/9iyp_61000_neut_trim.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 7 5.21 5 S 138 5.16 5 C 15042 2.51 5 N 3948 2.21 5 O 4306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23443 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 5951 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 32, 'TRANS': 755} Chain breaks: 3 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 7, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 3, 'GLU:plan': 13, 'ASN:plan1': 2, 'TYR:plan': 4, 'ASP:plan': 8, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 205 Chain: "B" Number of atoms: 5743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 5743 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 27, 'TRANS': 744} Chain breaks: 3 Unresolved non-hydrogen bonds: 358 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP:plan': 12, 'GLU:plan': 15, 'HIS:plan': 7, 'PHE:plan': 6, 'ARG:plan': 7, 'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 234 Chain: "C" Number of atoms: 5954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 5954 Classifications: {'peptide': 796} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 34, 'TRANS': 761} Chain breaks: 1 Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 431 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ARG:plan': 10, 'TRP:plan': 1, 'HIS:plan': 4, 'ASP:plan': 11, 'GLU:plan': 14, 'ASN:plan1': 7, 'TYR:plan': 2, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 221 Chain: "D" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 5704 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 26, 'TRANS': 743} Chain breaks: 3 Unresolved non-hydrogen bonds: 382 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 26, 'GLU:plan': 19, 'HIS:plan': 3, 'PHE:plan': 2, 'ARG:plan': 9, 'GLN:plan1': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 244 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 20 Unusual residues: {' MG': 4, '7RC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {' MG': 2, '7RC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.67, per 1000 atoms: 0.24 Number of scatterers: 23443 At special positions: 0 Unit cell: (110.26, 149.48, 186.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 138 16.00 P 2 15.00 Mg 7 11.99 O 4306 8.00 N 3948 7.00 C 15042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.37 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " 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=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " 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 NAG-ASN " NAG A 902 " - " ASN A 368 " " NAG C 901 " - " ASN C 203 " " NAG C 902 " - " ASN C 276 " Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 1.2 seconds 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5832 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 31 sheets defined 44.6% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 Processing helix chain 'A' and resid 70 through 82 Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.668A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (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 155 removed outlier: 3.749A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.918A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.654A pdb=" N ILE A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 256 through 262 Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.839A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.546A pdb=" N GLN A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 584 removed outlier: 3.745A pdb=" N ASP A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 Processing helix chain 'A' and resid 626 through 657 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 699 through 708 removed outlier: 4.000A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 768 through 783 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 812 through 840 removed outlier: 3.625A pdb=" N VAL A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE A 828 " --> pdb=" O ILE A 824 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.641A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 Processing helix chain 'B' and resid 105 through 120 removed outlier: 4.223A pdb=" N ALA B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 removed outlier: 4.003A pdb=" N SER B 130 " --> pdb=" O HIS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.660A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.623A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 296 through 312 Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 333 through 340 removed outlier: 3.783A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 removed outlier: 4.598A pdb=" N SER B 350 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.793A pdb=" N GLU B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 552 removed outlier: 4.425A pdb=" N PHE B 550 " --> pdb=" O PRO B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 578 removed outlier: 3.824A pdb=" N GLU B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 615 removed outlier: 3.905A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 615 " --> pdb=" O GLY B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 654 removed outlier: 3.782A pdb=" N LYS B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 707 Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 752 through 756 removed outlier: 4.001A pdb=" N VAL B 756 " --> pdb=" O SER B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 787 removed outlier: 4.629A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 796 removed outlier: 3.723A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 842 Processing helix chain 'C' and resid 35 through 53 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.805A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.792A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 4.029A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.883A pdb=" N ARG C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 298 removed outlier: 3.993A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 381 through 385 removed outlier: 4.239A pdb=" N GLU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.508A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 584 removed outlier: 3.628A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 615 Processing helix chain 'C' and resid 626 through 657 Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.978A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 removed outlier: 3.798A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 783 Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 809 through 840 removed outlier: 3.963A pdb=" N MET C 813 " --> pdb=" O THR C 809 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N MET C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 77 through 93 Processing helix chain 'D' and resid 106 through 119 removed outlier: 3.677A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 149 through 162 Processing helix chain 'D' and resid 178 through 192 Processing helix chain 'D' and resid 212 through 222 removed outlier: 4.140A pdb=" N LYS D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 288 through 312 Processing helix chain 'D' and resid 