Starting phenix.real_space_refine on Sat Jul 4 22:14:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sac_24948/07_2026/7sac_24948.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sac_24948/07_2026/7sac_24948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sac_24948/07_2026/7sac_24948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sac_24948/07_2026/7sac_24948.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sac_24948/07_2026/7sac_24948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sac_24948/07_2026/7sac_24948.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7sac_24948/07_2026/7sac_24948.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sac_24948/07_2026/7sac_24948.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.352 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 298 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 124 5.16 5 Cl 3 4.86 5 C 15067 2.51 5 N 3872 2.21 5 O 4408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23474 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5888 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved non-hydrogen bonds: 410 Unresolved non-hydrogen angles: 493 Unresolved non-hydrogen dihedrals: 353 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 20, 'HIS:plan': 4, 'GLU:plan': 17, 'GLN:plan1': 7, 'ASP:plan': 6, 'PHE:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 286 Chain: "B" Number of atoms: 5747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5747 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 476 Unresolved non-hydrogen angles: 582 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 25, 'HIS:plan': 5, 'PHE:plan': 6, 'ASN:plan1': 4, 'ARG:plan': 6, 'GLN:plan1': 7, 'TYR:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 333 Chain: "C" Number of atoms: 5870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5870 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved non-hydrogen bonds: 430 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 18, 'HIS:plan': 5, 'GLU:plan': 15, 'GLN:plan1': 7, 'PHE:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 10, 'TRP:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 295 Chain: "D" Number of atoms: 5709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5709 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 513 Unresolved non-hydrogen angles: 626 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 28, 'HIS:plan': 4, 'PHE:plan': 6, 'ARG:plan': 9, 'ASN:plan1': 5, 'GLN:plan1': 8, 'TYR:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 362 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 chiralities: 2 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 48 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 1, 16 Unusual residues: {'JC9': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 16 Unusual residues: {'JC9': 1} Classifications: {'undetermined': 1} Conformer: "C" Number of residues, atoms: 1, 16 Unusual residues: {'JC9': 1} Classifications: {'undetermined': 1} 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 chiralities: 2 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 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 chiralities: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 AJC9 B 903 " occ=0.33 ... (46 atoms not shown) pdb="CL1 CJC9 B 903 " occ=0.33 Time building chain proxies: 5.58, per 1000 atoms: 0.24 Number of scatterers: 23474 At special positions: 0 Unit cell: (124.976, 153.224, 179.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 3 17.00 S 124 16.00 O 4408 8.00 N 3872 7.00 C 15067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.65 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.04 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=2.04 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 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 902 " - " ASN A 368 " " NAG B 901 " - " ASN B 491 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN C 368 " " NAG G 1 " - " ASN D 688 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 847.9 milliseconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5908 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 33 sheets defined 43.8% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.878A pdb=" N SER A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.909A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 159 removed outlier: 3.814A pdb=" N GLN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 188 removed outlier: 3.556A pdb=" N ALA A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.616A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.579A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 256 through 262 removed outlier: 4.068A pdb=" N LEU A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 262 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.703A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLY A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 removed outlier: 4.020A pdb=" N ARG A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 removed outlier: 3.611A pdb=" N LEU A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 Processing helix chain 'A' and resid 559 through 584 removed outlier: 3.957A pdb=" N TRP A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.584A pdb=" N SER A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 615 " --> pdb=" O TRP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 655 removed outlier: 3.790A pdb=" N ARG A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE A 631 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.564A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.688A pdb=" N ARG A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.694A pdb=" N GLN A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP A 723 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.601A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 742 " --> pdb=" O PHE A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 783 removed outlier: 3.975A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 810 through 841 removed outlier: 4.274A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 820 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 824 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 830 " --> pdb=" O ALA A 826 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.512A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.541A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 119 removed outlier: 3.929A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.916A pdb=" N SER B 130 " --> pdb=" O HIS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 162 Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.508A pdb=" N VAL B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.667A pdb=" N LYS B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 289 through 312 removed outlier: 3.568A pdb=" N ARG B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.805A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR B 330 " --> pdb=" O LYS B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 330' Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.622A pdb=" N ILE B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 472 Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 518 through 522 removed outlier: 3.809A pdb=" N GLU B 521 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL B 522 " --> pdb=" O ARG B 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 518 through 522' Processing helix chain 'B' and resid 557 through 577 removed outlier: 3.524A pdb=" N MET B 565 " --> pdb=" O MET B 561 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.533A pdb=" N ALA B 605 " --> pdb=" O THR B 601 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 656 removed outlier: 3.507A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 634 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.521A pdb=" N ARG B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 707 removed outlier: 3.541A pdb=" N GLY B 707 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 724 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 771 through 787 removed outlier: 4.439A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 783 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY B 785 " --> pdb=" O LEU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 798 removed outlier: 3.618A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR B 798 " --> pdb=" O ALA B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 845 removed outlier: 4.017A pdb=" N GLN B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 