Starting phenix.real_space_refine on Thu Mar 5 17:21:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sab_24947/03_2026/7sab_24947.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sab_24947/03_2026/7sab_24947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sab_24947/03_2026/7sab_24947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sab_24947/03_2026/7sab_24947.map" model { file = "/net/cci-nas-00/data/ceres_data/7sab_24947/03_2026/7sab_24947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sab_24947/03_2026/7sab_24947.cif" } resolution = 4.3 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= -0.001 sd= 0.441 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 15083 2.51 5 N 3828 2.21 5 O 4471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23510 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5913 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 24, 'ASP:plan': 4, 'HIS:plan': 2, 'GLU:plan': 11, 'TRP:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 228 Chain: "B" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5760 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 456 Unresolved non-hydrogen angles: 542 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 24, 'HIS:plan': 3, 'ASN:plan1': 4, 'ARG:plan': 7, 'GLN:plan1': 8, 'TYR:plan': 7, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 281 Chain: "C" Number of atoms: 5896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5896 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved non-hydrogen bonds: 396 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 26, 'ASP:plan': 6, 'HIS:plan': 2, 'GLU:plan': 10, 'TRP:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 234 Chain: "D" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5755 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 464 Unresolved non-hydrogen angles: 556 Unresolved non-hydrogen dihedrals: 410 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 24, 'HIS:plan': 3, 'PHE:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 6, 'GLN:plan1': 6, 'TYR:plan': 8} Unresolved non-hydrogen planarities: 298 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'1PC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.07, per 1000 atoms: 0.22 Number of scatterers: 23510 At special positions: 0 Unit cell: (123.264, 154.08, 183.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 4471 8.00 N 3828 7.00 C 15083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.52 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 901 " - " ASN B 491 " " NAG C 901 " - " ASN C 203 " " NAG D 901 " - " ASN D 491 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN D 688 " Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 5904 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 36 sheets defined 43.6% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 35 through 52 removed outlier: 3.550A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.532A pdb=" N MET A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.712A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 143 through 150 removed outlier: 3.878A pdb=" N GLN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 158 removed outlier: 3.825A pdb=" N MET A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.749A pdb=" N GLU A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.815A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 removed outlier: 3.995A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.967A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.505A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 removed outlier: 4.100A pdb=" N LYS A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET A 326 " --> pdb=" O LYS A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 3.568A pdb=" N GLY A 384 " --> pdb=" O TRP A 381 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 385' Processing helix chain 'A' and resid 458 through 470 removed outlier: 3.690A pdb=" N LEU A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 removed outlier: 4.123A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A 505 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 580 removed outlier: 3.660A pdb=" N TRP A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 579 " --> pdb=" O VAL A 575 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 580 " --> pdb=" O MET A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 614 removed outlier: 3.691A pdb=" N SER A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 612 " --> pdb=" O TRP A 608 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 656 removed outlier: 3.525A pdb=" N ARG A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 631 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 640 " --> pdb=" O TRP A 636 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 removed outlier: 3.662A pdb=" N ARG A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 669 through 674' Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.529A pdb=" N TYR A 692 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 708 removed outlier: 3.593A pdb=" N ARG A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 722 removed outlier: 3.966A pdb=" N ARG A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.770A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 742 " --> pdb=" O PHE A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 783 removed outlier: 3.576A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS A 780 " --> pdb=" O ILE A 776 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 removed outlier: 3.531A pdb=" N ASP A 787 " --> pdb=" O GLY A 783 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 788 " --> pdb=" O PHE A 784 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 827 removed outlier: 3.860A pdb=" N MET A 813 " --> pdb=" O THR A 809 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 824 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 840 Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.068A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 106 through 119 Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.617A pdb=" N SER B 130 " --> pdb=" O HIS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.516A pdb=" N GLN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 193 removed outlier: 3.747A pdb=" N GLU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.506A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.840A pdb=" N VAL B 262 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 290 through 312 removed outlier: 3.814A pdb=" N SER B 309 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.939A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR B 330 " --> pdb=" O LYS B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.795A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 472 Processing helix chain 'B' and resid 496 through 503 removed outlier: 3.858A pdb=" N MET B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'B' and resid 557 through 577 removed outlier: 4.128A pdb=" N MET B 561 " --> pdb=" O ASP B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 613 Processing helix chain 'B' and resid 625 through 653 removed outlier: 3.693A pdb=" N PHE B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.728A pdb=" N ASN B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 4.127A pdb=" N ALA B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 708 removed outlier: 3.926A pdb=" N LYS B 708 " --> pdb=" O TYR B 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 705 through 708' Processing helix chain 'B' and resid 714 through 723 Processing helix chain 'B' and resid 733 through 743 removed outlier: 3.794A pdb=" N GLY B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP B 743 " --> pdb=" O MET B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 787 removed outlier: 4.623A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP B 786 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.994A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 817 removed outlier: 3.806A pdb=" N ASN B 817 " --> pdb=" O ASP B 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 814 through 817' Processing helix chain 'B' and resid 818 through 845 