334 through 340 Processing helix chain 'D' and resid 459 through 473 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 517 through 522 removed outlier: 3.548A pdb=" N GLU D 521 " --> pdb=" O GLU D 518 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL D 522 " --> pdb=" O ARG D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 552 Processing helix chain 'D' and resid 555 through 580 Processing helix chain 'D' and resid 601 through 614 Processing helix chain 'D' and resid 626 through 654 Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 674 through 677 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 707 Processing helix chain 'D' and resid 713 through 724 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 752 through 756 removed outlier: 3.858A pdb=" N VAL D 756 " --> pdb=" O SER D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 787 Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.665A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 820 through 840 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 66 removed outlier: 7.348A pdb=" N ASN A 28 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LEU A 91 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY A 30 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.346A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TRP A 247 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N LEU A 269 " --> pdb=" O TRP A 247 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE A 266 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 478 removed outlier: 3.530A pdb=" N GLY A 761 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA5, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.773A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.773A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU A 538 " --> pdb=" O PHE A 754 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE A 754 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 68 through 73 removed outlier: 6.450A pdb=" N ILE B 37 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL B 71 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY B 36 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL B 98 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.958A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 257 through 258 removed outlier: 3.627A pdb=" N VAL B 280 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 475 through 480 Processing sheet with id=AB2, first strand: chain 'B' and resid 434 through 438 removed outlier: 3.664A pdb=" N ILE B 453 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 683 through 685 Processing sheet with id=AB4, first strand: chain 'B' and resid 683 through 685 removed outlier: 4.082A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AB6, first strand: chain 'C' and resid 61 through 62 removed outlier: 6.299A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU C 121 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL C 92 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 197 removed outlier: 7.158A pdb=" N ILE C 163 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N LEU C 195 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER C 168 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 268 through 271 removed outlier: 3.644A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLN C 357 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LEU C 361 " --> pdb=" O GLN C 357 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 473 through 478 Processing sheet with id=AC1, first strand: chain 'C' and resid 409 through 412 removed outlier: 3.554A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 485 through 489 removed outlier: 3.725A pdb=" N THR C 486 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN C 499 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 488 " --> pdb=" O GLU C 497 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C 497 " --> pdb=" O GLU C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AC4, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.938A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 540 through 542 removed outlier: 3.647A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 67 through 73 removed outlier: 6.438A pdb=" N ILE D 37 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL D 71 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY D 36 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA D 100 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE D 123 " --> pdb=" O PHE D 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 170 through 171 Processing sheet with id=AC8, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.543A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY D 377 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AD1, first strand: chain 'D' and resid 475 through 480 removed outlier: 3.663A pdb=" N MET D 508 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N GLY D 511 " --> pdb=" O ALA D 765 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALA D 765 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU D 513 " --> pdb=" O GLY D 763 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE D 530 " --> pdb=" O TYR D 762 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 524 through 525 removed outlier: 5.861A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE D 530 " --> pdb=" O TYR D 762 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AD4, first strand: chain 'D' and resid 656 through 657 removed outlier: 3.585A pdb=" N GLN D 656 " --> pdb=" O MET D 809 " (cutoff:3.500A) 1105 hydrogen bonds defined for protein. 3198 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7578 1.35 - 1.48: 5939 1.48 - 1.61: 10177 1.61 - 1.73: 0 1.73 - 1.86: 239 Bond restraints: 23933 Sorted by residual: bond pdb=" C THR A 370 " pdb=" N HIS A 371 " ideal model delta sigma weight residual 1.331 1.297 0.034 1.28e-02 6.10e+03 6.86e+00 bond pdb=" C GLY A 200 " pdb=" N THR A 201 " ideal model delta sigma weight residual 1.331 1.374 -0.043 1.66e-02 3.63e+03 6.75e+00 bond pdb=" C GLY A 612 " pdb=" N VAL A 613 " ideal model delta sigma weight residual 1.334 1.304 0.031 1.26e-02 6.30e+03 5.97e+00 bond pdb=" C ARG C 801 " pdb=" N SER C 802 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.35e-02 5.49e+03 3.54e+00 bond pdb=" C PHE C 810 " pdb=" N GLU C 811 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.31e-02 5.83e+03 3.40e+00 ... (remaining 23928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 32234 1.65 - 3.29: 274 3.29 - 4.94: 40 4.94 - 6.59: 8 6.59 - 8.24: 3 Bond angle restraints: 32559 Sorted by residual: angle pdb=" N PHE B 313 " pdb=" CA PHE B 313 " pdb=" C PHE B 313 " ideal model delta sigma weight residual 108.42 113.84 -5.42 1.54e+00 4.22e-01 1.24e+01 angle pdb=" C ARG C 801 " pdb=" N SER C 802 " pdb=" CA SER C 802 " ideal model delta sigma weight residual 120.90 116.13 4.77 1.41e+00 5.03e-01 1.14e+01 angle pdb=" CA GLY A 200 " pdb=" C GLY A 200 " pdb=" N THR A 201 " ideal model delta sigma weight residual 118.48 114.86 3.62 1.17e+00 7.31e-01 9.56e+00 angle pdb=" N ILE D 340 " pdb=" CA ILE D 340 " pdb=" C ILE D 340 " ideal model delta sigma weight residual 112.29 109.59 2.70 9.40e-01 1.13e+00 8.22e+00 angle pdb=" O