Processing helix chain 'C' and resid 70 through 86 removed outlier: 3.986A pdb=" N MET C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.968A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 4.116A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 158 removed outlier: 4.335A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.851A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 214 removed outlier: 3.651A pdb=" N MET C 209 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 236 removed outlier: 3.501A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 255 through 256 No H-bonds generated for 'chain 'C' and resid 255 through 256' Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.762A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 296 removed outlier: 3.590A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 removed outlier: 4.175A pdb=" N LYS C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET C 326 " --> pdb=" O LYS C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 471 removed outlier: 3.530A pdb=" N LYS C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 507 removed outlier: 4.009A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 505 " --> pdb=" O MET C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 525 removed outlier: 3.946A pdb=" N GLN C 525 " --> pdb=" O GLU C 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 522 through 525' Processing helix chain 'C' and resid 559 through 584 removed outlier: 3.674A pdb=" N TRP C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 removed outlier: 3.506A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP C 611 " --> pdb=" O MET C 607 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 657 removed outlier: 3.606A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET C 634 " --> pdb=" O ARG C 630 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL C 635 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 637 " --> pdb=" O GLY C 633 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLY C 638 " --> pdb=" O MET C 634 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 651 " --> pdb=" O TYR C 647 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 removed outlier: 3.897A pdb=" N ASN C 674 " --> pdb=" O PRO C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.592A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 710 removed outlier: 4.014A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N HIS C 709 " --> pdb=" O HIS C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.534A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG C 722 " --> pdb=" O ILE C 718 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP C 723 " --> pdb=" O GLN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 removed outlier: 3.629A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 782 removed outlier: 3.831A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU C 781 " --> pdb=" O LEU C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 removed outlier: 3.526A pdb=" N ASP C 787 " --> pdb=" O GLY C 783 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 788 " --> pdb=" O PHE C 784 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP C 789 " --> pdb=" O MET C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 840 removed outlier: 3.824A pdb=" N MET C 813 " --> pdb=" O THR C 809 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 820 " --> pdb=" O VAL C 816 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 830 " --> pdb=" O ALA C 826 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 removed outlier: 4.390A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 93 Processing helix chain 'D' and resid 106 through 119 removed outlier: 3.583A pdb=" N PHE D 114 " --> pdb=" O GLN D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.683A pdb=" N SER D 130 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 157 Processing helix chain 'D' and resid 159 through 164 Processing helix chain 'D' and resid 179 through 192 removed outlier: 4.142A pdb=" N VAL D 183 " --> pdb=" O TYR D 179 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 259 through 264 removed outlier: 4.145A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 307 Processing helix chain 'D' and resid 324 through 330 removed outlier: 4.222A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR D 330 " --> pdb=" O LYS D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 340 Processing helix chain 'D' and resid 459 through 473 removed outlier: 3.751A pdb=" N ASP D 463 " --> pdb=" O GLY D 459 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE D 464 " --> pdb=" O PHE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 503 removed outlier: 3.836A pdb=" N MET D 503 " --> pdb=" O GLY D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 521 removed outlier: 3.667A pdb=" N GLU D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 579 removed outlier: 4.135A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 614 removed outlier: 3.960A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 656 removed outlier: 3.746A pdb=" N VAL D 634 " --> pdb=" O ILE D 630 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP D 635 " --> pdb=" O MET D 631 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA D 644 " --> pdb=" O VAL D 640 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE D 653 " --> pdb=" O ASN D 649 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 697 removed outlier: 3.908A pdb=" N ARG D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 708 through 710 No H-bonds generated for 'chain 'D' and resid 708 through 710' Processing helix chain 'D' and resid 713 through 723 removed outlier: 3.738A pdb=" N LYS D 722 " --> pdb=" O LEU D 718 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR D 723 " --> pdb=" O LEU D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 743 removed outlier: 3.526A pdb=" N ASN D 737 " --> pdb=" O ALA D 733 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY D 741 " --> pdb=" O ASN D 737 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 742 " --> pdb=" O TYR D 738 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP D 743 " --> pdb=" O MET D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 787 removed outlier: 3.522A pdb=" N PHE D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY D 785 " --> pdb=" O LEU D 781 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP D 786 " --> pdb=" O GLN D 782 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.654A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 845 removed outlier: 4.433A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 removed outlier: 7.567A pdb=" N GLY A 30 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.585A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 168 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 271 removed outlier: 4.027A pdb=" N TYR A 351 " --> pdb=" O TYR A 367 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE A 366 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 373 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.712A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 476 removed outlier: 3.506A pdb=" N LEU A 398 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 475 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 400 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 401 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 413 removed outlier: 3.674A pdb=" N LYS A 412 " --> pdb=" O CYS A 454 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS A 454 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 451 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA9, first strand: chain 'A' and resid 517 through 518 removed outlier: 4.719A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 759 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE A 753 " --> pdb=" O GLN A 536 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLN A 536 " --> pdb=" O PHE A 753 " (cutoff:3.500A) removed outlier: 10.229A pdb=" N ARG A 755 " --> pdb=" O LYS A 534 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N LYS A 534 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 682 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 730 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.509A pdb=" N GLU A 528 " --> pdb=" O MET A 762 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET A 762 " --> pdb=" O GLU A 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 67 through 73 removed outlier: 3.559A pdb=" N LEU B 41 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET B 73 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLY B 36 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N VAL B 98 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 203 removed outlier: 7.965A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE B 227 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 280 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 408 through 410 removed outlier: 6.401A pdb=" N ILE B 408 " --> pdb=" O TYR B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 418 through 420 removed outlier: 4.322A pdb=" N CYS B 456 " --> pdb=" O GLU B 420 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AB7, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB8, first strand: chain 'B' and resid 729 through 732 removed outlier: 3.506A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 59 through 62 removed outlier: 3.506A pdb=" N GLN C 61 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N LEU C 91 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 194 through 197 removed outlier: 7.147A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 267 through 268 removed outlier: 3.562A pdb=" N GLY C 268 " --> pdb=" O MET C 354 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET C 354 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 339 through 340 removed outlier: 3.920A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 473 through 478 removed outlier: 7.188A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET C 512 " --> pdb=" O LYS C 399 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.662A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS C 412 " --> pdb=" O CYS C 454 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS C 454 " --> pdb=" O LYS C 412 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 486 through 489 Processing sheet with id=AC7, first strand: chain 'C' and resid 681 through 682 removed outlier: 3.985A pdb=" N ALA C 682 " --> pdb=" O ALA C 728 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 681 through 682 removed outlier: 3.985A pdb=" N ALA C 682 " --> pdb=" O ALA C 728 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 67 through 73 removed outlier: 3.697A pdb=" N GLU D 69 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 39 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY D 36 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL D 97 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA D 38 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N PHE D 99 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE D 40 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 198 through 205 removed outlier: 7.770A pdb=" N PHE D 169 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLU D 201 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR D 173 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE D 227 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR D 174 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 230 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL D 280 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU D 362 " --> pdb=" O TRP D 379 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY D 377 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS D 378 " --> pdb=" O GLN D 385 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 385 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS D 380 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 408 through 410 Processing sheet with id=AD3, first strand: chain 'D' and resid 418 through 420 removed outlier: 4.082A pdb=" N CYS D 456 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 508 through 509 Processing sheet with id=AD5, first strand: chain 'D' and resid 683 through 684 removed outlier: 3.798A pdb=" N ILE D 730 " --> pdb=" O GLY D 684 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 683 through 684 removed outlier: 3.798A pdb=" N ILE D 730 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 944 hydrogen bonds defined for protein. 2706 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: 5.54 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 3852 1.28 - 1.42: 6085 1.42 - 1.56: 13807 1.56 - 1.70: 7 1.70 - 1.84: 213 Bond restraints: 23964 Sorted by residual: bond pdb=" CA LYS D 438 " pdb=" C LYS D 438 " ideal model delta sigma weight residual 1.524 1.401 0.123 1.23e-02 6.61e+03 9.97e+01 bond pdb=" CA PHE B 642 " pdb=" C PHE B 642 " ideal model delta sigma weight residual 1.524 1.418 0.106 1.24e-02 6.50e+03 7.32e+01 bond pdb=" C GLN B 437 " pdb=" O GLN B 437 " ideal model delta sigma weight residual 1.236 1.137 0.099 1.19e-02 7.06e+03 6.86e+01 bond pdb=" CA ALA D 636 " pdb=" C ALA D 636 " ideal model delta sigma weight residual 1.523 1.420 0.103 1.30e-02 5.92e+03 6.30e+01 bond pdb=" C TRP D 610 " pdb=" O TRP D 610 " ideal model delta sigma weight residual 1.237 1.146 0.091 1.17e-02 7.31e+03 6.03e+01 ... (remaining 23959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.11: 32582 5.11 - 10.23: 118 10.23 - 15.34: 11 15.34 - 20.46: 1 20.46 - 25.57: 1 Bond angle restraints: 32713 Sorted by residual: angle pdb=" C ILE D 606 " pdb=" CA ILE D 606 " pdb=" CB ILE D 606 " ideal model delta sigma weight residual 112.14 95.86 16.28 1.35e+00 5.49e-01 1.45e+02 angle pdb=" C VAL D 613 " pdb=" CA VAL D 613 " pdb=" CB VAL D 613 " ideal model delta sigma weight residual 112.14 99.54 12.60 1.35e+00 5.49e-01 8.71e+01 angle pdb=" N LEU C 655 " pdb=" CA LEU C 655 " pdb=" C LEU C 655 " ideal model delta sigma weight residual 111.14 119.84 -8.70 1.08e+00 8.57e-01 6.49e+01 angle pdb=" N GLN D 437 " pdb=" CA GLN D 437 " pdb=" C GLN D 437 " ideal model delta sigma weight residual 108.02 121.49 -13.47 1.75e+00 3.27e-01 5.93e+01 angle pdb=" CA LEU D 612 " pdb=" CB LEU D 612 " pdb=" CG LEU D 612 " ideal model delta sigma weight residual 116.30 90.73 25.57 3.50e+00 8.16e-02 5.34e+01 ... (remaining 32708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.15: 13411 25.15 - 50.30: 567 50.30 - 75.45: 73 75.45 - 100.60: 24 100.60 - 125.74: 7 Dihedral angle restraints: 14082 sinusoidal: 4929 harmonic: 9153 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 -162.29 76.29 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS D 429 " pdb=" SG CYS D 429 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual 93.00 166.62 -73.62 1 1.00e+01 1.00e-02 6.89e+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 93.00 165.48 -72.48 1 1.00e+01 1.00e-02 6.71e+01 ... (remaining 14079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 3873 0.175 - 0.350: 31 0.350 - 0.525: 11 0.525 - 0.700: 2 0.700 - 0.875: 1 Chirality restraints: 3918 Sorted by residual: chirality pdb=" CA VAL D 640 " pdb=" N VAL D 640 " pdb=" C VAL D 640 " pdb=" CB VAL D 640 " both_signs ideal model delta sigma weight residual False 2.44 1.57 0.87 2.00e-01 2.50e+01 1.91e+01 chirality pdb=" CA ILE D 641 " pdb=" N ILE D 641 " pdb=" C ILE D 641 " pdb=" CB ILE D 641 " both_signs ideal model delta sigma weight residual False 2.43 1.78 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA PHE D 642 " pdb=" N PHE D 642 " pdb=" C PHE D 642 " pdb=" CB PHE D 642 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.57e+00 ... (remaining 3915 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 435 " 0.031 2.00e-02 2.50e+03 6.13e-02 3.76e+01 pdb=" C PRO B 435 " -0.106 2.00e-02 2.50e+03 pdb=" O PRO B 435 " 0.039 2.00e-02 2.50e+03 pdb=" N CYS B 436 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 678 " 0.097 5.00e-02 4.00e+02 1.46e-01 3.42e+01 pdb=" N PRO B 679 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO B 679 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO B 679 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 678 " -0.082 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO D 679 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO D 679 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO D 679 " -0.064 5.00e-02 4.00e+02 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2145 2.74 - 3.28: 23677 3.28 - 3.82: 35271 3.82 - 4.36: 38379 4.36 - 4.90: 67916 Nonbonded interactions: 167388 Sorted by model distance: nonbonded pdb=" OE2 GLU D 151 " pdb=" NZ LYS D 185 " model vdw 2.202 3.120 nonbonded pdb=" OH TYR D 507 " pdb=" OG SER D 770 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASP B 101 " pdb=" N ASP B 102 " model vdw 2.210 3.120 nonbonded pdb=" O MET A 125 " pdb=" NH2 ARG A 139 " model vdw 2.217 3.120 nonbonded pdb=" N1 CJC9 B 903 " pdb="CL1 CJC9 B 903 " model vdw 2.239 3.350 ... (remaining 167383 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 25 through 41 or (resid 42 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 