Processing helix chain 'C' and resid 35 through 52 removed outlier: 4.004A pdb=" N LYS C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 removed outlier: 3.743A pdb=" N MET C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.701A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 143 through 150 removed outlier: 3.710A pdb=" N GLN C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 158 removed outlier: 4.031A pdb=" N MET C 154 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 204 through 214 removed outlier: 3.738A pdb=" N MET C 209 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 removed outlier: 3.536A pdb=" N ALA C 228 " --> pdb=" O SER C 224 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.767A pdb=" N ALA C 258 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 297 removed outlier: 3.550A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 removed outlier: 4.035A pdb=" N LYS C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C 326 " --> pdb=" O LYS C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 471 removed outlier: 3.729A pdb=" N LEU C 462 " --> pdb=" O PHE C 458 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 505 removed outlier: 3.718A pdb=" N LEU C 505 " --> pdb=" O MET C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 580 removed outlier: 3.873A pdb=" N TRP C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET C 576 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU C 577 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 614 removed outlier: 3.942A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 613 " --> pdb=" O PHE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 655 removed outlier: 3.546A pdb=" N ARG C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE C 631 " --> pdb=" O PHE C 627 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 638 " --> pdb=" O MET C 634 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 640 " --> pdb=" O TRP C 636 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA C 652 " --> pdb=" O THR C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 673 removed outlier: 3.786A pdb=" N ASN C 668 " --> pdb=" O THR C 665 " (cutoff:3.500A) Proline residue: C 670 - end of helix Processing helix chain 'C' and resid 687 through 695 removed outlier: 3.659A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 695 " --> pdb=" O ILE C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 removed outlier: 3.669A pdb=" N TYR C 703 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU C 707 " --> pdb=" O TYR C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.558A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP C 723 " --> pdb=" O GLN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 removed outlier: 4.607A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 739 " --> pdb=" O VAL C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 782 removed outlier: 4.537A pdb=" N GLN C 771 " --> pdb=" O PRO C 767 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS C 780 " --> pdb=" O ILE C 776 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU C 781 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN C 782 " --> pdb=" O LYS C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 809 through 812 Processing helix chain 'C' and resid 813 through 841 removed outlier: 5.389A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU C 830 " --> pdb=" O ALA C 826 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.852A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 93 removed outlier: 3.502A pdb=" N ILE D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 119 Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.684A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.679A pdb=" N THR D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 233 through 248 removed outlier: 4.259A pdb=" N THR D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.614A pdb=" N VAL D 262 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 312 removed outlier: 4.159A pdb=" N VAL D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG D 294 " --> pdb=" O PRO D 290 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER D 309 " --> pdb=" O SER D 305 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 329 removed outlier: 4.078A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 removed outlier: 4.023A pdb=" N ILE D 340 " --> pdb=" O ASN D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 Processing helix chain 'D' and resid 495 through 503 removed outlier: 3.808A pdb=" N MET D 503 " --> pdb=" O GLY D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 523 removed outlier: 3.866A pdb=" N VAL D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 570 removed outlier: 3.890A pdb=" N MET D 561 " --> pdb=" O ASP D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 578 removed outlier: 3.951A pdb=" N PHE D 575 " --> pdb=" O ALA D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 613 removed outlier: 3.562A pdb=" N ILE D 606 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU D 609 " --> pdb=" O ALA D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 656 Processing helix chain 'D' and resid 668 through 672 Processing helix chain 'D' and resid 673 through 677 Processing helix chain 'D' and resid 689 through 696 removed outlier: 4.042A pdb=" N ARG D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 removed outlier: 3.788A pdb=" N GLY D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 723 Processing helix chain 'D' and resid 733 through 741 removed outlier: 4.244A pdb=" N GLY D 741 " --> pdb=" O ASN D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 787 removed outlier: 3.939A pdb=" N LEU D 781 " --> pdb=" O ASP D 777 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN D 782 " --> pdb=" O LEU D 778 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 796 removed outlier: 4.049A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 845 removed outlier: 4.349A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLY D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 6.287A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 197 removed outlier: 7.500A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 3.520A pdb=" N GLY A 268 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS A 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.178A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 400 through 401 removed outlier: 3.797A pdb=" N VAL A 401 " --> pdb=" O MET A 512 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.656A pdb=" N VAL A 451 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 487 through 489 removed outlier: 3.886A pdb=" N GLU A 488 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 528 through 536 removed outlier: 7.468A pdb=" N SER A 530 " --> pdb=" O MET A 762 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N MET A 762 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE A 760 " --> pdb=" O PRO A 532 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 756 " --> pdb=" O GLN A 536 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 731 through 732 removed outlier: 3.506A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 747 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.932A pdb=" N ALA A 682 " --> pdb=" O ALA A 728 " (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 72 removed outlier: 6.734A pdb=" N ILE B 37 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL B 71 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY B 36 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL B 98 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N LEU B 124 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 203 through 204 removed outlier: 6.321A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N TYR B 231 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 228 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 257 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 280 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 279 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.789A pdb=" N PHE B 344 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 407 through 409 removed outlier: 5.852A