GLY A 200 " pdb=" C GLY A 200 " pdb=" N THR A 201 " ideal model delta sigma weight residual 122.43 126.00 -3.57 1.27e+00 6.20e-01 7.89e+00 ... (remaining 32554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 13899 34.77 - 69.55: 320 69.55 - 104.32: 27 104.32 - 139.10: 4 139.10 - 173.87: 2 Dihedral angle restraints: 14252 sinusoidal: 5209 harmonic: 9043 Sorted by residual: dihedral pdb=" CB CYS C 436 " pdb=" SG CYS C 436 " pdb=" SG CYS C 455 " pdb=" CB CYS C 455 " ideal model delta sinusoidal sigma weight residual -86.00 -155.22 69.22 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CB CYS B 436 " pdb=" SG CYS B 436 " pdb=" SG CYS B 457 " pdb=" CB CYS B 457 " ideal model delta sinusoidal sigma weight residual -86.00 -141.09 55.09 1 1.00e+01 1.00e-02 4.11e+01 dihedral pdb=" C03 7RC D 901 " pdb=" C04 7RC D 901 " pdb=" N01 7RC D 901 " pdb=" C06 7RC D 901 " ideal model delta sinusoidal sigma weight residual 291.68 117.81 173.87 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 14249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3437 0.066 - 0.133: 333 0.133 - 0.199: 3 0.199 - 0.266: 0 0.266 - 0.332: 1 Chirality restraints: 3774 Sorted by residual: chirality pdb=" C1 NAG C 901 " pdb=" ND2 ASN C 203 " pdb=" C2 NAG C 901 " pdb=" O5 NAG C 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CG LEU A 830 " pdb=" CB LEU A 830 " pdb=" CD1 LEU A 830 " pdb=" CD2 LEU A 830 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" C01 7RC B 901 " pdb=" C02 7RC B 901 " pdb=" C08 7RC B 901 " pdb=" N02 7RC B 901 " both_signs ideal model delta sigma weight residual False 2.45 2.61 -0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 3771 not shown) Planarity restraints: 4148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 78 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.99e+00 pdb=" C PRO B 78 " -0.046 2.00e-02 2.50e+03 pdb=" O PRO B 78 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS B 79 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 366 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C ILE A 366 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE A 366 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR A 367 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 318 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO A 319 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 319 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 319 " 0.022 5.00e-02 4.00e+02 ... (remaining 4145 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 131 2.54 - 3.13: 18421 3.13 - 3.72: 35074 3.72 - 4.31: 46294 4.31 - 4.90: 80884 Nonbonded interactions: 180804 Sorted by model distance: nonbonded pdb=" OD1 ASN C 616 " pdb="MG MG C 904 " model vdw 1.949 2.170 nonbonded pdb=" OG SER B 690 " pdb=" O04 7RC B 901 " model vdw 2.091 3.040 nonbonded pdb=" OE2 GLU B 657 " pdb=" OG SER C 802 " model vdw 2.117 3.040 nonbonded pdb=" NH2 ARG A 523 " pdb=" O GLY A 901 " model vdw 2.156 3.120 nonbonded pdb=" OD1 ASN A 341 " pdb=" NZ LYS A 347 " model vdw 2.197 3.120 ... (remaining 180799 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 109 or (resid 110 through 111 and \ (name N or name CA or name C or name O or name CB )) or resid 112 through 167 or \ (resid 168 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 9 or (resid 170 and (name N or name CA or name C or name O or name CB )) or resi \ d 171 or (resid 172 and (name N or name CA or name C or name O or name CB )) or \ resid 173 through 181 or (resid 182 and (name N or name CA or name C or name O o \ r name CB )) or resid 183 through 187 or (resid 188 and (name N or name CA or na \ me C or name O or name CB )) or resid 189 through 207 or (resid 208 and (name N \ or name CA or name C or name O or name CB )) or resid 209 through 212 or (resid \ 213 through 216 and (name N or name CA or name C or name O or name CB )) or resi \ d 217 through 225 or (resid 226 through 230 and (name N or name CA or name C or \ name O or name CB )) or resid 231 through 237 or (resid 238 and (name N or name \ CA or name C or name O or name CB )) or resid 239 through 240 or (resid 241 and \ (name N or name CA or name C or name O or name CB )) or resid 242 or (resid 243 \ and (name N or name CA or name C or name O or name CB )) or resid 244 through 24 \ 8 or (resid 249 and (name N or name CA or name C or name O or name CB )) or resi \ d 250 or (resid 251 and (name N or name CA or name C or name O or name CB )) or \ resid 252 or (resid 253 and (name N or name CA or name C or name O or name CB )) \ or resid 254 through 258 or (resid 259 through 260 and (name N or name CA or na \ me C or name O or name CB )) or resid 261 through 263 or (resid 264 and (name N \ or name CA or name C or name O or name CB )) or resid 265 through 272 or (resid \ 273 and (name N or name CA or name C or name O or name CB )) or resid 274 or (re \ sid 275 and (name N or name CA or name C or name O or name CB )) or resid 276 th \ rough 281 or (resid 282 through 284 and (name N or name CA or name C or name O o \ r name CB )) or resid 285 through 294 or (resid 295 through 299 and (name N or n \ ame CA or name C or name O or name CB )) or resid 300 through 307 or (resid 308 \ and (name N or name CA or name C or name O or name CB )) or resid 309 through 31 \ 5 or (resid 316 and (name N or name CA or name C or name O or name CB )) or resi \ d 317 through 355 or (resid 356 and (name N or name CA or name C or name O or na \ me CB )) or resid 357 or (resid 358 and (name N or name CA or name C or name O o \ r name CB )) or resid 359 through 376 or (resid 377 through 378 and (name N or n \ ame CA or name C or name O or name CB )) or resid 379 through 385 or (resid 386 \ through 387 and (name N or name CA or name C or name O or name CB )) or resid 38 \ 8 through 413 or (resid 414 and (name N or name CA or name C or name O or name C \ B )) or resid 415 through 420 or (resid 421 and (name N or name CA or name C or \ name O or name CB )) or resid 422 through 425 or (resid 426 through 427 and (nam \ e N or name CA or name C or name O or name CB )) or resid 428 or (resid 429 and \ (name N or name CA or name C or name O or name CB )) or resid 430 through 448 or \ (resid 449 and (name N or name CA or name C or name O or name CB )) or resid 45 \ 0 through 460 or (resid 461 and (name N or name CA or name C or name O or name C \ B )) or resid 462 through 491 or (resid 492 and (name N or name CA or name C or \ name O or name CB )) or resid 493 or (resid 494 through 495 and (name N or name \ CA or name C or name O or name CB )) or resid 496 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB )) or resid 569 through 603 or \ (resid 604 through 607 and (name N or name CA or name C or name O or name CB )) \ or resid 608 through 656 or (resid 657 and (name N or name CA or name C or name \ O or name CB )) or resid 658 through 673 or (resid 674 and (name N or name CA o \ r name C or name O or name CB )) or resid 675 through 798 or (resid 799 and (nam \ e N or name CA or name C or name O or name CB )) or resid 800 through 817 or (re \ sid 818 and (name N or name CA or name C or name O or name CB )) or resid 819 th \ rough 828 or (resid 829 and (name N or name CA or name C or name O or name CB )) \ or resid 830 through 901)) selection = (chain 'C' and (resid 27 through 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 97 or (resid 101 through 102 and ( \ name N or name CA or name C or name O or name CB )) or resid 103 through 121 or \ (resid 122 and (name N or name CA or name C or name O or name CB )) or resid 123 \ through 148 or (resid 149 and (name N or name CA or name C or name O or name CB \ )) or resid 150 through 156 or (resid 157 and (name N or name CA or name C or n \ ame O or name CB )) or resid 158 through 201 or (resid 202 and (name N or name C \ A or name C or name O or name CB )) or resid 203 through 213 or (resid 214 throu \ gh 216 and (name N or name CA or name C or name O or name CB )) or resid 217 thr \ ough 293 or (resid 294 through 299 and (name N or name CA or name C or name O or \ name CB )) or resid 300 through 314 or (resid 315 through 316 and (name N or na \ me CA or name C or name O or name CB )) or resid 317 through 323 or (resid 324 a \ nd (name N or name CA or name C or name O or name CB )) or resid 325 through 328 \ or (resid 329 through 331 and (name N or name CA or name C or name O or name CB \ )) or resid 332 through 375 or (resid 376 through 378 and (name N or name CA or \ name C or name O or name CB )) or resid 379 through 416 or (resid 417 and (name \ N or name CA or name C or name O or name CB )) or resid 418 or (resid 419 and ( \ name N or name CA or name C or name O or name CB )) or resid 420 through 441 or \ resid 447 through 620 or (resid 621 and (name N or name CA or name C or name O o \ r name CB )) or resid 622 through 664 or (resid 665 and (name N or name CA or na \ me C or name O or name CB )) or resid 666 through 676 or (resid 677 through 678 \ and (name N or name CA or name C or name O or name CB )) or resid 679 through 70 \ 0 or (resid 701 and (name N or name CA or name C or name O or name CB )) or resi \ d 702 through 723 or (resid 724 and (name N or name CA or name C or name O or na \ me CB )) or resid 725 through 732 or (resid 733 through 734 and (name N or name \ CA or name C or name O or name CB )) or resid 735 through 736 or (resid 737 and \ (name N or name CA or name C or name O or name CB )) or resid 738 or (resid 739 \ through 740 and (name N or name CA or name C or name O or name CB )) or resid 74 \ 1 through 748 or (resid 749 and (name N or name CA or name C or name O or name C \ B )) or resid 750 through 764 or (resid 765 and (name N or name CA or name C or \ name O or name CB )) or resid 766 through 768 or (resid 769 through 770 and (nam \ e N or name CA or name C or name O or name CB )) or resid 771 through 785 or (re \ sid 786 through 787 and (name N or name CA or name C or name O or name CB )) or \ resid 788 or (resid 789 through 790 and (name N or name CA or name C or name O o \ r name CB )) or resid 791 through 794 or (resid 795 and (name N or name CA or na \ me C or name O or name CB )) or resid 796 through 840 or resid 903)) } ncs_group { reference = (chain 'B' and (resid 35 through 61 or (resid 62 and (name N or name CA or name \ C or name O or name CB )) or resid 63 through 64 or (resid 65 and (name N or nam \ e CA or name C or name O or name CB )) or resid 66 or (resid 67 and (name N or n \ ame CA or name C or name O or name CB )) or resid 68 through 72 or (resid 73 and \ (name N or name CA or name C or name O or name CB )) or resid 74 through 76 or \ (resid 77 and (name N or name CA or name C or name O or name CB )) or resid 78 o \ r (resid 79 through 80 and (name N or name CA or name C or name O or name CB )) \ or resid 81 through 100 or (resid 101 through 102 and (name N or name CA or name \ C or name O or name CB )) or resid 103 through 107 or (resid 108 through 109 an \ d (name N or name CA or name C or name O or name CB )) or resid 110 through 112 \ or (resid 113 and (name N or name CA or name C or name O or name CB )) or resid \ 114 through 122 or (resid 123 and (name N or name CA or name C or name O or name \ CB )) or resid 124 through 138 or (resid 139 and (name N or name CA or name C o \ r name O or name CB )) or resid 140 through 199 or (resid 200 through 201 and (n \ ame N or name CA or name C or name O or name CB )) or resid 202 through 205 or ( \ resid 206 and (name N or name CA or name C or name O or name CB )) or resid 207 \ through 212 or (resid 213 and (name N or name CA or name C or name O or name CB \ )) or resid 214 through 223 or (resid 224 and (name N or name CA or name C or na \ me O or name CB )) or resid 225 through 234 or (resid 235 and (name N or name CA \ or name C or name O or name CB )) or resid 236 through 241 or (resid 242 and (n \ ame N or name CA or name C or name O or name CB )) or resid 243 through 267 or ( \ resid 268 and (name N or name CA or name C or name O or name CB )) or resid 269 \ through 293 or (resid 294 and (name N or name CA or name C or name O or name CB \ )) or resid 295 through 298 or (resid 299 and (name N or name CA or name C or na \ me O or name CB )) or resid 300 through 304 or (resid 305 through 308 and (name \ N or name CA or name C or name O or name CB )) or resid 309 through 336 or (resi \ d 337 through 338 and (name N or name CA or name C or name O or name CB )) or re \ sid 339 through 351 or (resid 352 and (name N or name CA or name C or name O or \ name CB )) or resid 353 through 373 or (resid 374 through 375 and (name N or nam \ e CA or name C or name O or name CB )) or resid 376 through 379 or (resid 380 th \ rough 382 and (name N or name CA or name C or name O or name CB )) or resid 383 \ through 388 or (resid 389 and (name N or name CA or name C or name O or name CB \ )) or resid 390 through 403 or (resid 404 and (name N or name CA or name C or na \ me O or name CB )) or resid 405 through 429 or (resid 430 through 431 and (name \ N or name CA or name C or name O or name CB )) or resid 432 or (resid 433 and (n \ ame N or name CA or name C or name O or name CB )) or resid 434 through 451 or ( \ resid 452 and (name N or name CA or name C or name O or name CB )) or resid 453 \ through 476 or (resid 477 and (name N or name CA or name C or name O or name CB \ )) or resid 478 through 520 or (resid 521 and (name N or name CA or name C or na \ me O or name CB )) or resid 522 through 537 or (resid 538 and (name N or name CA \ or name C or name O or name CB )) or resid 539 through 562 or (resid 563 and (n \ ame N or name CA or name C or name O or name CB )) or resid 564 or (resid 565 an \ d (name N or name CA or name C or name O or name CB )) or resid 566 through 579 \ or resid 600 through 603 or (resid 604 through 605 and (name N or name CA or nam \ e C or name O or name CB )) or resid 606 through 623 or (resid 624 and (name N o \ r name CA or name C or name O or name CB )) or resid 625 through 628 or (resid 6 \ 29 and (name N or name CA or name C or name O or name CB )) or resid 630 through \ 663 or (resid 664 and (name N or name CA or name C or name O or name CB )) or r \ esid 665 through 667 or (resid 668 through 669 and (name N or name CA or name C \ or name O or name CB )) or resid 670 through 681 or (resid 682 and (name N or na \ me CA or name C or name O or name CB )) or resid 683 through 691 or (resid 692 a \ nd (name N or name CA or name C or name O or name CB )) or resid 693 through 701 \ or (resid 702 and (name