or (resid 47 through 52 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 72 or (res \ id 73 through 75 and (name N or name CA or name C or name O or name CB )) or res \ id 76 through 129 or (resid 130 through 131 and (name N or name CA or name C or \ name O or name CB )) or resid 132 through 214 or (resid 215 through 216 and (nam \ e N or name CA or name C or name O or name CB )) or resid 217 through 259 or (re \ sid 260 and (name N or name CA or name C or name O or name CB )) or resid 261 th \ rough 274 or (resid 275 and (name N or name CA or name C or name O or name CB )) \ or resid 276 through 289 or (resid 290 through 291 and (name N or name CA or na \ me C or name O or name CB )) or resid 292 or (resid 293 through 294 and (name N \ or name CA or name C or name O or name CB )) or resid 295 through 325 or (resid \ 326 and (name N or name CA or name C or name O or name CB )) or resid 327 throug \ h 338 or (resid 339 and (name N or name CA or name C or name O or name CB )) or \ resid 340 through 342 or (resid 343 and (name N or name CA or name C or name O o \ r name CB )) or (resid 344 through 346 and (name N or name CA or name C or name \ O or name CB )) or resid 347 through 358 or (resid 359 through 360 and (name N o \ r name CA or name C or name O or name CB )) or resid 361 through 377 or (resid 3 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 379 through \ 575 or (resid 576 and (name N or name CA or name C or name O or name CB )) or r \ esid 577 or (resid 578 and (name N or name CA or name C or name O or name CB )) \ or resid 579 through 580 or (resid 581 through 583 and (name N or name CA or nam \ e C or name O or name CB )) or resid 584 through 606 or (resid 607 and (name N o \ r name CA or name C or name O or name CB )) or resid 608 through 657 or (resid 6 \ 58 through 659 and (name N or name CA or name C or name O or name CB )) or resid \ 660 through 677 or (resid 678 and (name N or name CA or name C or name O or nam \ e CB )) or resid 679 through 707 or (resid 708 and (name N or name CA or name C \ or name O or name CB )) or resid 709 through 798 or (resid 799 and (name N or na \ me CA or name C or name O or name CB )) or resid 800 through 903)) selection = (chain 'C' and (resid 25 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 or (resid 61 through 62 and (name N or nam \ e CA or name C or name O or name CB )) or resid 63 through 82 or (resid 83 and ( \ name N or name CA or name C or name O or name CB )) or resid 84 through 101 or ( \ resid 102 and (name N or name CA or name C or name O or name CB )) or resid 103 \ through 114 or (resid 115 and (name N or name CA or name C or name O or name CB \ )) or resid 116 through 130 or (resid 131 and (name N or name CA or name C or na \ me O or name CB )) or resid 132 through 155 or (resid 156 and (name N or name CA \ or name C or name O or name CB )) or resid 157 through 184 or (resid 185 throug \ h 188 and (name N or name CA or name C or name O or name CB )) or resid 189 thro \ ugh 224 or (resid 225 and (name N or name CA or name C or name O or name CB )) o \ r resid 226 through 271 or (resid 272 and (name N or name CA or name C or name O \ or name CB )) or resid 273 through 386 or (resid 387 through 388 and (name N or \ name CA or name C or name O or name CB )) or resid 389 or (resid 390 and (name \ N or name CA or name C or name O or name CB )) or resid 391 through 633 or (resi \ d 634 and (name N or name CA or name C or name O or name CB )) or resid 635 thro \ ugh 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 781 or (resid 782 and (name N or name CA or name \ C or name O or name CB )) or resid 783 through 789 or (resid 790 and (name N or \ name CA or name C or name O or name CB )) or resid 791 through 793 or (resid 79 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 795 through \ 903)) } ncs_group { reference = (chain 'B' and (resid 34 through 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 or (resid 69 and (name N or name CA or nam \ e C or name O or name CB )) or resid 70 through 83 or (resid 84 and (name N or n \ ame CA or name C or name O or name CB )) or resid 85 through 117 or (resid 118 a \ nd (name N or name CA or name C or name O or name CB )) or resid 119 through 136 \ or (resid 137 and (name N or name CA or name C or name O or name CB )) or resid \ 138 or (resid 139 and (name N or name CA or name C or name O or name CB )) or r \ esid 140 through 212 or (resid 213 and (name N or name CA or name C or name O or \ name CB )) or resid 214 through 305 or (resid 306 through 308 and (name N or na \ me CA or name C or name O or name CB )) or resid 309 or (resid 310 and (name N o \ r name CA or name C or name O or name CB )) or resid 311 through 315 or (resid 3 \ 16 and (name N or name CA or name C or name O or name CB )) or resid 317 through \ 332 or (resid 333 through 334 and (name N or name CA or name C or name O or nam \ e CB )) or resid 335 through 346 or (resid 347 through 348 and (name N or name C \ A or name C or name O or name CB )) or resid 349 through 360 or (resid 361 and ( \ name N or name CA or name C or name O or name CB )) or resid 362 through 440 or \ (resid 441 and (name N or name CA or name C or name O or name CB )) or resid 442 \ through 520 or (resid 521 and (name N or name CA or name C or name O or name CB \ )) or resid 522 through 562 or (resid 563 and (name N or name CA or name C or n \ ame O or name CB )) or resid 564 through 711 or (resid 712 and (name N or name C \ A or name C or name O or name CB )) or resid 713 through 746 or (resid 747 and ( \ name N or name CA or name C or name O or name CB )) or resid 748 through 802 or \ (resid 803 through 807 and (name N or name CA or name C or name O or name CB )) \ or resid 808 through 811 or (resid 812 and (name N or name CA or name C or name \ O or name CB )) or resid 813 through 817 or (resid 818 through 819 and (name N o \ r name CA or name C or name O or name CB )) or resid 820 through 823 or (resid 8 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 825 through \ 828 or (resid 829 through 830 and (name N or name CA or name C or name O or nam \ e CB )) or resid 831 through 835 or (resid 836 and (name N or name CA or name C \ or name O or name CB )) or resid 837 through 901)) selection = (chain 'D' and (resid 34 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 197 or (resid 198 and (name N or n \ ame CA or name C or name O or name CB )) or resid 199 or (resid 200 through 201 \ and (name N or name CA or name C or name O or name CB )) or resid 202 through 20 \ 6 or (resid 207 and (name N or name CA or name C or name O or name CB )) or resi \ d 208 or (resid 209 through 211 and (name N or name CA or name C or name O or na \ me CB )) or resid 212 through 377 or (resid 378 and (name N or name CA or name C \ or name O or name CB )) or resid 379 through 502 or (resid 503 and (name N or n \ ame CA or name C or name O or name CB )) or resid 504 through 560 or (resid 561 \ and (name N or name CA or name C or name O or name CB )) or resid 562 through 57 \ 4 or (resid 575 and (name N or name CA or name C or name O or name CB )) or resi \ d 576 through 628 or (resid 629 and (name N or name CA or name C or name O or na \ me CB )) or resid 630 through 661 or (resid 662 and (name N or name CA or name C \ or name O or name CB )) or resid 663 through 669 or (resid 670 and (name N or n \ ame CA or name C or name O or name CB )) or resid 671 through 672 or (resid 673 \ and (name N or name CA or name C or name O or name CB )) or resid 674 through 67 \ 5 or (resid 676 through 677 and (name N or name CA or name C or name O or name C \ B )) or resid 678 through 805 or (resid 806 through 807 and (name N or name CA o \ r name C or name O or name CB )) or resid 808 through 815 or (resid 816 and (nam \ e N or name CA or name C or name O or name CB )) or resid 817 through 901)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.270 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 : 0.009 0.620 23988 Z= 0.597 Angle : 0.828 25.573 32767 Z= 0.460 Chirality : 0.057 0.875 3918 Planarity : 0.006 0.146 4139 Dihedral : 14.490 125.744 8129 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.01 % Favored : 94.64 % Rotamer: Outliers : 0.90 % Allowed : 0.73 % Favored : 98.37 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.77 (0.15), residues: 3136 helix: 0.95 (0.15), residues: 1121 sheet: -0.18 (0.29), residues: 359 loop : -1.69 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 156 TYR 0.064 0.001 TYR D 646 PHE 0.061 0.001 PHE D 642 TRP 0.031 0.001 TRP D 607 HIS 0.014 0.001 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00805 / 0.51 (23964) covalent geometry : angle 0.82090 / 0.46 (32713) SS BOND : bond 0.16007 / 12.91 ( 15) SS BOND : angle 3.14188 / 1.97 ( 30) hydrogen bonds : bond 0.24780 / 16.81 ( 931) hydrogen bonds : angle 7.16221 / 5.07 ( 2706) Misc. bond : bond 0.35406 / 18.63 ( 1) link_BETA1-4 : bond 0.00319 / 0.16 ( 3) link_BETA1-4 : angle 0.74417 / 0.45 ( 9) link_NAG-ASN : bond 0.00876 / 0.44 ( 5) link_NAG-ASN : angle 2.93569 / 1.78 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 355 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8180 (tpp) cc_final: 0.7849 (tpp) REVERT: B 307 MET cc_start: 0.6990 (ppp) cc_final: 0.6420 (tmm) REVERT: B 347 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7533 (mtm-85) REVERT: B 432 ASN cc_start: 0.8784 (m-40) cc_final: 0.8576 (p0) REVERT: B 782 GLN cc_start: 0.8309 (tp-100) cc_final: 0.7812 (tp-100) REVERT: C 153 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7719 (mm-30) REVERT: C 209 MET cc_start: 0.7611 (tpp) cc_final: 0.7085 (tpp) REVERT: C 528 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7380 (tm-30) REVERT: C 651 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9192 (tt) REVERT: D 89 MET cc_start: 0.5658 (mmp) cc_final: 0.4711 (ttp) REVERT: D 95 GLN cc_start: 0.7360 (mm-40) cc_final: 0.6851 (tt0) REVERT: D 436 CYS cc_start: 0.5619 (p) cc_final: 0.5404 (p) REVERT: D 561 MET cc_start: 0.8577 (ppp) cc_final: 0.8145 (ppp) REVERT: D 612 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9377 (tt) REVERT: D 645 SER cc_start: 0.9667 (OUTLIER) cc_final: 0.9419 (p) REVERT: D 706 MET cc_start: 0.7248 (tmm) cc_final: 0.7009 (tmm) outliers start: 21 outliers final: 13 residues processed: 375 average time/residue: 0.1151 time to fit residues: 73.5606 Evaluate side-chains 303 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 286 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 642 PHE Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 654 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN A 404 HIS A 471 GLN A 796 GLN B 437 GLN C 146 HIS C 276 ASN D 95 GLN D 219 GLN D 311 HIS D 656 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.124288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.096843 restraints weight = 54929.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.098605 restraints weight = 39534.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099154 restraints weight = 28014.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099483 restraints weight = 23829.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.099672 restraints weight = 22071.963| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 23988 Z= 0.182 Angle : 0.654 11.492 32767 Z= 0.339 Chirality : 0.045 0.236 3918 Planarity : 0.006 0.146 4139 Dihedral : 7.382 86.786 3436 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.15 % Favored : 93.56 % Rotamer: Outliers : 1.63 % Allowed : 8.97 % Favored : 89.40 % 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: -0.76 (0.15), residues: 3136 helix: 0.93 (0.15), residues: 1198 sheet: -0.27 (0.27), residues: 408 loop : -1.81 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 774 TYR 0.015 0.001 TYR D 479 PHE 0.028 0.002 PHE D 114 TRP 0.018 0.001 TRP B 379 HIS 0.006 0.001 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (23964) covalent geometry : angle 0.64993 / 0.34 (32713) SS BOND : bond 0.01633 / 1.15 ( 15) SS BOND : angle 2.01401 / 1.48 ( 30) hydrogen bonds : bond 0.05852 / 4.03 ( 931) hydrogen bonds : angle 5.08325 / 3.61 ( 2706) Misc. bond : bond 0.00201 / 0.11 ( 1) link_BETA1-4 : bond 0.00345 / 0.17 ( 3) link_BETA1-4 : angle 1.14171 / 0.70 ( 9) link_NAG-ASN : bond 0.00725 / 0.36 ( 5) link_NAG-ASN : angle 2.05913 / 1.19 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 309 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 341 ASN cc_start: 0.7145 (p0) cc_final: 0.6905 (p0) REVERT: B 101 ASP cc_start: 0.6657 (t0) cc_final: 0.6249 (t0) REVERT: B 142 MET cc_start: 0.8189 (mmp) cc_final: 0.7986 (mmp) REVERT: B 309 SER cc_start: 0.7503 (t) cc_final: 0.7127 (m) REVERT: B 432 ASN cc_start: 0.8751 (m-40) cc_final: 0.8458 (p0) REVERT: B 782 GLN cc_start: 0.7720 (tp-100) cc_final: 0.7240 (tp-100) REVERT: C 209 MET cc_start: 0.7777 (tpp) cc_final: 0.7270 (tpp) REVERT: C 354 MET cc_start: 0.7650 (ppp) cc_final: 0.7404 (ppp) REVERT: C 355 ASN cc_start: 0.8332 (t0) cc_final: 0.7602 (t0) REVERT: C 634 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.7002 (tpt) REVERT: C 691 ILE cc_start: 0.8998 (mm) cc_final: 0.8692 (mm) REVERT: C 737 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7618 (mt-10) REVERT: D 89 MET cc_start: 0.5751 (mmp) cc_final: 0.5174 (ttp) REVERT: D 95 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.7062 (mm-40) REVERT: D 386 MET cc_start: 0.8654 (mmm) cc_final: 0.8229 (tpt) REVERT: D 430 MET cc_start: 0.8392 (ppp) cc_final: 0.7566 (ppp) REVERT: D 561 MET cc_start: 0.8455 (ppp) cc_final: 0.8178 (ppp) REVERT: D 562 MET cc_start: 0.8738 (ttt) cc_final: 0.8487 (ttt) REVERT: D 706 MET cc_start: 0.7253 (tmm) cc_final: 0.6968 (tmm) outliers start: 38 outliers final: 22 residues processed: 327 average time/residue: 0.1107 time to fit residues: 63.0579 Evaluate side-chains 297 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 273 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 654 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 48 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 306 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 146 HIS C 571 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.126455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.100120 restraints weight = 54642.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.099906 restraints weight = 33868.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100921 restraints weight = 27984.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.101541 restraints weight = 22870.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.101682 restraints weight = 20930.750| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 23988 Z= 0.118 Angle : 0.586 11.737 32767 Z= 0.299 Chirality : 0.042 0.250 3918 Planarity : 0.005 0.143 4139 Dihedral : 6.311 77.991 3414 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.78 % Favored : 94.93 % Rotamer: Outliers : 1.42 % Allowed : 11.71 % Favored : 86.87 % 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: -0.59 (0.15), residues: 3136 helix: 1.10 (0.15), residues: 1204 sheet: -0.17 (0.28), residues: 378 loop : -1.73 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 774 TYR 0.018 0.001 TYR A 578 PHE 0.021 0.001 PHE D 114 TRP 0.008 0.001 TRP B 379 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (23964) covalent geometry : angle 0.58219 / 0.30 (32713) SS BOND : bond 0.00333 / 0.24 ( 15) SS BOND : angle 1.57452 / 1.04 ( 30) hydrogen bonds : bond 0.04631 / 3.17 ( 931) hydrogen bonds : angle 4.64095 / 3.30 ( 2706) Misc. bond : bond 0.00087 / 0.05 ( 1) link_BETA1-4 : bond 0.00425 / 0.22 ( 3) link_BETA1-4 : angle 0.95423 / 0.57 ( 9) link_NAG-ASN : bond 0.00758 / 0.38 ( 5) link_NAG-ASN : angle 2.14773 / 1.30 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 309 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9244 (tt) cc_final: 0.8815 (pp) REVERT: B 101 ASP cc_start: 0.6804 (t0) cc_final: 0.6351 (t0) REVERT: B 309 SER cc_start: 0.7299 (t) cc_final: 0.7047 (m) REVERT: B 420 GLU cc_start: 0.8052 (tp30) cc_final: 0.7768 (mm-30) REVERT: B 432 ASN cc_start: 0.8803 (m-40) cc_final: 0.8420 (p0) REVERT: B 565 MET cc_start: 0.8111 (mtm) cc_final: 0.7621 (mtp) REVERT: C 209 MET cc_start: 0.7809 (tpp) cc_final: 0.7266 (tpp) REVERT: C 354 MET cc_start: 0.7745 (ppp) cc_final: 0.7420 (ppp) REVERT: C 355 ASN cc_start: 0.8348 (t0) cc_final: 0.7543 (t0) REVERT: C 691 ILE cc_start: 0.8796 (mm) cc_final: 0.8509 (mm) REVERT: C 737 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7552 (mt-10) REVERT: D 89 MET cc_start: 0.6109 (mmp) cc_final: 0.5105 (ttp) REVERT: D 561 MET cc_start: 0.8540 (ppp) cc_final: 0.8262 (ppp) REVERT: D 562 MET cc_start: 0.8780 (ttt) cc_final: 0.8480 (ttt) REVERT: D 645 SER cc_start: 0.9532 (m) cc_final: 0.9141 (p) REVERT: D 702 MET cc_start: 0.8498 (mmm) cc_final: 0.8140 (tpt) REVERT: D 706 MET cc_start: 0.7238 (tmm) cc_final: 0.7005 (tmm) outliers start: 33 outliers final: 22 residues processed: 328 average time/residue: 0.1266 time to fit residues: 72.4175 Evaluate side-chains 300 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 278 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 808 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 295 optimal weight: 3.9990 chunk 144 optimal weight: 0.2980 chunk 279 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 290 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 277 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS B 782 GLN C 146 HIS C 559 GLN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.121403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.093634 restraints weight = 55264.