pdb=" N ILE B 408 " --> pdb=" O TYR B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 417 through 420 removed outlier: 3.725A pdb=" N CYS B 456 " --> pdb=" O GLU B 420 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS B 438 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS B 455 " --> pdb=" O CYS B 436 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AB8, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB9, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.918A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 538 " --> pdb=" O VAL B 749 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 749 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 59 through 65 removed outlier: 8.992A pdb=" N LEU C 91 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 163 through 167 removed outlier: 4.217A pdb=" N SER C 222 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 269 through 271 removed outlier: 6.343A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 366 " --> pdb=" O ILE C 373 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 339 through 340 removed outlier: 4.638A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 473 through 477 removed outlier: 4.334A pdb=" N LEU C 398 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU C 475 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE C 400 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL C 401 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET C 762 " --> pdb=" O GLU C 528 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU C 528 " --> pdb=" O MET C 762 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 435 through 439 Processing sheet with id=AC7, first strand: chain 'C' and resid 487 through 490 removed outlier: 3.527A pdb=" N GLU C 488 " --> pdb=" O GLU C 497 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU C 497 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 490 " --> pdb=" O LYS C 495 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LYS C 495 " --> pdb=" O VAL C 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 535 through 536 removed outlier: 3.756A pdb=" N SER C 756 " --> pdb=" O GLN C 536 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 729 through 732 removed outlier: 3.911A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 542 " --> pdb=" O VAL C 747 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C 747 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 67 through 73 removed outlier: 3.545A pdb=" N ILE D 37 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU D 69 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 41 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET D 73 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY D 36 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N VAL D 97 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA D 38 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE D 99 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE D 40 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE D 126 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE D 123 " --> pdb=" O PHE D 144 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 203 through 204 removed outlier: 6.377A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N SER D 170 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N TYR D 231 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 9.680A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 362 " --> pdb=" O TRP D 379 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY D 377 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN D 385 " --> pdb=" O LYS D 378 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 343 through 344 removed outlier: 3.619A pdb=" N PHE D 344 " --> pdb=" O ARG D 347 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 405 through 409 removed outlier: 7.318A pdb=" N LEU D 406 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N TYR D 479 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE D 408 " --> pdb=" O TYR D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 417 through 420 removed outlier: 3.540A pdb=" N CYS D 456 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD7, first strand: chain 'D' and resid 508 through 509 Processing sheet with id=AD8, first strand: chain 'D' and resid 531 through 532 Processing sheet with id=AD9, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.883A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL D 538 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 749 " --> pdb=" O VAL D 538 " (cutoff:3.500A) 857 hydrogen bonds defined for protein. 2457 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.54 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3931 1.30 - 1.44: 6448 1.44 - 1.57: 13428 1.57 - 1.71: 1 1.71 - 1.84: 218 Bond restraints: 24026 Sorted by residual: bond pdb=" CG 1PC C 903 " pdb=" NM 1PC C 903 " ideal model delta sigma weight residual 1.461 1.212 0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" CA ASN D 616 " pdb=" C ASN D 616 " ideal model delta sigma weight residual 1.523 1.408 0.116 1.34e-02 5.57e+03 7.45e+01 bond pdb=" CA VAL D 640 " pdb=" C VAL D 640 " ideal model delta sigma weight residual 1.524 1.413 0.111 1.30e-02 5.92e+03 7.26e+01 bond pdb=" N ALA D 639 " pdb=" CA ALA D 639 " ideal model delta sigma weight residual 1.459 1.359 0.100 1.19e-02 7.06e+03 7.11e+01 bond pdb=" N PHE B 642 " pdb=" CA PHE B 642 " ideal model delta sigma weight residual 1.459 1.365 0.094 1.19e-02 7.06e+03 6.29e+01 ... (remaining 24021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.71: 32603 3.71 - 7.43: 199 7.43 - 11.14: 26 11.14 - 14.86: 9 14.86 - 18.57: 1 Bond angle restraints: 32838 Sorted by residual: angle pdb=" N GLU B 658 " pdb=" CA GLU B 658 " pdb=" C GLU B 658 " ideal model delta sigma weight residual 110.28 124.61 -14.33 1.48e+00 4.57e-01 9.37e+01 angle pdb=" CA PHE D 638 " pdb=" C PHE D 638 " pdb=" N ALA D 639 " ideal model delta sigma weight residual 118.01 105.57 12.44 1.30e+00 5.92e-01 9.15e+01 angle pdb=" C TYR B 175 " pdb=" N PHE B 176 " pdb=" CA PHE B 176 " ideal model delta sigma weight residual 121.80 140.37 -18.57 2.44e+00 1.68e-01 5.79e+01 angle pdb=" C ASN D 616 " pdb=" N SER D 617 " pdb=" CA SER D 617 " ideal model delta sigma weight residual 120.58 107.61 12.97 1.71e+00 3.42e-01 5.75e+01 angle pdb=" C TYR D 646 " pdb=" CA TYR D 646 " pdb=" CB TYR D 646 " ideal model delta sigma weight residual 110.79 98.98 11.81 1.66e+00 3.63e-01 5.06e+01 ... (remaining 32833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.97: 13572 24.97 - 49.94: 629 49.94 - 74.91: 43 74.91 - 99.89: 12 99.89 - 124.86: 2 Dihedral angle restraints: 14258 sinusoidal: 5109 harmonic: 9149 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 -169.37 83.37 1 1.00e+01 1.00e-02 8.49e+01 dihedral pdb=" CA THR A 550 " pdb=" C THR A 550 " pdb=" N LEU A 551 " pdb=" CA LEU A 551 " ideal model delta harmonic sigma weight residual 180.00 146.65 33.35 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" C ASN D 615 " pdb=" N ASN D 615 " pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " ideal model delta harmonic sigma weight residual -122.60 -138.95 16.35 0 2.50e+00 1.60e-01 4.28e+01 ... (remaining 14255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 3877 0.170 - 0.340: 22 0.340 - 0.510: 6 0.510 - 0.679: 1 0.679 - 0.849: 4 Chirality restraints: 3910 Sorted by residual: chirality pdb=" CA ASN D 615 " pdb=" N ASN D 615 " pdb=" C ASN D 615 " pdb=" CB ASN D 615 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.80e+01 chirality pdb=" CA THR D 647 " pdb=" N THR D 647 " pdb=" C THR D 647 " pdb=" CB THR D 647 " both_signs ideal model delta sigma weight residual False 2.53 1.75 0.78 2.00e-01 2.50e+01 1.52e+01 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 1.70 0.75 2.00e-01 2.50e+01 1.39e+01 ... (remaining 3907 not shown) Planarity restraints: 4189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 638 " 0.031 2.00e-02 2.50e+03 6.94e-02 4.82e+01 pdb=" C PHE D 638 " -0.120 2.00e-02 2.50e+03 pdb=" O PHE D 638 " 0.048 2.00e-02 2.50e+03 pdb=" N ALA D 639 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 652 " -0.034 2.00e-02 2.50e+03 6.87e-02 4.73e+01 pdb=" C