N or name CA or name C or name O or name CB )) or resid \ 703 through 714 or (resid 715 and (name N or name CA or name C or name O or nam \ e CB )) or resid 716 through 718 or (resid 719 and (name N or name CA or name C \ or name O or name CB )) or resid 720 or (resid 721 and (name N or name CA or nam \ e C or name O or name CB )) or resid 722 through 724 or (resid 725 and (name N o \ r name CA or name C or name O or name CB )) or resid 726 or (resid 727 through 7 \ 28 and (name N or name CA or name C or name O or name CB )) or resid 729 through \ 742 or (resid 743 through 744 and (name N or name CA or name C or name O or nam \ e CB )) or resid 745 through 785 or (resid 786 and (name N or name CA or name C \ or name O or name CB )) or resid 787 through 789 or (resid 790 and (name N or na \ me CA or name C or name O or name CB )) or resid 791 through 813 or (resid 814 a \ nd (name N or name CA or name C or name O or name CB )) or resid 815 or (resid 8 \ 16 and (name N or name CA or name C or name O or name CB )) or resid 817 through \ 903)) selection = (chain 'D' and (resid 35 through 60 or (resid 61 through 62 and (name N or name \ CA or name C or name O or name CB )) or resid 63 through 79 or (resid 80 and (na \ me N or name CA or name C or name O or name CB )) or resid 81 through 82 or (res \ id 83 and (name N or name CA or name C or name O or name CB )) or resid 84 throu \ gh 87 or (resid 88 through 89 and (name N or name CA or name C or name O or name \ CB )) or resid 90 through 93 or (resid 94 through 95 and (name N or name CA or \ name C or name O or name CB )) or resid 96 through 137 or (resid 138 through 139 \ and (name N or name CA or name C or name O or name CB )) or resid 140 through 1 \ 67 or (resid 168 and (name N or name CA or name C or name O or name CB )) or res \ id 169 through 193 or (resid 194 and (name N or name CA or name C or name O or n \ ame CB )) or resid 195 through 208 or (resid 209 through 211 and (name N or name \ CA or name C or name O or name CB )) or resid 212 through 214 or (resid 215 and \ (name N or name CA or name C or name O or name CB )) or resid 216 through 313 o \ r (resid 314 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 15 through 318 or (resid 319 and (name N or name CA or name C or name O or name \ CB )) or resid 320 through 321 or (resid 322 and (name N or name CA or name C or \ name O or name CB )) or resid 323 or (resid 324 through 328 and (name N or name \ CA or name C or name O or name CB )) or resid 329 or (resid 330 and (name N or \ name CA or name C or name O or name CB )) or resid 331 through 337 or (resid 338 \ and (name N or name CA or name C or name O or name CB )) or resid 339 or (resid \ 340 and (name N or name CA or name C or name O or name CB or name CG1 or name C \ G2)) or resid 341 through 342 or (resid 343 and (name N or name CA or name C or \ name O or name CB )) or resid 344 through 346 or (resid 347 and (name N or name \ CA or name C or name O or name CB )) or resid 348 through 369 or (resid 370 and \ (name N or name CA or name C or name O or name CB )) or resid 371 through 374 or \ (resid 375 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 6 through 419 or (resid 420 and (name N or name CA or name C or name O or name C \ B )) or resid 421 through 439 or (resid 440 and (name N or name CA or name C or \ name O or name CB )) or resid 451 through 481 or (resid 482 and (name N or name \ CA or name C or name O or name CB )) or resid 483 through 560 or (resid 561 and \ (name N or name CA or name C or name O or name CB )) or resid 562 through 574 or \ (resid 575 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 6 or (resid 577 and (name N or name CA or name C or name O or name CB )) or resi \ d 578 through 579 or resid 600 through 625 or (resid 626 through 627 and (name N \ or name CA or name C or name O or name CB )) or resid 628 through 648 or (resid \ 649 and (name N or name CA or name C or name O or name CB )) or resid 650 throu \ gh 661 or (resid 662 and (name N or name CA or name C or name O or name CB )) or \ resid 663 through 668 or (resid 669 and (name N or name CA or name C or name O \ or name CB )) or resid 670 through 672 or (resid 673 and (name N or name CA or n \ ame C or name O or name CB )) or resid 674 through 743 or (resid 744 and (name N \ or name CA or name C or name O or name CB )) or resid 745 through 768 or (resid \ 769 through 770 and (name N or name CA or name C or name O or name CB )) or res \ id 771 through 776 or (resid 777 and (name N or name CA or name C or name O or n \ ame CB )) or resid 778 through 787 or (resid 788 and (name N or name CA or name \ C or name O or name CB )) or resid 789 through 801 or (resid 802 and (name N or \ name CA or name C or name O or name CB )) or resid 803 through 832 or (resid 833 \ and (name N or name CA or name C or name O or name CB )) or resid 834 through 8 \ 35 or (resid 836 through 837 and (name N or name CA or name C or name O or name \ CB )) or resid 838 or (resid 839 through 842 and (name N or name CA or name C or \ name O or name CB )) or resid 901 through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.410 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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 : 0.003 0.334 23947 Z= 0.144 Angle : 0.397 8.236 32590 Z= 0.213 Chirality : 0.038 0.332 3774 Planarity : 0.002 0.040 4145 Dihedral : 15.166 173.873 8387 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.13 % Allowed : 20.16 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.17), residues: 3098 helix: 3.25 (0.15), residues: 1327 sheet: -0.51 (0.28), residues: 375 loop : -1.46 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 489 TYR 0.009 0.000 TYR C 681 PHE 0.007 0.001 PHE D 460 TRP 0.005 0.000 TRP D 197 HIS 0.002 0.000 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.10 (23933) covalent geometry : angle 0.39115 / 0.21 (32559) SS BOND : bond 0.10088 / 3.74 ( 11) SS BOND : angle 1.93183 / 1.00 ( 22) hydrogen bonds : bond 0.13945 / 9.30 ( 1091) hydrogen bonds : angle 5.27177 / 3.87 ( 3198) link_NAG-ASN : bond 0.00514 / 0.24 ( 3) link_NAG-ASN : angle 3.04456 / 1.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 216 time to evaluate : 0.975 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 218 average time/residue: 0.1433 time to fit residues: 51.8442 Evaluate side-chains 209 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 559 GLN B 710 ASN D 336 ASN D 432 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.108117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.079540 restraints weight = 48832.280| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.69 r_work: 0.2916 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23947 Z= 0.161 Angle : 0.509 10.386 32590 Z= 0.267 Chirality : 0.043 0.365 3774 Planarity : 0.003 0.048 4145 Dihedral : 7.504 176.025 3419 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.77 % Allowed : 18.29 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.16), residues: 3098 helix: 2.55 (0.15), residues: 1331 sheet: -0.70 (0.27), residues: 385 loop : -1.49 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 139 TYR 0.022 0.001 TYR C 681 PHE 0.017 0.002 PHE B 313 TRP 0.011 0.001 TRP D 197 HIS 0.003 0.001 