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.095309 restraints weight = 41519.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.095720 restraints weight = 29523.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096119 restraints weight = 25162.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096362 restraints weight = 23142.114| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 23988 Z= 0.235 Angle : 0.668 12.353 32767 Z= 0.346 Chirality : 0.045 0.253 3918 Planarity : 0.005 0.144 4139 Dihedral : 6.140 66.640 3406 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.17 % Favored : 92.57 % Rotamer: Outliers : 2.49 % Allowed : 14.50 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % 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: -0.79 (0.15), residues: 3136 helix: 0.98 (0.15), residues: 1204 sheet: -0.53 (0.27), residues: 407 loop : -1.83 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 292 TYR 0.020 0.002 TYR D 479 PHE 0.026 0.002 PHE D 642 TRP 0.012 0.001 TRP A 151 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.23 (23964) covalent geometry : angle 0.66353 / 0.34 (32713) SS BOND : bond 0.00643 / 0.44 ( 15) SS BOND : angle 2.34314 / 1.60 ( 30) hydrogen bonds : bond 0.05450 / 3.78 ( 931) hydrogen bonds : angle 4.73238 / 3.36 ( 2706) Misc. bond : bond 0.00099 / 0.05 ( 1) link_BETA1-4 : bond 0.00615 / 0.32 ( 3) link_BETA1-4 : angle 1.14288 / 0.69 ( 9) link_NAG-ASN : bond 0.00800 / 0.40 ( 5) link_NAG-ASN : angle 2.02364 / 1.18 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 282 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7854 (pp20) REVERT: A 261 TYR cc_start: 0.7125 (m-80) cc_final: 0.6709 (m-10) REVERT: B 134 MET cc_start: 0.6510 (tmm) cc_final: 0.6290 (tmm) REVERT: B 142 MET cc_start: 0.8381 (mmp) cc_final: 0.8175 (mmp) REVERT: B 309 SER cc_start: 0.7297 (t) cc_final: 0.7046 (m) REVERT: B 727 ASP cc_start: 0.7746 (t0) cc_final: 0.7210 (t0) REVERT: C 354 MET cc_start: 0.7953 (ppp) cc_final: 0.7712 (ppp) REVERT: C 355 ASN cc_start: 0.8604 (t0) cc_final: 0.7782 (t0) REVERT: C 737 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7688 (mt-10) REVERT: D 386 MET cc_start: 0.8519 (mmm) cc_final: 0.8110 (tpp) REVERT: D 565 MET cc_start: 0.8414 (tpp) cc_final: 0.8213 (tpp) REVERT: D 788 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8662 (mp0) outliers start: 58 outliers final: 35 residues processed: 320 average time/residue: 0.1251 time to fit residues: 69.4210 Evaluate side-chains 304 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 267 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 788 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 245 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 189 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 264 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 298 optimal weight: 0.7980 chunk 157 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 709 HIS ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.124876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098063 restraints weight = 54449.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098298 restraints weight = 33257.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.099051 restraints weight = 27049.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.099390 restraints weight = 23094.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.099700 restraints weight = 21591.043| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 23988 Z= 0.114 Angle : 0.590 13.454 32767 Z= 0.299 Chirality : 0.042 0.249 3918 Planarity : 0.005 0.141 4139 Dihedral : 5.783 61.214 3406 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.10 % Favored : 94.61 % Rotamer: Outliers : 1.93 % Allowed : 16.60 % Favored : 81.47 % 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: -0.61 (0.15), residues: 3136 helix: 1.14 (0.15), residues: 1220 sheet: -0.50 (0.26), residues: 414 loop : -1.73 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 468 TYR 0.016 0.001 TYR D 479 PHE 0.033 0.001 PHE C 817 TRP 0.009 0.001 TRP B 379 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (23964) covalent geometry : angle 0.58586 / 0.30 (32713) SS BOND : bond 0.00448 / 0.31 ( 15) SS BOND : angle 1.81986 / 1.18 ( 30) hydrogen bonds : bond 0.04144 / 2.85 ( 931) hydrogen bonds : angle 4.39513 / 3.13 ( 2706) Misc. bond : bond 0.00071 / 0.04 ( 1) link_BETA1-4 : bond 0.00493 / 0.25 ( 3) link_BETA1-4 : angle 0.99826 / 0.60 ( 9) link_NAG-ASN : bond 0.00801 / 0.40 ( 5) link_NAG-ASN : angle 2.17928 / 1.36 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 291 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 261 TYR cc_start: 0.7124 (m-80) cc_final: 0.6741 (m-10) REVERT: A 437 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8788 (p) REVERT: A 745 ASP cc_start: 0.7181 (p0) cc_final: 0.6979 (t0) REVERT: B 134 MET cc_start: 0.6459 (tmm) cc_final: 0.6223 (tmm) REVERT: B 142 MET cc_start: 0.8271 (mmp) cc_final: 0.8018 (mmp) REVERT: B 309 SER cc_start: 0.7135 (t) cc_final: 0.6925 (m) REVERT: B 432 ASN cc_start: 0.8767 (m-40) cc_final: 0.8451 (p0) REVERT: B 532 THR cc_start: 0.9199 (t) cc_final: 0.8962 (p) REVERT: B 565 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7214 (ptp) REVERT: B 653 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7732 (t80) REVERT: B 727 ASP cc_start: 0.7773 (t0) cc_final: 0.7186 (t0) REVERT: B 791 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7682 (tm-30) REVERT: C 209 MET cc_start: 0.7970 (tpp) cc_final: 0.7688 (tpp) REVERT: C 354 MET cc_start: 0.7784 (ppp) cc_final: 0.7575 (ppp) REVERT: C 355 ASN cc_start: 0.8582 (t0) cc_final: 0.7767 (t0) REVERT: C 460 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8304 (mp) REVERT: C 461 ASP cc_start: 0.8198 (t0) cc_final: 0.7996 (t0) REVERT: C 536 GLN cc_start: 0.8547 (pp30) cc_final: 0.8293 (pp30) REVERT: C 737 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7634 (mt-10) REVERT: D 386 MET cc_start: 0.8634 (mmm) cc_final: 0.8283 (tpp) REVERT: D 565 MET cc_start: 0.8424 (tpp) cc_final: 0.8175 (tpp) REVERT: D 654 MET cc_start: 0.8548 (mmp) cc_final: 0.8150 (mmt) REVERT: D 788 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8633 (mp0) outliers start: 45 outliers final: 25 residues processed: 318 average time/residue: 0.1239 time to fit residues: 68.8344 Evaluate side-chains 304 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 274 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 788 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 56 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 294 optimal weight: 0.9990 chunk 201 optimal weight: 0.0980 chunk 251 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 185 optimal weight: 0.0370 chunk 244 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 650 ASN ** 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 = 0.3770 r_free = 0.3770 target = 0.125866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.098705 restraints weight = 54687.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099722 restraints weight = 32086.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100808 restraints weight = 24731.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.101025 restraints weight = 21286.