ALA B 652 " 0.119 2.00e-02 2.50e+03 pdb=" O ALA B 652 " -0.045 2.00e-02 2.50e+03 pdb=" N PHE B 653 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 615 " -0.026 2.00e-02 2.50e+03 5.39e-02 2.91e+01 pdb=" C ASN D 615 " 0.093 2.00e-02 2.50e+03 pdb=" O ASN D 615 " -0.036 2.00e-02 2.50e+03 pdb=" N ASN D 616 " -0.031 2.00e-02 2.50e+03 ... (remaining 4186 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 180 2.54 - 3.13: 19488 3.13 - 3.72: 34650 3.72 - 4.31: 42982 4.31 - 4.90: 69731 Nonbonded interactions: 167031 Sorted by model distance: nonbonded pdb=" O ALA D 636 " pdb=" CB ALA D 639 " model vdw 1.955 3.460 nonbonded pdb=" O GLN D 437 " pdb=" NE2 GLN D 437 " model vdw 2.071 3.120 nonbonded pdb=" O LEU C 655 " pdb=" CG2 VAL C 656 " model vdw 2.121 3.460 nonbonded pdb=" CG1 VAL D 613 " pdb=" CE1 PHE D 614 " model vdw 2.151 3.760 nonbonded pdb=" O ALA D 648 " pdb=" C ASN D 649 " model vdw 2.170 3.270 ... (remaining 167026 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 186 or (resid 187 through 188 and (name N or na \ me CA or name C or name O or name CB )) or resid 189 through 259 or (resid 260 a \ nd (name N or name CA or name C or name O or name CB )) or resid 261 through 344 \ or (resid 345 and (name N or name CA or name C or name O or name CB )) or resid \ 346 through 482 or (resid 483 and (name N or name CA or name C or name O or nam \ e CB )) or resid 484 through 508 or (resid 509 through 510 and (name N or name C \ A or name C or name O or name CB )) or resid 511 through 542 or (resid 543 and ( \ name N or name CA or name C or name O or name CB )) or resid 544 through 657 or \ (resid 658 through 659 and (name N or name CA or name C or name O or name CB )) \ or resid 660 through 662 or (resid 663 and (name N or name CA or name C or name \ O or name CB )) or resid 664 through 693 or (resid 694 and (name N or name CA or \ name C or name O or name CB )) or resid 695 through 707 or (resid 708 and (name \ N or name CA or name C or name O or name CB )) or resid 709 through 724 or (res \ id 725 and (name N or name CA or name C or name O or name CB )) or resid 726 thr \ ough 902)) selection = (chain 'C' and (resid 25 through 386 or (resid 387 through 388 and (name N or na \ me CA or name C or name O or name CB )) or resid 389 through 396 or (resid 397 a \ nd (name N or name CA or name C or name O or name CB )) or resid 398 through 535 \ or (resid 536 and (name N or name CA or name C or name O or name CB )) or resid \ 537 through 629 or (resid 630 and (name N or name CA or name C or name O or nam \ e CB )) or resid 631 through 763 or (resid 764 and (name N or name CA or name C \ or name O or name CB )) or resid 765 through 817 or (resid 818 through 819 and ( \ name N or name CA or name C or name O or name CB )) or resid 820 through 828 or \ (resid 829 and (name N or name CA or name C or name O or name CB )) or resid 830 \ through 902)) } ncs_group { reference = (chain 'B' and (resid 34 through 54 or (resid 55 through 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 or (resid 59 and (name N or nam \ e CA or name C or name O or name CB )) or resid 60 through 66 or (resid 67 and ( \ name N or name CA or name C or name O or name CB )) or resid 68 through 178 or ( \ resid 179 and (name N or name CA or name C or name O or name CB )) or resid 180 \ through 233 or (resid 234 and (name N or name CA or name C or name O or name CB \ )) or resid 235 through 283 or (resid 284 and (name N or name CA or name C or na \ me O or name CB )) or resid 285 through 482 or (resid 483 and (name N or name CA \ or name C or name O or name CB )) or resid 484 or (resid 485 and (name N or nam \ e CA or name C or name O or name CB )) or resid 486 through 488 or (resid 489 an \ d (name N or name CA or name C or name O or name CB )) or resid 490 through 556 \ or (resid 557 and (name N or name CA or name C or name O or name CB )) or resid \ 558 through 746 or (resid 747 and (name N or name CA or name C or name O or name \ CB )) or resid 748 through 801 or (resid 802 through 807 and (name N or name CA \ or name C or name O or name CB )) or resid 808 through 835 or (resid 836 and (n \ ame N or name CA or name C or name O or name CB )) or resid 837 through 902)) 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 487 or (resid 488 through 489 and \ (name N or name CA or name C or name O or name CB )) or resid 490 through 502 or \ (resid 503 through 504 and (name N or name CA or name C or name O or name CB )) \ or resid 505 through 560 or (resid 561 and (name N or name CA or name C or name \ O or name CB )) or resid 562 through 655 or (resid 656 through 659 and (name N \ or name CA or name C or name O or name CB )) or resid 660 through 672 or (resid \ 673 and (name N or name CA or name C or name O or name CB )) or resid 674 throug \ h 721 or (resid 722 and (name N or name CA or name C or name O or name CB )) or \ resid 723 through 772 or (resid 773 and (name N or name CA or name C or name O o \ r name CB )) or resid 774 through 844 or (resid 845 and (name N or name CA or na \ me C or name O or name CB )) or resid 901 through 902)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.390 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 19.980 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.493 24049 Z= 0.411 Angle : 0.818 18.574 32891 Z= 0.453 Chirality : 0.055 0.849 3910 Planarity : 0.006 0.128 4184 Dihedral : 13.431 124.857 8306 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.31 % Favored : 93.49 % Rotamer: Outliers : 0.38 % Allowed : 0.42 % Favored : 99.19 % Cbeta Deviations : 0.30 % 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: -1.48 (0.15), residues: 3136 helix: 0.12 (0.16), residues: 1080 sheet: -0.92 (0.29), residues: 354 loop : -1.77 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 115 TYR 0.042 0.001 TYR D 646 PHE 0.039 0.002 PHE D 642 TRP 0.026 0.001 TRP A 636 HIS 0.003 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00614 (24026) covalent geometry : angle 0.80786 (32838) SS BOND : bond 0.12339 ( 16) SS BOND : angle 2.04386 ( 32) hydrogen bonds : bond 0.24843 ( 857) hydrogen bonds : angle 7.53079 ( 2457) link_BETA1-4 : bond 0.00278 ( 2) link_BETA1-4 : angle 0.89227 ( 6) link_NAG-ASN : bond 0.00906 ( 5) link_NAG-ASN : angle 5.38001 ( 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 479 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 470 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.9008 (mtp-110) cc_final: 0.8336 (tpt90) REVERT: A 197 PHE cc_start: 0.7940 (t80) cc_final: 0.7664 (t80) REVERT: A 198 ASP cc_start: 0.8985 (p0) cc_final: 0.8363 (p0) REVERT: A 240 MET cc_start: 0.8761 (mpp) cc_final: 0.8530 (mpp) REVERT: A 354 MET cc_start: 0.8528 (mmm) cc_final: 0.8217 (mmm) REVERT: A 394 MET cc_start: 0.9112 (pmm) cc_final: 0.8708 (ppp) REVERT: A 461 ASP cc_start: 0.9122 (m-30) cc_final: 0.8845 (m-30) REVERT: A 681 TYR cc_start: 0.8205 (p90) cc_final: 0.7969 (p90) REVERT: B 158 LEU cc_start: 0.8480 (tp) cc_final: 0.8142 (tp) REVERT: B 574 VAL cc_start: 0.8482 (t) cc_final: 0.8196 (t) REVERT: B 716 ASP cc_start: 0.9044 (m-30) cc_final: 0.8803 (m-30) REVERT: C 154 MET cc_start: 0.8145 (tpt) cc_final: 0.7932 (tpt) REVERT: C 171 HIS cc_start: 0.9102 (m90) cc_final: 0.8806 (m90) REVERT: C 198 ASP cc_start: 0.8814 (t70) cc_final: 0.8562 (t0) REVERT: C 240 MET cc_start: 0.8430 (mmp) cc_final: 0.7731 (mmm) REVERT: C 317 THR cc_start: 0.8088 (p) cc_final: 0.7392 (p) REVERT: C 354 MET cc_start: 0.8227 (mmp) cc_final: 0.7646 (mmm) REVERT: C 501 MET cc_start: 0.9349 (ppp) cc_final: 0.9138 (ppp) REVERT: C 520 ASN cc_start: 0.8921 (t0) cc_final: 0.8661 (t0) REVERT: C 631 ILE cc_start: 0.9237 (mp) cc_final: 0.8755 (tp) REVERT: C 641 MET cc_start: 0.8911 (tmm) cc_final: 0.8482 (tmm) REVERT: C 642 ILE cc_start: 0.9729 (mm) cc_final: 0.9513 (mm) REVERT: C 760 ILE cc_start: 0.8911 (mm) cc_final: 0.8708 (mt) REVERT: D 142 MET cc_start: 0.8269 (ttm) cc_final: 0.7771 (ttm) REVERT: D 168 ILE cc_start: 0.8500 (pt) cc_final: 0.8059 (mt) REVERT: D 457 CYS cc_start: 0.8151 (m) cc_final: 0.7810 (m) REVERT: D 554 PHE cc_start: 0.8832 (t80) cc_final: 0.8040 (t80) REVERT: D 569 VAL cc_start: 0.9374 (t) cc_final: 0.9097 (t) REVERT: D 654 MET cc_start: 0.8928 (tpp) cc_final: 0.8372 (tmm) REVERT: D 702 MET cc_start: 0.8583 (tmm) cc_final: 0.7693 (tpp) REVERT: D 715 ASP cc_start: 0.8957 (p0) cc_final: 0.8753 (p0) REVERT: D 743 ASP cc_start: 0.7693 (t70) cc_final: 0.7382 (t0) outliers start: 9 outliers final: 7 residues processed: 479 average time/residue: 0.1231 time to fit residues: 101.4427 Evaluate side-chains 377 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 370 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN B 145 GLN C 161 ASN C 162 HIS ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.122123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.089145 restraints weight = 66176.