HIS C 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (23933) covalent geometry : angle 0.50481 / 0.27 (32559) SS BOND : bond 0.00280 / 0.14 ( 11) SS BOND : angle 0.86044 / 0.55 ( 22) hydrogen bonds : bond 0.04413 / 2.97 ( 1091) hydrogen bonds : angle 4.47721 / 3.22 ( 3198) link_NAG-ASN : bond 0.00783 / 0.37 ( 3) link_NAG-ASN : angle 3.99633 / 2.37 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 218 time to evaluate : 0.906 Fit side-chains REVERT: A 125 MET cc_start: 0.8942 (mmm) cc_final: 0.8675 (mmm) REVERT: C 470 MET cc_start: 0.8174 (mtt) cc_final: 0.7908 (mtt) REVERT: C 479 VAL cc_start: 0.9560 (OUTLIER) cc_final: 0.9360 (m) REVERT: D 171 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8824 (mm) outliers start: 65 outliers final: 33 residues processed: 271 average time/residue: 0.1363 time to fit residues: 61.4026 Evaluate side-chains 236 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 838 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 179 optimal weight: 10.0000 chunk 219 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 432 ASN D 782 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.108979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.081245 restraints weight = 48736.121| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.75 r_work: 0.2929 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23947 Z= 0.108 Angle : 0.473 10.890 32590 Z= 0.247 Chirality : 0.041 0.356 3774 Planarity : 0.003 0.051 4145 Dihedral : 7.264 172.286 3419 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.47 % Allowed : 19.65 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.16), residues: 3098 helix: 2.40 (0.15), residues: 1335 sheet: -0.57 (0.28), residues: 365 loop : -1.54 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 489 TYR 0.019 0.001 TYR C 681 PHE 0.014 0.001 PHE A 472 TRP 0.012 0.001 TRP B 197 HIS 0.003 0.001 HIS D 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (23933) covalent geometry : angle 0.46768 / 0.25 (32559) SS BOND : bond 0.00228 / 0.15 ( 11) SS BOND : angle 0.81738 / 0.50 ( 22) hydrogen bonds : bond 0.03559 / 2.37 ( 1091) hydrogen bonds : angle 4.22272 / 3.04 ( 3198) link_NAG-ASN : bond 0.00827 / 0.39 ( 3) link_NAG-ASN : angle 4.12579 / 2.44 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 217 time to evaluate : 0.943 Fit side-chains REVERT: A 354 MET cc_start: 0.7581 (ptp) cc_final: 0.7147 (ptp) REVERT: A 611 TRP cc_start: 0.8166 (m100) cc_final: 0.7810 (m100) REVERT: B 132 MET cc_start: 0.8147 (mtt) cc_final: 0.7843 (mtt) REVERT: B 252 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.6801 (t80) REVERT: B 307 MET cc_start: 0.7407 (tpt) cc_final: 0.7164 (ttt) REVERT: B 453 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7878 (mp) REVERT: D 142 MET cc_start: 0.8827 (mmt) cc_final: 0.8169 (mmt) REVERT: D 171 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8971 (mt) REVERT: D 615 ASN cc_start: 0.7099 (t0) cc_final: 0.6730 (t0) REVERT: D 661 ASP cc_start: 0.6270 (m-30) cc_final: 0.5842 (m-30) outliers start: 58 outliers final: 30 residues processed: 265 average time/residue: 0.1406 time to fit residues: 61.8648 Evaluate side-chains 234 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 252 TYR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 838 CYS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 618 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 271 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 186 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 300 optimal weight: 0.9990 chunk 273 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 81 optimal weight: 30.0000 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 432 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.106567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.077840 restraints weight = 48680.541| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.68 r_work: 0.2885 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23947 Z= 0.176 Angle : 0.528 11.417 32590 Z= 0.274 Chirality : 0.043 0.382 3774 Planarity : 0.003 0.052 4145 Dihedral : 7.286 175.093 3419 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.24 % Allowed : 19.61 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.16), residues: 3098 helix: 2.28 (0.15), residues: 1328 sheet: -0.78 (0.27), residues: 390 loop : -1.53 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 505 TYR 0.022 0.001 TYR C 681 PHE 0.017 0.002 PHE C 472 TRP 0.013 0.001 TRP D 197 HIS 0.004 0.001 HIS D 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (23933) covalent geometry : angle 0.52285 / 0.27 (32559) SS BOND : bond 0.00259 / 0.15 ( 11) SS BOND : angle 0.93099 / 0.62 ( 22) hydrogen bonds : bond 0.04278 / 2.88 ( 1091) hydrogen bonds : angle 4.27486 / 3.06 ( 3198) link_NAG-ASN : bond 0.00747 / 0.36 ( 3) link_NAG-ASN : angle 4.40135 / 2.61 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 218 time to evaluate : 0.930 Fit side-chains REVERT: A 354 MET cc_start: 0.7678 (ptp) cc_final: 0.7314 (ptp) REVERT: B 132 MET cc_start: 0.8416 (mtt) cc_final: 0.8153 (mtt) REVERT: B 307 MET cc_start: 0.7516 (tpt) cc_final: 0.7119 (ttt) REVERT: B 309 SER cc_start: 0.7633 (OUTLIER) cc_final: 0.7413 (m) REVERT: C 789 ASP cc_start: 0.8449 (t0) cc_final: 0.8236 (t0) REVERT: D 142 MET cc_start: 0.8851 (mmt) cc_final: 0.8257 (mmt) REVERT: D 171 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.9052 (mt) REVERT: D 661 ASP cc_start: 0.6305 (m-30) cc_final: 0.5889 (m-30) outliers start: 76 outliers final: 53 residues processed: 282 average time/residue: 0.1442 time to fit residues: 67.9043 Evaluate side-chains 254 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 199 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 838 CYS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 429 CYS Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 618 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 36 optimal weight: 7.9990 chunk 248 optimal weight: 0.5980 chunk 6 optimal weight: 0.0570 chunk 39 optimal weight: 20.0000 chunk 286 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 203 optimal weight: 0.7980 chunk 127 optimal weight: 9.9990 chunk 154 optimal weight: 30.0000 overall best weight: 2.