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.101184 restraints weight = 20957.576| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 23988 Z= 0.106 Angle : 0.574 13.979 32767 Z= 0.290 Chirality : 0.042 0.262 3918 Planarity : 0.005 0.139 4139 Dihedral : 5.504 55.982 3405 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.36 % Favored : 94.39 % Rotamer: Outliers : 1.67 % Allowed : 17.89 % Favored : 80.44 % 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: -0.45 (0.15), residues: 3136 helix: 1.28 (0.15), residues: 1216 sheet: -0.35 (0.27), residues: 410 loop : -1.66 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 774 TYR 0.017 0.001 TYR A 578 PHE 0.036 0.001 PHE C 817 TRP 0.007 0.001 TRP C 636 HIS 0.005 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (23964) covalent geometry : angle 0.56901 / 0.29 (32713) SS BOND : bond 0.00437 / 0.30 ( 15) SS BOND : angle 1.98420 / 1.35 ( 30) hydrogen bonds : bond 0.03601 / 2.47 ( 931) hydrogen bonds : angle 4.23383 / 3.01 ( 2706) Misc. bond : bond 0.00097 / 0.05 ( 1) link_BETA1-4 : bond 0.00439 / 0.22 ( 3) link_BETA1-4 : angle 0.90152 / 0.55 ( 9) link_NAG-ASN : bond 0.00813 / 0.41 ( 5) link_NAG-ASN : angle 2.26094 / 1.41 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 291 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 261 TYR cc_start: 0.7004 (m-80) cc_final: 0.6714 (m-80) REVERT: A 437 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8843 (p) REVERT: A 501 MET cc_start: 0.7497 (mtt) cc_final: 0.7271 (mtt) REVERT: A 536 GLN cc_start: 0.8554 (pp30) cc_final: 0.8228 (pp30) REVERT: B 134 MET cc_start: 0.6397 (OUTLIER) cc_final: 0.6186 (tmm) REVERT: B 432 ASN cc_start: 0.8711 (m-40) cc_final: 0.8370 (p0) REVERT: B 563 PHE cc_start: 0.8223 (t80) cc_final: 0.7743 (t80) REVERT: B 653 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7735 (t80) REVERT: B 727 ASP cc_start: 0.7768 (t0) cc_final: 0.7241 (t0) REVERT: C 355 ASN cc_start: 0.8450 (t0) cc_final: 0.7824 (t0) REVERT: C 460 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8305 (mp) REVERT: C 470 MET cc_start: 0.8733 (mpp) cc_final: 0.8425 (mpp) REVERT: C 536 GLN cc_start: 0.8558 (pp30) cc_final: 0.8304 (pp30) REVERT: C 737 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7589 (mt-10) REVERT: C 817 PHE cc_start: 0.8131 (m-80) cc_final: 0.7341 (m-80) REVERT: D 386 MET cc_start: 0.8576 (mmm) cc_final: 0.8235 (tpp) REVERT: D 565 MET cc_start: 0.8433 (tpp) cc_final: 0.8203 (tpp) outliers start: 39 outliers final: 24 residues processed: 315 average time/residue: 0.1108 time to fit residues: 60.6357 Evaluate side-chains 302 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 749 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 65 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 225 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 235 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 650 ASN ** 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 = 0.3723 r_free = 0.3723 target = 0.122569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.094750 restraints weight = 55362.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096814 restraints weight = 40997.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097308 restraints weight = 28219.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.097610 restraints weight = 24036.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.097854 restraints weight = 22322.441| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 23988 Z= 0.191 Angle : 0.629 14.180 32767 Z= 0.322 Chirality : 0.044 0.268 3918 Planarity : 0.005 0.138 4139 Dihedral : 5.609 54.049 3405 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.76 % Favored : 92.95 % Rotamer: Outliers : 2.15 % Allowed : 18.40 % Favored : 79.45 % 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: -0.58 (0.15), residues: 3136 helix: 1.20 (0.15), residues: 1220 sheet: -0.53 (0.26), residues: 422 loop : -1.74 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 468 TYR 0.018 0.001 TYR D 479 PHE 0.022 0.002 PHE C 817 TRP 0.009 0.001 TRP B 635 HIS 0.004 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (23964) covalent geometry : angle 0.62471 / 0.32 (32713) SS BOND : bond 0.00454 / 0.29 ( 15) SS BOND : angle 2.07751 / 1.37 ( 30) hydrogen bonds : bond 0.04517 / 3.13 ( 931) hydrogen bonds : angle 4.35529 / 3.10 ( 2706) Misc. bond : bond 0.00083 / 0.04 ( 1) link_BETA1-4 : bond 0.00525 / 0.26 ( 3) link_BETA1-4 : angle 0.92627 / 0.56 ( 9) link_NAG-ASN : bond 0.00782 / 0.39 ( 5) link_NAG-ASN : angle 2.11965 / 1.29 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 261 TYR cc_start: 0.7126 (m-80) cc_final: 0.6826 (m-80) REVERT: A 354 MET cc_start: 0.7955 (tpp) cc_final: 0.7725 (tpp) REVERT: A 536 GLN cc_start: 0.8688 (pp30) cc_final: 0.8209 (pp30) REVERT: B 142 MET cc_start: 0.8279 (mmp) cc_final: 0.8045 (mmp) REVERT: B 432 ASN cc_start: 0.8712 (m-40) cc_final: 0.8378 (p0) REVERT: B 563 PHE cc_start: 0.8204 (t80) cc_final: 0.7744 (t80) REVERT: B 653 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7829 (t80) REVERT: B 727 ASP cc_start: 0.7819 (t0) cc_final: 0.7411 (t0) REVERT: C 355 ASN cc_start: 0.8457 (t0) cc_final: 0.8081 (t0) REVERT: C 368 ASN cc_start: 0.6435 (m-40) cc_final: 0.6235 (p0) REVERT: C 460 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8471 (mp) REVERT: C 470 MET cc_start: 0.8877 (mpp) cc_final: 0.8533 (mpp) REVERT: C 536 GLN cc_start: 0.8634 (pp30) cc_final: 0.8370 (pp30) REVERT: C 737 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7667 (mt-10) REVERT: C 752 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8577 (mt) REVERT: C 817 PHE cc_start: 0.8175 (m-80) cc_final: 0.7728 (m-80) REVERT: D 386 MET cc_start: 0.8580 (mmm) cc_final: 0.8280 (tpp) REVERT: D 561 MET cc_start: 0.8471 (ppp) cc_final: 0.8083 (ppp) REVERT: D 562 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8140 (tpp) REVERT: D 565 MET cc_start: 0.8495 (tpp) cc_final: 0.8245 (tpp) REVERT: D 746 CYS cc_start: 0.4521 (OUTLIER) cc_final: 0.4119 (m) outliers start: 50 outliers final: 33 residues processed: 314 average time/residue: 0.1072 time to fit residues: 59.2401 Evaluate side-chains 315 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 277 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 749 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 269 optimal weight: 0.9990 chunk 185 optimal weight: 0.1980 chunk 1 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 184 optimal weight: 0.0000 chunk 17 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 ASN C 146 HIS ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.125525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.097985 restraints weight = 54671.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099786 restraints weight = 38456.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.100133 restraints weight = 26444.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.101153 restraints weight = 23945.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.101182 restraints weight = 21569.960| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 23988 Z= 0.107 Angle : 0.587 16.004 32767 Z= 0.295 Chirality : 0.042 0.262 3918 Planarity : 0.005 0.135 4139 Dihedral : 5.396 55.894 3405 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.26 % Favored : 94.45 % Rotamer: Outliers : 1.67 % Allowed : 19.18 % Favored : 79.15 % 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 (0.15), residues: 3136 helix: 1.36 (0.15), residues: 1215 sheet: -0.34 (0.27), residues: 396 loop : -1.63 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 774 TYR 0.015 0.001 TYR A 578 PHE 0.019 0.001 PHE C 817 TRP 0.009 0.001 TRP A 608 HIS 0.003 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (23964) covalent geometry : angle 0.58275 / 0.29 (32713) SS BOND : bond 0.00347 / 0.24 ( 15) SS BOND : angle 1.82399 / 1.26 ( 30) hydrogen bonds : bond 0.03506 / 2.41 ( 931) hydrogen bonds : angle 4.16472 / 2.96 ( 2706) Misc. bond : bond 0.00078 / 0.04 ( 1) link_BETA1-4 : bond 0.00425 / 0.21 ( 3) link_BETA1-4 : angle 0.88289 / 0.53 ( 9) link_NAG-ASN : bond 0.00762 / 0.38 ( 5) link_NAG-ASN : angle 2.25487 / 1.40 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 288 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 261 TYR cc_start: 0.7005 (m-80) cc_final: 0.6726 (m-80) REVERT: A 354 MET cc_start: 0.7920 (tpp) cc_final: 0.7718 (tpp) REVERT: A 437 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8838 (p) REVERT: A 536 GLN cc_start: 0.8597 (pp30) cc_final: 0.8198 (pp30) REVERT: B 142 MET cc_start: 0.8062 (mmp) cc_final: 0.7769 (mmp) REVERT: B 432 ASN cc_start: 0.8709 (m-40) cc_final: 0.8398 (p0) REVERT: B 563 PHE cc_start: 0.8116 (t80) cc_final: 0.7677 (t80) REVERT: B 653 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7775 (t80) REVERT: B 727 ASP cc_start: 0.7770 (t0) cc_final: 0.7369 (t0) REVERT: C 355 ASN cc_start: 0.8349 (t0) cc_final: 0.7876 (t0) REVERT: C 460 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8423 (mp) REVERT: C 536 GLN cc_start: 0.8563 (pp30) cc_final: 0.8317 (pp30) REVERT: C 737 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7579 (mt-10) REVERT: C 817 PHE cc_start: 0.8090 (m-80) cc_final: 0.7755 (m-80) REVERT: D 386 MET cc_start: 0.8554 (mmm) cc_final: 0.8250 (tpp) REVERT: D 561 MET cc_start: 0.8544 (ppp) cc_final: 0.8310 (ppp) REVERT: D 565 MET cc_start: 0.8474 (tpp) cc_final: 0.8229 (tpp) REVERT: D 746 CYS cc_start: 0.4360 (OUTLIER) cc_final: 0.3969 (m) outliers start: 39 outliers final: 29 residues processed: 315 average time/residue: 0.1271 time to fit residues: 69.4343 Evaluate side-chains 315 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 282 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 749 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 193 optimal weight: 0.9990 chunk 237 optimal weight: 9.9990 chunk 249 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 158 optimal weight: 20.0000 chunk 220 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 146 HIS ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.125246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.095263 restraints weight = 55585.