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.091953 restraints weight = 39726.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.093849 restraints weight = 28372.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.095130 restraints weight = 22640.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096008 restraints weight = 19433.738| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 24049 Z= 0.201 Angle : 0.663 14.888 32891 Z= 0.352 Chirality : 0.045 0.443 3910 Planarity : 0.005 0.104 4184 Dihedral : 6.439 112.031 3583 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.97 % Favored : 91.87 % Rotamer: Outliers : 0.08 % Allowed : 5.21 % Favored : 94.70 % Cbeta Deviations : 0.00 % 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: -1.43 (0.15), residues: 3136 helix: 0.20 (0.15), residues: 1144 sheet: -0.99 (0.28), residues: 364 loop : -1.82 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 292 TYR 0.030 0.002 TYR A 109 PHE 0.045 0.002 PHE B 176 TRP 0.018 0.001 TRP B 197 HIS 0.007 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00445 (24026) covalent geometry : angle 0.65581 (32838) SS BOND : bond 0.00388 ( 16) SS BOND : angle 1.79496 ( 32) hydrogen bonds : bond 0.05958 ( 857) hydrogen bonds : angle 5.61729 ( 2457) link_BETA1-4 : bond 0.00422 ( 2) link_BETA1-4 : angle 0.97947 ( 6) link_NAG-ASN : bond 0.00573 ( 5) link_NAG-ASN : angle 3.88290 ( 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 455 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 453 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8882 (mtp-110) cc_final: 0.8101 (ttp80) REVERT: A 155 MET cc_start: 0.8315 (tmm) cc_final: 0.8087 (tmm) REVERT: A 240 MET cc_start: 0.8762 (mpp) cc_final: 0.8510 (mpp) REVERT: A 347 LYS cc_start: 0.8296 (tmmt) cc_final: 0.7852 (ttpp) REVERT: A 354 MET cc_start: 0.8446 (mmm) cc_final: 0.8241 (mmm) REVERT: A 461 ASP cc_start: 0.9019 (m-30) cc_final: 0.8791 (m-30) REVERT: A 470 MET cc_start: 0.9055 (mmm) cc_final: 0.8821 (mmm) REVERT: A 520 ASN cc_start: 0.9201 (t0) cc_final: 0.8825 (t0) REVERT: A 565 LEU cc_start: 0.9285 (pp) cc_final: 0.8953 (tt) REVERT: A 706 MET cc_start: 0.8944 (ttp) cc_final: 0.7953 (tmm) REVERT: B 158 LEU cc_start: 0.8668 (tp) cc_final: 0.8315 (tp) REVERT: B 289 LEU cc_start: 0.8187 (mm) cc_final: 0.7915 (mm) REVERT: B 498 ILE cc_start: 0.8787 (mm) cc_final: 0.8574 (mm) REVERT: B 562 MET cc_start: 0.8567 (tmm) cc_final: 0.8255 (tmm) REVERT: C 154 MET cc_start: 0.8200 (tpt) cc_final: 0.7986 (tpt) REVERT: C 198 ASP cc_start: 0.8607 (t70) cc_final: 0.8406 (t0) REVERT: C 240 MET cc_start: 0.8369 (mmp) cc_final: 0.7796 (mmm) REVERT: C 354 MET cc_start: 0.8367 (mmp) cc_final: 0.7999 (mmm) REVERT: C 501 MET cc_start: 0.9276 (ppp) cc_final: 0.9064 (ppp) REVERT: C 732 ASP cc_start: 0.6921 (t0) cc_final: 0.6569 (t0) REVERT: D 101 ASP cc_start: 0.8631 (t0) cc_final: 0.8421 (t0) REVERT: D 142 MET cc_start: 0.8317 (ttm) cc_final: 0.7878 (ttm) REVERT: D 457 CYS cc_start: 0.7214 (m) cc_final: 0.6994 (m) REVERT: D 524 ASP cc_start: 0.8236 (t70) cc_final: 0.7899 (t70) REVERT: D 554 PHE cc_start: 0.8559 (t80) cc_final: 0.8173 (t80) REVERT: D 692 GLU cc_start: 0.8567 (pt0) cc_final: 0.8358 (pt0) REVERT: D 702 MET cc_start: 0.8490 (tmm) cc_final: 0.7472 (tpp) REVERT: D 715 ASP cc_start: 0.8906 (p0) cc_final: 0.8602 (p0) REVERT: D 743 ASP cc_start: 0.7374 (t70) cc_final: 0.7076 (t0) outliers start: 2 outliers final: 0 residues processed: 454 average time/residue: 0.1211 time to fit residues: 96.1060 Evaluate side-chains 380 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 313 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 236 optimal weight: 20.0000 chunk 259 optimal weight: 20.0000 chunk 112 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 chunk 310 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 247 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN A 710 ASN B 145 GLN C 161 ASN C 162 HIS C 536 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.122284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.089315 restraints weight = 66189.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.092117 restraints weight = 39754.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094021 restraints weight = 28455.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.095272 restraints weight = 22675.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.096186 restraints weight = 19457.870| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 24049 Z= 0.180 Angle : 0.638 13.917 32891 Z= 0.333 Chirality : 0.044 0.402 3910 Planarity : 0.004 0.102 4184 Dihedral : 6.410 113.785 3583 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.40 % Favored : 92.47 % Rotamer: Outliers : 0.17 % Allowed : 3.94 % Favored : 95.89 % 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: -1.45 (0.15), residues: 3136 helix: 0.23 (0.15), residues: 1154 sheet: -0.98 (0.28), residues: 372 loop : -1.88 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 704 TYR 0.025 0.001 TYR A 109 PHE 0.034 0.002 PHE B 176 TRP 0.015 0.001 TRP D 635 HIS 0.006 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00405 (24026) covalent geometry : angle 0.63135 (32838) SS BOND : bond 0.00466 ( 16) SS BOND : angle 1.72023 ( 32) hydrogen bonds : bond 0.05146 ( 857) hydrogen bonds : angle 5.23504 ( 2457) link_BETA1-4 : bond 0.00645 ( 2) link_BETA1-4 : angle 0.85476 ( 6) link_NAG-ASN : bond 0.00571 ( 5) link_NAG-ASN : angle 3.51074 ( 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 461 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 457 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8884 (mtp-110) cc_final: 0.8084 (ttp80) REVERT: A 461 ASP cc_start: 0.9067 (m-30) cc_final: 0.8841 (m-30) REVERT: A 470 MET cc_start: 0.9064 (mmm) cc_final: 0.8764 (mmm) REVERT: A 565 LEU cc_start: 0.9280 (pp) cc_final: 0.8909 (tt) REVERT: A 706 MET cc_start: 0.8722 (tmm) cc_final: 0.8380 (tmm) REVERT: B 150 ILE cc_start: 0.8974 (pt) cc_final: 0.8665 (pt) REVERT: B 158 LEU cc_start: 0.8747 (tp) cc_final: 0.8401 (tp) REVERT: B 289 LEU cc_start: 0.8219 (mm) cc_final: 0.7942 (mm) REVERT: B 477 ASP cc_start: 0.8750 (t70) cc_final: 0.8529 (t0) REVERT: B 562 MET cc_start: 0.8623 (tmm) cc_final: 0.8368 (tmm) REVERT: C 109 TYR cc_start: 0.8146 (p90) cc_final: 0.7922 (p90) REVERT: C 154 MET cc_start: 0.8223 (tpt) cc_final: 0.7978 (tpt) REVERT: C 198 ASP cc_start: 0.8361 (t70) cc_final: 0.8148 (t0) REVERT: C 240 MET cc_start: 0.8352 (mmp) cc_final: 0.7809 (mmm) REVERT: C 354 MET cc_start: 0.8445 (mmp) cc_final: 0.8067 (mmm) REVERT: C 631 ILE cc_start: 0.8820 (mp) cc_final: 0.8576 (mm) REVERT: C 643 ILE cc_start: 0.9596 (mm) cc_final: 0.9383 (mm) REVERT: D 101 ASP cc_start: 0.8656 (t0) cc_final: 0.8388 (t0) REVERT: D 142 MET cc_start: 0.8339 (ttm) cc_final: 0.7901 (ttm) REVERT: D 457 CYS cc_start: 0.7149 (m) cc_final: 0.6941 (m) REVERT: D 554 PHE cc_start: 0.8499 (t80) cc_final: 0.8098 (t80) REVERT: D 715 ASP cc_start: 0.8890 (p0) cc_final: 0.8578 (p0) outliers start: 4 outliers final: 0 residues processed: 459 average time/residue: 0.1174 time to fit residues: 93.8416 Evaluate side-chains 369 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 88 optimal weight: 7.9990 chunk 181 optimal weight: 8.9990 chunk 130 optimal weight: 0.0470 chunk 269 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 2.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 521 ASN A 710 ASN B 145 GLN B 615 ASN C 47 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.122086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.089350 restraints weight = 65851.