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.107299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.078633 restraints weight = 48628.686| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.69 r_work: 0.2899 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23947 Z= 0.126 Angle : 0.498 11.412 32590 Z= 0.259 Chirality : 0.042 0.375 3774 Planarity : 0.003 0.063 4145 Dihedral : 7.198 170.326 3419 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.86 % Allowed : 20.42 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.16), residues: 3098 helix: 2.26 (0.15), residues: 1328 sheet: -0.66 (0.28), residues: 366 loop : -1.57 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 794 TYR 0.021 0.001 TYR C 681 PHE 0.016 0.001 PHE A 472 TRP 0.010 0.001 TRP D 197 HIS 0.004 0.001 HIS D 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (23933) covalent geometry : angle 0.49263 / 0.26 (32559) SS BOND : bond 0.00239 / 0.15 ( 11) SS BOND : angle 0.84336 / 0.53 ( 22) hydrogen bonds : bond 0.03815 / 2.54 ( 1091) hydrogen bonds : angle 4.18996 / 3.00 ( 3198) link_NAG-ASN : bond 0.00795 / 0.38 ( 3) link_NAG-ASN : angle 4.36466 / 2.59 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 211 time to evaluate : 0.899 Fit side-chains REVERT: A 354 MET cc_start: 0.7648 (ptp) cc_final: 0.7282 (ptp) REVERT: B 132 MET cc_start: 0.8405 (mtt) cc_final: 0.8166 (mtt) REVERT: B 307 MET cc_start: 0.7567 (tpt) cc_final: 0.7160 (ttt) REVERT: D 142 MET cc_start: 0.8869 (mmt) cc_final: 0.8333 (mmt) REVERT: D 615 ASN cc_start: 0.7303 (t0) cc_final: 0.6971 (t0) outliers start: 67 outliers final: 50 residues processed: 266 average time/residue: 0.1400 time to fit residues: 62.3755 Evaluate side-chains 254 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 838 CYS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 618 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 139 optimal weight: 8.9990 chunk 208 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 283 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.106220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.078079 restraints weight = 48826.727| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.78 r_work: 0.2869 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23947 Z= 0.162 Angle : 0.527 11.606 32590 Z= 0.274 Chirality : 0.043 0.389 3774 Planarity : 0.004 0.054 4145 Dihedral : 7.231 154.659 3419 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.54 % Allowed : 20.12 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.16), residues: 3098 helix: 2.19 (0.15), residues: 1328 sheet: -0.89 (0.27), residues: 388 loop : -1.61 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 794 TYR 0.022 0.001 TYR C 681 PHE 0.016 0.001 PHE A 533 TRP 0.012 0.001 TRP D 197 HIS 0.005 0.001 HIS D 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (23933) covalent geometry : angle 0.52172 / 0.27 (32559) SS BOND : bond 0.00253 / 0.15 ( 11) SS BOND : angle 0.91134 / 0.60 ( 22) hydrogen bonds : bond 0.04144 / 2.77 ( 1091) hydrogen bonds : angle 4.21413 / 3.02 ( 3198) link_NAG-ASN : bond 0.00766 / 0.37 ( 3) link_NAG-ASN : angle 4.48208 / 2.66 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 204 time to evaluate : 0.904 Fit side-chains REVERT: A 354 MET cc_start: 0.7646 (ptp) cc_final: 0.7342 (ptp) REVERT: A 388 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8093 (ptmm) REVERT: B 307 MET cc_start: 0.7622 (tpt) cc_final: 0.7197 (ttt) REVERT: B 393 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6507 (ptm160) REVERT: D 142 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8413 (mmt) REVERT: D 615 ASN cc_start: 0.7460 (t0) cc_final: 0.6958 (t0) REVERT: D 631 MET cc_start: 0.8280 (tpp) cc_final: 0.8007 (tpp) outliers start: 83 outliers final: 59 residues processed: 272 average time/residue: 0.1423 time to fit residues: 64.8749 Evaluate side-chains 260 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 198 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 838 CYS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 429 CYS Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 801 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 168 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 266 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.106067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.078023 restraints weight = 48477.071| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.77 r_work: 0.2866 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23947 Z= 0.159 Angle : 0.529 11.854 32590 Z= 0.275 Chirality : 0.043 0.389 3774 Planarity : 0.004 0.054 4145 Dihedral : 7.322 143.241 3419 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.28 % Allowed : 20.25 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.16), residues: 3098 helix: 2.16 (0.15), residues: 1328 sheet: -0.91 (0.26), residues: 390 loop : -1.63 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 673 TYR 0.022 0.001 TYR C 681 PHE 0.015 0.001 PHE A 472 TRP 0.011 0.001 TRP D 197 HIS 0.004 0.001 HIS D 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (23933) covalent geometry : angle 0.52303 / 0.27 (32559) SS BOND : bond 0.00356 / 0.25 ( 11) SS BOND : angle 1.17048 / 0.79 ( 22) hydrogen bonds : bond 0.04124 / 2.75 ( 1091) hydrogen bonds : angle 4.20046 / 3.02 ( 3198) link_NAG-ASN : bond 0.00755 / 0.36 ( 3) link_NAG-ASN : angle 4.55205 / 2.70 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 207 time to evaluate : 0.977 Fit side-chains REVERT: A 354 MET cc_start: 0.7648 (ptp) cc_final: 0.7357 (ptp) REVERT: A 388 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8091 (ptmm) REVERT: B 204 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8137 (tt) REVERT: B 307 MET cc_start: 0.7644 (tpt) cc_final: 0.7251 (ttt) REVERT: B 393 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6528 (ptm160) REVERT: D 142 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8378 (mmt) REVERT: D 615 ASN cc_start: 0.7476 (t0) cc_final: 0.7022 (t0) REVERT: D 631 MET cc_start: 0.8315 (tpp) cc_final: 0.8056 (tpp) outliers start: 77 outliers final: 60 residues processed: 268 average time/residue: 0.1523 time to fit residues: 66.9745 Evaluate side-chains 259 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 195 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 838 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 429 CYS Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 801 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 196 optimal weight: 0.0670 chunk 206 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 309 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 257 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.106578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.077934 restraints weight = 48389.373| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.68 r_work: 0.2885 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23947 Z= 0.130 Angle : 0.514 11.818 32590 Z= 0.266 Chirality : 0.042 0.385 3774 Planarity : 0.004 0.053 4145 Dihedral : 7.301 148.604 3419 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.20 % Allowed : 20.76 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.16), residues: 3098 helix: 2.18 (0.15), residues: 1329 sheet: -0.85 (0.27), residues: 386 loop : -1.62 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 673 TYR 0.021 0.001 TYR C 681 PHE 0.019 0.001 PHE B 563 TRP 0.010 0.001 TRP C 768 HIS 0.004 0.001 HIS D 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (23933) covalent geometry : angle 0.50829 / 0.26 (32559) SS BOND : bond 0.00273 / 0.18 ( 11) SS BOND : angle 0.97368 / 0.65 ( 22) hydrogen bonds : bond 0.03871 / 2.58 ( 1091) hydrogen bonds : angle 4.14688 / 2.98 ( 3198) link_NAG-ASN : bond 0.00809 / 0.39 ( 3) link_NAG-ASN : angle 4.53703 / 2.69 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 202 time to evaluate : 0.928 Fit side-chains REVERT: A 354 MET cc_start: 0.7599 (ptp) cc_final: 0.7315 (ptp) REVERT: A 388 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8090 (ptmm) REVERT: B 307 MET cc_start: 0.7667 (tpt) cc_final: 0.7250 (ttt) REVERT: B 393 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6536 (ptm160) REVERT: B 739 MET cc_start: 0.8601 (mmm) cc_final: 0.8200 (mmm) REVERT: D 142 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8376 (mmt) REVERT: D 615 ASN cc_start: 0.7501 (t0) cc_final: 0.7057 (t0) REVERT: D 631 MET cc_start: 0.8309 (tpp) cc_final: 0.8105 (tpp) outliers start: 75 outliers final: 58 residues processed: 261 average time/residue: 0.1412 time to fit residues: 60.8644 Evaluate side-chains 262 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 201 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 838 CYS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 429 CYS Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 766 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 30 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 280 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 279 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN B 711 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.105401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.076697 restraints weight = 48545.972| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.66 r_work: 0.2863 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23947 Z= 0.177 Angle : 0.549 11.924 32590 Z= 0.286 Chirality : 0.044 0.396 3774 Planarity : 0.004 0.054 4145 Dihedral : 7.481 153.885 3419 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.11 % Allowed : 20.93 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 3098 helix: 2.11 (0.15), residues: 1325 sheet: -0.95 (0.26), residues: 388 loop : -1.65 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 673 TYR 0.023 0.001 TYR C 681 PHE 0.018 0.002 PHE C 472 TRP 0.013 0.001 TRP D 197 HIS 0.005 0.001 HIS D 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (23933) covalent geometry : angle 0.54314 / 0.28 (32559) SS BOND : bond 0.00305 / 0.19 ( 11) SS BOND : angle 1.07263 / 0.72 ( 22) hydrogen bonds : bond 0.04406 / 2.95 ( 1091) hydrogen bonds : angle 4.23351 / 3.04 ( 3198) link_NAG-ASN : bond 0.00759 / 0.36 ( 3) link_NAG-ASN : angle 4.61851 / 2.75 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 198 time to evaluate : 0.836 Fit side-chains REVERT: A 354 MET cc_start: 0.7560 (ptp) cc_final: 0.7346 (ptp) REVERT: A 388 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8099 (ptmm) REVERT: B 307 MET cc_start: 0.7668 (tpt) cc_final: 0.7247 (ttt) REVERT: B 393 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6614 (ptm160) REVERT: B 739 MET cc_start: 0.8640 (mmm) cc_final: 0.8220 (mmm) REVERT: C 41 MET cc_start: 0.8267 (ptt) cc_final: 0.8039 (ptp) REVERT: D 142 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8343 (mmt) REVERT: D 615 ASN cc_start: 0.7612 (t0) cc_final: 0.7158 (t0) REVERT: D 631 MET cc_start: 0.8345 (tpp) cc_final: 0.8115 (tpp) outliers start: 73 outliers final: 63 residues processed: 259 average time/residue: 0.1416 time to fit residues: 61.1817 Evaluate side-chains 265 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 199 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 838 CYS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 429 CYS Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 801 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 255 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 110 optimal weight: 0.1980 chunk 295 optimal weight: 9.9990 chunk 238 optimal weight: 0.3980 chunk 219 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 166 optimal weight: 0.3980 chunk 244 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.108807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.080547 restraints weight = 48132.840| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.66 r_work: 0.2934 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23947 Z= 0.095 Angle : 0.492 12.980 32590 Z= 0.253 Chirality : 0.041 0.364 3774 Planarity : 0.003 0.054 4145 Dihedral : 7.190 160.764 3419 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.00 % Allowed : 22.25 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.16), residues: 3098 helix: 2.24 (0.15), residues: 1332 sheet: -0.56 (0.27), residues: 372 loop : -1.63 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 794 TYR 0.015 0.001 TYR C 681 PHE 0.017 0.001 PHE A 472 TRP 0.013 0.001 TRP B 373 HIS 0.004 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (23933) covalent geometry : angle 0.48609 / 0.25 (32559) SS BOND : bond 0.00253 / 0.18 ( 11) SS BOND : angle 0.72118 / 0.46 ( 22) hydrogen bonds : bond 0.03054 / 2.03 ( 1091) hydrogen bonds : angle 4.01845 / 2.90 ( 3198) link_NAG-ASN : bond 0.00892 / 0.43 ( 3) link_NAG-ASN : angle 4.38533 / 2.60 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 217 time to evaluate : 0.879 Fit side-chains REVERT: A 354 MET cc_start: 0.7515 (ptp) cc_final: 0.7228 (ptp) REVERT: B 307 MET cc_start: 0.7612 (tpt) cc_final: 0.7209 (ttt) REVERT: B 337 ARG cc_start: 0.6934 (ptt90) cc_final: 0.6659 (tmm160) REVERT: B 393 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6533 (ptm160) REVERT: B 739 MET cc_start: 0.8683 (mmm) cc_final: 0.8316 (mmt) REVERT: C 41 MET cc_start: 0.8333 (ptt) cc_final: 0.8104 (ptp) REVERT: C 181 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8393 (mm-30) REVERT: C 790 LYS cc_start: 0.9104 (ptmm) cc_final: 0.8737 (pttt) REVERT: D 142 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8324 (mmt) REVERT: D 615 ASN cc_start: 0.7358 (t0) cc_final: 0.7047 (t0) REVERT: D 631 MET cc_start: 0.8237 (tpp) cc_final: 0.8028 (tpp) outliers start: 47 outliers final: 36 residues processed: 255 average time/residue: 0.1445 time to fit residues: 60.6512 Evaluate side-chains 244 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 429 CYS Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 766 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 310 optimal weight: 8.9990 chunk 305 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 241 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 285 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 308 optimal weight: 0.6980 chunk 210 optimal weight: 20.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN D 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.108758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.080450 restraints weight = 48301.860| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.67 r_work: 0.2932 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.140 23947 Z= 0.129 Angle : 0.653 59.200 32590 Z= 0.367 Chirality : 0.041 0.366 3774 Planarity : 0.003 0.055 4145 Dihedral : 7.193 160.748 3419 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.83 % Allowed : 22.59 % Favored : 75.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.16), residues: 3098 helix: 2.22 (0.14), residues: 1332 sheet: -0.55 (0.27), residues: 372 loop : -1.63 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 323 TYR 0.017 0.001 TYR C 681 PHE 0.031 0.001 PHE C 817 TRP 0.011 0.001 TRP B 373 HIS 0.004 0.000 HIS D 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (23933) covalent geometry : angle 0.64942 / 0.37 (32559) SS BOND : bond 0.00248 / 0.17 ( 11) SS BOND : angle 0.71319 / 0.46 ( 22) hydrogen bonds : bond 0.03075 / 2.04 ( 1091) hydrogen bonds : angle 4.01760 / 2.90 ( 3198) link_NAG-ASN : bond 0.00890 / 0.42 ( 3) link_NAG-ASN : angle 4.38671 / 2.60 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5483.22 seconds wall clock time: 94 minutes 48.96 seconds (5688.96 seconds total)