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098070 restraints weight = 33275.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099990 restraints weight = 23842.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.101259 restraints weight = 19102.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.102065 restraints weight = 16503.071| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 23988 Z= 0.112 Angle : 0.585 16.221 32767 Z= 0.293 Chirality : 0.042 0.267 3918 Planarity : 0.005 0.133 4139 Dihedral : 5.294 55.636 3405 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.23 % Favored : 94.48 % Rotamer: Outliers : 1.80 % Allowed : 19.39 % Favored : 78.81 % 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: -0.34 (0.15), residues: 3136 helix: 1.40 (0.15), residues: 1215 sheet: -0.34 (0.27), residues: 408 loop : -1.61 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 774 TYR 0.016 0.001 TYR A 578 PHE 0.019 0.001 PHE C 817 TRP 0.007 0.001 TRP C 636 HIS 0.002 0.000 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (23964) covalent geometry : angle 0.58043 / 0.29 (32713) SS BOND : bond 0.00392 / 0.27 ( 15) SS BOND : angle 1.81741 / 1.17 ( 30) hydrogen bonds : bond 0.03526 / 2.43 ( 931) hydrogen bonds : angle 4.10424 / 2.92 ( 2706) Misc. bond : bond 0.00083 / 0.04 ( 1) link_BETA1-4 : bond 0.00481 / 0.25 ( 3) link_BETA1-4 : angle 0.86409 / 0.52 ( 9) link_NAG-ASN : bond 0.00736 / 0.37 ( 5) link_NAG-ASN : angle 2.20979 / 1.37 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 288 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 261 TYR cc_start: 0.6909 (m-80) cc_final: 0.6628 (m-80) REVERT: A 437 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8797 (p) REVERT: A 536 GLN cc_start: 0.8548 (pp30) cc_final: 0.8201 (pp30) REVERT: B 132 MET cc_start: 0.7684 (mmp) cc_final: 0.7137 (mtt) REVERT: B 142 MET cc_start: 0.8087 (mmp) cc_final: 0.7778 (mmp) REVERT: B 432 ASN cc_start: 0.8698 (m-40) cc_final: 0.8346 (p0) REVERT: B 563 PHE cc_start: 0.8219 (t80) cc_final: 0.7786 (t80) REVERT: B 653 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7771 (t80) REVERT: B 654 MET cc_start: 0.8300 (ttt) cc_final: 0.8085 (ttm) REVERT: B 727 ASP cc_start: 0.7876 (t0) cc_final: 0.7401 (t0) REVERT: C 355 ASN cc_start: 0.8334 (t0) cc_final: 0.8057 (t0) REVERT: C 737 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7596 (mt-10) REVERT: C 817 PHE cc_start: 0.8222 (m-80) cc_final: 0.7945 (m-80) REVERT: D 386 MET cc_start: 0.8558 (mmm) cc_final: 0.8209 (tpp) REVERT: D 565 MET cc_start: 0.8530 (tpp) cc_final: 0.8280 (tpp) REVERT: D 746 CYS cc_start: 0.4474 (OUTLIER) cc_final: 0.4105 (m) outliers start: 42 outliers final: 32 residues processed: 318 average time/residue: 0.1273 time to fit residues: 70.9213 Evaluate side-chains 315 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 749 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 273 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 185 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 146 HIS ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.124819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.094337 restraints weight = 57477.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097936 restraints weight = 35538.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.099519 restraints weight = 24154.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101573 restraints weight = 18466.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101304 restraints weight = 16064.439| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 23988 Z= 0.130 Angle : 0.597 16.391 32767 Z= 0.301 Chirality : 0.042 0.271 3918 Planarity : 0.005 0.132 4139 Dihedral : 5.320 55.335 3405 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.29 % Favored : 94.42 % Rotamer: Outliers : 1.72 % Allowed : 19.95 % Favored : 78.34 % 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: -0.37 (0.15), residues: 3136 helix: 1.40 (0.15), residues: 1218 sheet: -0.36 (0.27), residues: 405 loop : -1.65 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 468 TYR 0.016 0.001 TYR A 578 PHE 0.020 0.001 PHE C 817 TRP 0.008 0.001 TRP C 636 HIS 0.003 0.001 HIS D 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (23964) covalent geometry : angle 0.59253 / 0.30 (32713) SS BOND : bond 0.00424 / 0.27 ( 15) SS BOND : angle 1.81312 / 1.29 ( 30) hydrogen bonds : bond 0.03720 / 2.57 ( 931) hydrogen bonds : angle 4.11403 / 2.92 ( 2706) Misc. bond : bond 0.00084 / 0.04 ( 1) link_BETA1-4 : bond 0.00412 / 0.21 ( 3) link_BETA1-4 : angle 0.86300 / 0.52 ( 9) link_NAG-ASN : bond 0.00745 / 0.37 ( 5) link_NAG-ASN : angle 2.17567 / 1.34 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 284 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 261 TYR cc_start: 0.6938 (m-80) cc_final: 0.6648 (m-80) REVERT: A 536 GLN cc_start: 0.8563 (pp30) cc_final: 0.8232 (pp30) REVERT: B 132 MET cc_start: 0.7686 (mmp) cc_final: 0.7172 (mtt) REVERT: B 142 MET cc_start: 0.8148 (mmp) cc_final: 0.7861 (mmp) REVERT: B 432 ASN cc_start: 0.8679 (m-40) cc_final: 0.8315 (p0) REVERT: B 653 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7779 (t80) REVERT: B 727 ASP cc_start: 0.7905 (t0) cc_final: 0.7443 (t0) REVERT: C 355 ASN cc_start: 0.8393 (t0) cc_final: 0.7972 (t0) REVERT: C 737 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7597 (mt-10) REVERT: C 817 PHE cc_start: 0.8374 (m-80) cc_final: 0.8009 (m-80) REVERT: D 132 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7885 (mpp) REVERT: D 151 GLU cc_start: 0.7910 (pt0) cc_final: 0.7346 (pp20) REVERT: D 386 MET cc_start: 0.8559 (mmm) cc_final: 0.8222 (tpp) REVERT: D 565 MET cc_start: 0.8593 (tpp) cc_final: 0.8319 (tpp) REVERT: D 746 CYS cc_start: 0.4387 (OUTLIER) cc_final: 0.4035 (m) outliers start: 40 outliers final: 33 residues processed: 312 average time/residue: 0.1226 time to fit residues: 66.8182 Evaluate side-chains 316 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 749 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 254 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 chunk 127 optimal weight: 0.5980 chunk 186 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 chunk 285 optimal weight: 8.9990 chunk 191 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 119 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 146 HIS ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.124163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.094172 restraints weight = 59185.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.097261 restraints weight = 36605.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.099279 restraints weight = 23337.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.099596 restraints weight = 19652.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.099637 restraints weight = 18162.814| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 23988 Z= 0.134 Angle : 0.613 16.413 32767 Z= 0.305 Chirality : 0.043 0.395 3918 Planarity : 0.005 0.131 4139 Dihedral : 5.326 55.427 3405 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.61 % Favored : 94.10 % Rotamer: Outliers : 1.84 % Allowed : 19.95 % Favored : 78.21 % 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: -0.34 (0.15), residues: 3136 helix: 1.44 (0.15), residues: 1213 sheet: -0.35 (0.27), residues: 405 loop : -1.64 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 468 TYR 0.016 0.001 TYR A 578 PHE 0.021 0.001 PHE C 817 TRP 0.007 0.001 TRP A 381 HIS 0.002 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (23964) covalent geometry : angle 0.60708 / 0.30 (32713) SS BOND : bond 0.00514 / 0.38 ( 15) SS BOND : angle 1.45126 / 1.09 ( 30) hydrogen bonds : bond 0.03794 / 2.62 ( 931) hydrogen bonds : angle 4.11834 / 2.92 ( 2706) Misc. bond : bond 0.00078 / 0.04 ( 1) link_BETA1-4 : bond 0.00832 / 0.40 ( 3) link_BETA1-4 : angle 0.95033 / 0.58 ( 9) link_NAG-ASN : bond 0.00415 / 0.21 ( 5) link_NAG-ASN : angle 3.39069 / 2.72 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3875.66 seconds wall clock time: 67 minutes 33.04 seconds (4053.04 seconds total)