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.092226 restraints weight = 38868.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.094179 restraints weight = 27560.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.095514 restraints weight = 21794.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.096445 restraints weight = 18573.842| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 24049 Z= 0.136 Angle : 0.608 16.500 32891 Z= 0.315 Chirality : 0.044 0.374 3910 Planarity : 0.004 0.100 4184 Dihedral : 6.144 112.601 3583 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.24 % Favored : 92.63 % Rotamer: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.15), residues: 3136 helix: 0.30 (0.15), residues: 1155 sheet: -0.74 (0.28), residues: 374 loop : -1.80 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 704 TYR 0.027 0.001 TYR A 109 PHE 0.024 0.002 PHE B 176 TRP 0.013 0.001 TRP B 379 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00306 (24026) covalent geometry : angle 0.60193 (32838) SS BOND : bond 0.00370 ( 16) SS BOND : angle 1.74502 ( 32) hydrogen bonds : bond 0.04400 ( 857) hydrogen bonds : angle 4.87627 ( 2457) link_BETA1-4 : bond 0.00398 ( 2) link_BETA1-4 : angle 0.94705 ( 6) link_NAG-ASN : bond 0.00567 ( 5) link_NAG-ASN : angle 3.25958 ( 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 471 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 469 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8907 (mtp-110) cc_final: 0.8104 (ttp80) REVERT: A 155 MET cc_start: 0.8338 (tmm) cc_final: 0.8074 (tmm) REVERT: A 347 LYS cc_start: 0.8354 (tmmt) cc_final: 0.7957 (ttpp) REVERT: A 354 MET cc_start: 0.8364 (mmp) cc_final: 0.7952 (mmm) REVERT: A 461 ASP cc_start: 0.9054 (m-30) cc_final: 0.8813 (m-30) REVERT: A 520 ASN cc_start: 0.9163 (t0) cc_final: 0.8793 (t0) REVERT: A 565 LEU cc_start: 0.9253 (pp) cc_final: 0.8837 (tt) REVERT: A 641 MET cc_start: 0.8386 (tmm) cc_final: 0.8170 (tmm) REVERT: A 706 MET cc_start: 0.8816 (tmm) cc_final: 0.8181 (tpp) REVERT: B 158 LEU cc_start: 0.8669 (tp) cc_final: 0.8281 (tp) REVERT: B 285 TRP cc_start: 0.7666 (t60) cc_final: 0.7465 (t60) REVERT: B 477 ASP cc_start: 0.8736 (t70) cc_final: 0.8490 (t0) REVERT: B 574 VAL cc_start: 0.8553 (t) cc_final: 0.8296 (t) REVERT: B 791 GLU cc_start: 0.8802 (mp0) cc_final: 0.8558 (mp0) REVERT: C 109 TYR cc_start: 0.8061 (p90) cc_final: 0.7859 (p90) REVERT: C 154 MET cc_start: 0.8295 (tpt) cc_final: 0.8059 (tpt) REVERT: C 354 MET cc_start: 0.8536 (mmp) cc_final: 0.8092 (mmm) REVERT: C 501 MET cc_start: 0.9180 (ppp) cc_final: 0.8959 (ppp) REVERT: C 520 ASN cc_start: 0.8893 (t0) cc_final: 0.8668 (t0) REVERT: C 527 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.6768 (tt) REVERT: C 528 GLU cc_start: 0.7953 (mp0) cc_final: 0.7731 (mp0) REVERT: C 641 MET cc_start: 0.8912 (tmm) cc_final: 0.8441 (tmm) REVERT: C 642 ILE cc_start: 0.9598 (mm) cc_final: 0.9337 (mm) REVERT: C 755 ARG cc_start: 0.8573 (mtt-85) cc_final: 0.8312 (mtp85) REVERT: D 101 ASP cc_start: 0.8659 (t0) cc_final: 0.8320 (t0) REVERT: D 142 MET cc_start: 0.8457 (ttm) cc_final: 0.7955 (ttm) REVERT: D 457 CYS cc_start: 0.7334 (m) cc_final: 0.7095 (m) REVERT: D 537 MET cc_start: 0.8802 (tmm) cc_final: 0.8350 (tmm) REVERT: D 554 PHE cc_start: 0.8462 (t80) cc_final: 0.7938 (t80) REVERT: D 654 MET cc_start: 0.8989 (tpp) cc_final: 0.8516 (tpp) REVERT: D 692 GLU cc_start: 0.8595 (pt0) cc_final: 0.8344 (pt0) REVERT: D 702 MET cc_start: 0.8399 (tmm) cc_final: 0.7881 (tpp) REVERT: D 715 ASP cc_start: 0.8932 (p0) cc_final: 0.8623 (p0) REVERT: D 732 ASP cc_start: 0.8511 (m-30) cc_final: 0.7817 (t0) REVERT: D 743 ASP cc_start: 0.7437 (t70) cc_final: 0.7082 (t70) outliers start: 2 outliers final: 0 residues processed: 470 average time/residue: 0.1200 time to fit residues: 97.3358 Evaluate side-chains 375 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 34 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 306 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 274 optimal weight: 0.0030 chunk 95 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 overall best weight: 2.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN B 145 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.121468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.088564 restraints weight = 65450.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.091448 restraints weight = 38941.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.093391 restraints weight = 27593.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.094708 restraints weight = 21879.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.095631 restraints weight = 18671.516| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 24049 Z= 0.160 Angle : 0.629 14.837 32891 Z= 0.324 Chirality : 0.044 0.439 3910 Planarity : 0.004 0.097 4184 Dihedral : 6.029 112.335 3583 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.53 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % 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: -1.25 (0.15), residues: 3136 helix: 0.40 (0.15), residues: 1145 sheet: -0.79 (0.29), residues: 360 loop : -1.79 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 704 TYR 0.022 0.001 TYR A 109 PHE 0.030 0.002 PHE B 176 TRP 0.017 0.001 TRP D 635 HIS 0.011 0.001 HIS C 293 Details of bonding type rmsd covalent geometry : bond 0.00363 (24026) covalent geometry : angle 0.62319 (32838) SS BOND : bond 0.00457 ( 16) SS BOND : angle 1.79202 ( 32) hydrogen bonds : bond 0.04393 ( 857) hydrogen bonds : angle 4.88297 ( 2457) link_BETA1-4 : bond 0.00624 ( 2) link_BETA1-4 : angle 1.23157 ( 6) link_NAG-ASN : bond 0.00501 ( 5) link_NAG-ASN : angle 3.19333 ( 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 450 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8910 (mtp-110) cc_final: 0.8077 (ttp80) REVERT: A 240 MET cc_start: 0.8671 (mpp) cc_final: 0.8382 (mpp) REVERT: A 354 MET cc_start: 0.8383 (mmp) cc_final: 0.8010 (mmm) REVERT: A 461 ASP cc_start: 0.9071 (m-30) cc_final: 0.8831 (m-30) REVERT: A 502 MET cc_start: 0.9573 (tpp) cc_final: 0.9371 (tpp) REVERT: A 706 MET cc_start: 0.8885 (tmm) cc_final: 0.8388 (tmm) REVERT: B 158 LEU cc_start: 0.8696 (tp) cc_final: 0.8311 (tp) REVERT: B 477 ASP cc_start: 0.8750 (t70) cc_final: 0.8508 (t0) REVERT: B 498 ILE cc_start: 0.8798 (mm) cc_final: 0.8577 (mm) REVERT: B 562 MET cc_start: 0.8805 (tmm) cc_final: 0.8542 (tmm) REVERT: B 818 MET cc_start: 0.8978 (mmt) cc_final: 0.8608 (mmm) REVERT: C 154 MET cc_start: 0.8244 (tpt) cc_final: 0.7957 (tpt) REVERT: C 354 MET cc_start: 0.8533 (mmp) cc_final: 0.8092 (mmm) REVERT: C 520 ASN cc_start: 0.8941 (t0) cc_final: 0.8704 (t0) REVERT: C 732 ASP cc_start: 0.7234 (t70) cc_final: 0.6825 (t0) REVERT: C 795 TYR cc_start: 0.8063 (p90) cc_final: 0.7820 (p90) REVERT: D 101 ASP cc_start: 0.8692 (t0) cc_final: 0.8246 (t0) REVERT: D 142 MET cc_start: 0.8488 (ttm) cc_final: 0.8233 (mmt) REVERT: D 411 LEU cc_start: 0.9071 (tp) cc_final: 0.8806 (tp) REVERT: D 412 GLU cc_start: 0.8494 (pm20) cc_final: 0.7781 (pp20) REVERT: D 554 PHE cc_start: 0.8447 (t80) cc_final: 0.7916 (t80) REVERT: D 654 MET cc_start: 0.8950 (tpp) cc_final: 0.8500 (tpp) REVERT: D 702 MET cc_start: 0.8335 (tmm) cc_final: 0.7367 (tmm) REVERT: D 706 MET cc_start: 0.5944 (mmm) cc_final: 0.5184 (mmm) REVERT: D 715 ASP cc_start: 0.8916 (p0) cc_final: 0.8581 (p0) REVERT: D 732 ASP cc_start: 0.8623 (m-30) cc_final: 0.7833 (t0) REVERT: D 743 ASP cc_start: 0.7504 (t70) cc_final: 0.7198 (t70) outliers start: 0 outliers final: 0 residues processed: 450 average time/residue: 0.1223 time to fit residues: 94.9324 Evaluate side-chains 364 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 229 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 262 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 206 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 295 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN B 145 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS C 311 ASN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.123785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.091044 restraints weight = 65269.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.094017 restraints weight = 38419.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096047 restraints weight = 27029.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.097457 restraints weight = 21233.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.098402 restraints weight = 17965.372| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24049 Z= 0.113 Angle : 0.605 15.562 32891 Z= 0.307 Chirality : 0.043 0.426 3910 Planarity : 0.004 0.095 4184 Dihedral : 5.754 112.866 3583 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.57 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % 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: -1.16 (0.15), residues: 3136 helix: 0.45 (0.15), residues: 1150 sheet: -0.58 (0.29), residues: 358 loop : -1.76 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 704 TYR 0.024 0.001 TYR A 526 PHE 0.034 0.001 PHE B 176 TRP 0.012 0.001 TRP B 285 HIS 0.005 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00256 (24026) covalent geometry : angle 0.59997 (32838) SS BOND : bond 0.00458 ( 16) SS BOND : angle 1.68987 ( 32) hydrogen bonds : bond 0.03892 ( 857) hydrogen bonds : angle 4.63370 ( 2457) link_BETA1-4 : bond 0.00403 ( 2) link_BETA1-4 : angle 0.97140 ( 6) link_NAG-ASN : bond 0.00588 ( 5) link_NAG-ASN : angle 3.04946 ( 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 475 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 475 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9324 (ppp) cc_final: 0.9086 (ppp) REVERT: A 115 ARG cc_start: 0.8900 (mtp-110) cc_final: 0.8233 (tpt90) REVERT: A 155 MET cc_start: 0.8292 (tmm) cc_final: 0.8040 (tmm) REVERT: A 240 MET cc_start: 0.8663 (mpp) cc_final: 0.8413 (mpp) REVERT: A 354 MET cc_start: 0.8426 (mmp) cc_final: 0.8102 (mmm) REVERT: A 461 ASP cc_start: 0.9078 (m-30) cc_final: 0.8789 (m-30) REVERT: A 577 LEU cc_start: 0.9499 (mm) cc_final: 0.9284 (mm) REVERT: A 706 MET cc_start: 0.8835 (tmm) cc_final: 0.8290 (tmm) REVERT: B 105 GLN cc_start: 0.8391 (mp10) cc_final: 0.8053 (pm20) REVERT: B 158 LEU cc_start: 0.8643 (tp) cc_final: 0.8271 (tp) REVERT: B 477 ASP cc_start: 0.8701 (t70) cc_final: 0.8451 (t0) REVERT: B 818 MET cc_start: 0.8946 (mmt) cc_final: 0.8621 (mmm) REVERT: C 109 TYR cc_start: 0.8097 (p90) cc_final: 0.7710 (p90) REVERT: C 154 MET cc_start: 0.8226 (tpt) cc_final: 0.7986 (tpt) REVERT: C 198 ASP cc_start: 0.8408 (t70) cc_final: 0.8184 (t0) REVERT: C 354 MET cc_start: 0.8534 (mmp) cc_final: 0.8113 (mmm) REVERT: C 501 MET cc_start: 0.9105 (ppp) cc_final: 0.8873 (ppp) REVERT: C 502 MET cc_start: 0.9069 (tpp) cc_final: 0.8828 (tpp) REVERT: C 520 ASN cc_start: 0.8922 (t0) cc_final: 0.8698 (t0) REVERT: C 641 MET cc_start: 0.8899 (tmm) cc_final: 0.8428 (tmm) REVERT: C 642 ILE cc_start: 0.9607 (mm) cc_final: 0.9333 (mm) REVERT: C 643 ILE cc_start: 0.9601 (mm) cc_final: 0.9361 (mm) REVERT: C 707 GLU cc_start: 0.8907 (pp20) cc_final: 0.8675 (pp20) REVERT: D 101 ASP cc_start: 0.8642 (t0) cc_final: 0.8128 (t0) REVERT: D 142 MET cc_start: 0.8505 (ttm) cc_final: 0.8236 (mmt) REVERT: D 358 MET cc_start: 0.8471 (mmt) cc_final: 0.8179 (mmp) REVERT: D 537 MET cc_start: 0.8734 (tmm) cc_final: 0.8356 (tmm) REVERT: D 554 PHE cc_start: 0.8377 (t80) cc_final: 0.7853 (t80) REVERT: D 637 PHE cc_start: 0.9324 (t80) cc_final: 0.9114 (t80) REVERT: D 654 MET cc_start: 0.8898 (tpp) cc_final: 0.8530 (tpp) REVERT: D 702 MET cc_start: 0.8348 (tmm) cc_final: 0.7975 (tpp) REVERT: D 715 ASP cc_start: 0.8921 (p0) cc_final: 0.8599 (p0) REVERT: D 732 ASP cc_start: 0.8487 (m-30) cc_final: 0.7858 (t70) REVERT: D 743 ASP cc_start: 0.7285 (t70) cc_final: 0.6965 (t70) outliers start: 0 outliers final: 0 residues processed: 475 average time/residue: 0.1172 time to fit residues: 96.6002 Evaluate side-chains 380 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 214 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 187 optimal weight: 30.0000 chunk 139 optimal weight: 0.3980 chunk 19 optimal weight: 10.0000 chunk 102 optimal weight: 0.0770 chunk 189 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 180 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 overall best weight: 1.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN A 710 ASN B 145 GLN C 270 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 = 0.3743 r_free = 0.3743 target = 0.123939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.091030 restraints weight = 65855.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.094004 restraints weight = 39022.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096023 restraints weight = 27583.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097356 restraints weight = 21782.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.098334 restraints weight = 18552.790| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 24049 Z= 0.120 Angle : 0.609 18.210 32891 Z= 0.308 Chirality : 0.044 0.418 3910 Planarity : 0.004 0.094 4184 Dihedral : 5.627 112.778 3583 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.86 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.15), residues: 3136 helix: 0.49 (0.16), residues: 1148 sheet: -0.66 (0.28), residues: 374 loop : -1.69 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 704 TYR 0.030 0.001 TYR D 389 PHE 0.022 0.001 PHE A 639 TRP 0.013 0.001 TRP B 285 HIS 0.006 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00274 (24026) covalent geometry : angle 0.60404 (32838) SS BOND : bond 0.00407 ( 16) SS BOND : angle 1.61593 ( 32) hydrogen bonds : bond 0.03821 ( 857) hydrogen bonds : angle 4.60407 ( 2457) link_BETA1-4 : bond 0.00390 ( 2) link_BETA1-4 : angle 1.00235 ( 6) link_NAG-ASN : bond 0.00546 ( 5) link_NAG-ASN : angle 2.99877 ( 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 461 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9328 (ppp) cc_final: 0.9109 (ppp) REVERT: A 115 ARG cc_start: 0.8917 (mtp-110) cc_final: 0.8249 (tpt90) REVERT: A 155 MET cc_start: 0.8299 (tmm) cc_final: 0.8055 (tmm) REVERT: A 354 MET cc_start: 0.8417 (mmp) cc_final: 0.8095 (mmm) REVERT: A 461 ASP cc_start: 0.9077 (m-30) cc_final: 0.8793 (m-30) REVERT: A 520 ASN cc_start: 0.9176 (t0) cc_final: 0.8815 (t0) REVERT: A 642 ILE cc_start: 0.9471 (mm) cc_final: 0.9267 (mm) REVERT: A 706 MET cc_start: 0.8821 (tmm) cc_final: 0.8071 (tpp) REVERT: B 105 GLN cc_start: 0.8393 (mp10) cc_final: 0.8023 (pm20) REVERT: B 158 LEU cc_start: 0.8651 (tp) cc_final: 0.8281 (tp) REVERT: B 477 ASP cc_start: 0.8718 (t70) cc_final: 0.8440 (t0) REVERT: C 61 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7562 (tm-30) REVERT: C 109 TYR cc_start: 0.7978 (p90) cc_final: 0.7663 (p90) REVERT: C 154 MET cc_start: 0.8184 (tpt) cc_final: 0.7944 (tpt) REVERT: C 198 ASP cc_start: 0.8426 (t70) cc_final: 0.8219 (t0) REVERT: C 240 MET cc_start: 0.8116 (mmm) cc_final: 0.7349 (mmm) REVERT: C 354 MET cc_start: 0.8529 (mmp) cc_final: 0.8100 (mmm) REVERT: C 502 MET cc_start: 0.9171 (tpp) cc_final: 0.8836 (tpp) REVERT: C 520 ASN cc_start: 0.8933 (t0) cc_final: 0.8698 (t0) REVERT: C 641 MET cc_start: 0.8894 (tmm) cc_final: 0.8409 (tmm) REVERT: C 642 ILE cc_start: 0.9612 (mm) cc_final: 0.9343 (mm) REVERT: C 643 ILE cc_start: 0.9601 (mm) cc_final: 0.9385 (mm) REVERT: C 762 MET cc_start: 0.8479 (mtm) cc_final: 0.8149 (mtm) REVERT: D 101 ASP cc_start: 0.8665 (t0) cc_final: 0.8116 (t0) REVERT: D 282 TYR cc_start: 0.7699 (t80) cc_final: 0.7297 (t80) REVERT: D 358 MET cc_start: 0.8474 (mmt) cc_final: 0.8144 (mmp) REVERT: D 508 MET cc_start: 0.8876 (tpp) cc_final: 0.8625 (mmm) REVERT: D 537 MET cc_start: 0.8701 (tmm) cc_final: 0.8280 (tmm) REVERT: D 554 PHE cc_start: 0.8381 (t80) cc_final: 0.7847 (t80) REVERT: D 637 PHE cc_start: 0.9323 (t80) cc_final: 0.9114 (t80) REVERT: D 654 MET cc_start: 0.8823 (tpp) cc_final: 0.8503 (tpp) REVERT: D 692 GLU cc_start: 0.8636 (pt0) cc_final: 0.8360 (pt0) REVERT: D 702 MET cc_start: 0.8331 (tmm) cc_final: 0.8055 (tpp) REVERT: D 715 ASP cc_start: 0.8906 (p0) cc_final: 0.8616 (p0) REVERT: D 732 ASP cc_start: 0.8505 (m-30) cc_final: 0.7827 (t70) REVERT: D 743 ASP cc_start: 0.7176 (t70) cc_final: 0.6857 (t70) REVERT: D 793 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8503 (mm-30) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.1144 time to fit residues: 92.1965 Evaluate side-chains 384 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 183 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 chunk 287 optimal weight: 0.4980 chunk 231 optimal weight: 1.9990 chunk 7 optimal weight: 0.0060 chunk 3 optimal weight: 30.0000 chunk 80 optimal weight: 0.0000 chunk 95 optimal weight: 7.9990 overall best weight: 1.7004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN A 710 ASN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN B 649 ASN ** 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 = 0.3746 r_free = 0.3746 target = 0.124056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.091184 restraints weight = 66052.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094131 restraints weight = 39070.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.096138 restraints weight = 27651.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.097493 restraints weight = 21813.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098462 restraints weight = 18559.020| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24049 Z= 0.122 Angle : 0.618 17.676 32891 Z= 0.309 Chirality : 0.043 0.377 3910 Planarity : 0.004 0.092 4184 Dihedral : 5.530 112.589 3583 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.57 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.15), residues: 3136 helix: 0.54 (0.16), residues: 1151 sheet: -0.57 (0.29), residues: 369 loop : -1.67 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 704 TYR 0.022 0.001 TYR A 109 PHE 0.023 0.001 PHE A 639 TRP 0.015 0.001 TRP D 635 HIS 0.007 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00280 (24026) covalent geometry : angle 0.61298 (32838) SS BOND : bond 0.00406 ( 16) SS BOND : angle 1.52626 ( 32) hydrogen bonds : bond 0.03788 ( 857) hydrogen bonds : angle 4.56889 ( 2457) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 0.95126 ( 6) link_NAG-ASN : bond 0.00566 ( 5) link_NAG-ASN : angle 2.93165 ( 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 464 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9356 (ppp) cc_final: 0.9149 (ppp) REVERT: A 115 ARG cc_start: 0.8939 (mtp-110) cc_final: 0.8236 (tpt90) REVERT: A 155 MET cc_start: 0.8336 (tmm) cc_final: 0.8075 (tmm) REVERT: A 354 MET cc_start: 0.8443 (mmp) cc_final: 0.8110 (mmm) REVERT: A 461 ASP cc_start: 0.9084 (m-30) cc_final: 0.8792 (m-30) REVERT: A 520 ASN cc_start: 0.9249 (t0) cc_final: 0.8841 (t0) REVERT: A 642 ILE cc_start: 0.9470 (mm) cc_final: 0.9241 (mm) REVERT: A 706 MET cc_start: 0.8821 (tmm) cc_final: 0.8084 (tpp) REVERT: B 105 GLN cc_start: 0.8413 (mp10) cc_final: 0.8098 (pm20) REVERT: B 158 LEU cc_start: 0.8637 (tp) cc_final: 0.8269 (tp) REVERT: B 477 ASP cc_start: 0.8700 (t70) cc_final: 0.8432 (t0) REVERT: B 649 ASN cc_start: 0.8663 (t0) cc_final: 0.8463 (t0) REVERT: C 109 TYR cc_start: 0.7919 (p90) cc_final: 0.7631 (p90) REVERT: C 154 MET cc_start: 0.8153 (tpt) cc_final: 0.7939 (tpt) REVERT: C 198 ASP cc_start: 0.8404 (t70) cc_final: 0.8199 (t0) REVERT: C 354 MET cc_start: 0.8499 (mmp) cc_final: 0.8089 (mmm) REVERT: C 502 MET cc_start: 0.9157 (tpp) cc_final: 0.8817 (tpp) REVERT: C 520 ASN cc_start: 0.8939 (t0) cc_final: 0.8671 (t0) REVERT: C 641 MET cc_start: 0.8901 (tmm) cc_final: 0.8405 (tmm) REVERT: C 642 ILE cc_start: 0.9615 (mm) cc_final: 0.9342 (mm) REVERT: C 643 ILE cc_start: 0.9608 (mm) cc_final: 0.9403 (mm) REVERT: C 669 ASP cc_start: 0.9275 (t0) cc_final: 0.8912 (t0) REVERT: D 101 ASP cc_start: 0.8700 (t0) cc_final: 0.8158 (t0) REVERT: D 142 MET cc_start: 0.8624 (tpp) cc_final: 0.8027 (ttm) REVERT: D 168 ILE cc_start: 0.8835 (pt) cc_final: 0.8459 (mt) REVERT: D 282 TYR cc_start: 0.7710 (t80) cc_final: 0.7317 (t80) REVERT: D 358 MET cc_start: 0.8480 (mmt) cc_final: 0.8133 (mmp) REVERT: D 508 MET cc_start: 0.8906 (tpp) cc_final: 0.8643 (mmm) REVERT: D 537 MET cc_start: 0.8719 (tmm) cc_final: 0.8321 (tmm) REVERT: D 554 PHE cc_start: 0.8355 (t80) cc_final: 0.7812 (t80) REVERT: D 654 MET cc_start: 0.8774 (tpp) cc_final: 0.8461 (tpp) REVERT: D 692 GLU cc_start: 0.8669 (pt0) cc_final: 0.8412 (pt0) REVERT: D 702 MET cc_start: 0.8300 (tmm) cc_final: 0.8035 (tpp) REVERT: D 715 ASP cc_start: 0.8872 (p0) cc_final: 0.8557 (p0) REVERT: D 732 ASP cc_start: 0.8549 (m-30) cc_final: 0.7784 (t0) REVERT: D 743 ASP cc_start: 0.7060 (t70) cc_final: 0.6730 (t70) outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.1189 time to fit residues: 96.1610 Evaluate side-chains 382 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 212 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 173 optimal weight: 8.9990 chunk 115 optimal weight: 0.0670 chunk 254 optimal weight: 0.0870 chunk 246 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN B 145 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3735 r_free = 0.3735 target = 0.123646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.090733 restraints weight = 65603.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.093730 restraints weight = 38732.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095761 restraints weight = 27276.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097095 restraints weight = 21496.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098091 restraints weight = 18296.647| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 24049 Z= 0.127 Angle : 0.633 17.659 32891 Z= 0.315 Chirality : 0.043 0.367 3910 Planarity : 0.004 0.090 4184 Dihedral : 5.585 112.488 3583 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.73 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.15), residues: 3136 helix: 0.59 (0.16), residues: 1151 sheet: -0.55 (0.29), residues: 369 loop : -1.69 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 704 TYR 0.029 0.001 TYR D 389 PHE 0.025 0.001 PHE A 639 TRP 0.028 0.001 TRP B 197 HIS 0.006 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00292 (24026) covalent geometry : angle 0.62459 (32838) SS BOND : bond 0.00450 ( 16) SS BOND : angle 1.65711 ( 32) hydrogen bonds : bond 0.03765 ( 857) hydrogen bonds : angle 4.58629 ( 2457) link_BETA1-4 : bond 0.00548 ( 2) link_BETA1-4 : angle 2.33275 ( 6) link_NAG-ASN : bond 0.01407 ( 5) link_NAG-ASN : angle 4.21787 ( 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 458 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9358 (ppp) cc_final: 0.9137 (ppp) REVERT: A 115 ARG cc_start: 0.8954 (mtp-110) cc_final: 0.8274 (tpt90) REVERT: A 155 MET cc_start: 0.8295 (tmm) cc_final: 0.8044 (tmm) REVERT: A 240 MET cc_start: 0.8565 (mpp) cc_final: 0.8343 (mpp) REVERT: A 354 MET cc_start: 0.8451 (mmp) cc_final: 0.8118 (mmm) REVERT: A 461 ASP cc_start: 0.9106 (m-30) cc_final: 0.8849 (m-30) REVERT: A 520 ASN cc_start: 0.9191 (t0) cc_final: 0.8775 (t0) REVERT: A 706 MET cc_start: 0.8827 (tmm) cc_final: 0.8417 (tmm) REVERT: A 711 TYR cc_start: 0.8436 (m-10) cc_final: 0.8054 (m-10) REVERT: B 105 GLN cc_start: 0.8463 (mp10) cc_final: 0.8131 (pm20) REVERT: B 158 LEU cc_start: 0.8662 (tp) cc_final: 0.8297 (tp) REVERT: B 477 ASP cc_start: 0.8656 (t70) cc_final: 0.8381 (t0) REVERT: C 109 TYR cc_start: 0.7892 (p90) cc_final: 0.7592 (p90) REVERT: C 154 MET cc_start: 0.8161 (tpt) cc_final: 0.7944 (tpt) REVERT: C 198 ASP cc_start: 0.8394 (t70) cc_final: 0.8186 (t0) REVERT: C 354 MET cc_start: 0.8538 (mmp) cc_final: 0.8123 (mmm) REVERT: C 502 MET cc_start: 0.9193 (tpp) cc_final: 0.8855 (tpp) REVERT: C 520 ASN cc_start: 0.8903 (t0) cc_final: 0.8630 (t0) REVERT: C 641 MET cc_start: 0.8889 (tmm) cc_final: 0.8387 (tmm) REVERT: C 642 ILE cc_start: 0.9614 (mm) cc_final: 0.9337 (mm) REVERT: C 643 ILE cc_start: 0.9614 (mm) cc_final: 0.9410 (mm) REVERT: C 669 ASP cc_start: 0.9280 (t0) cc_final: 0.8914 (t0) REVERT: C 817 PHE cc_start: 0.9253 (m-80) cc_final: 0.8926 (m-80) REVERT: D 101 ASP cc_start: 0.8714 (t0) cc_final: 0.8172 (t0) REVERT: D 142 MET cc_start: 0.8632 (tpp) cc_final: 0.8034 (ttm) REVERT: D 168 ILE cc_start: 0.8856 (pt) cc_final: 0.8488 (mt) REVERT: D 358 MET cc_start: 0.8509 (mmt) cc_final: 0.8173 (mmp) REVERT: D 508 MET cc_start: 0.8914 (tpp) cc_final: 0.8678 (mmm) REVERT: D 537 MET cc_start: 0.8712 (tmm) cc_final: 0.8343 (tmm) REVERT: D 554 PHE cc_start: 0.8305 (t80) cc_final: 0.7785 (t80) REVERT: D 654 MET cc_start: 0.8739 (tpp) cc_final: 0.8507 (tpp) REVERT: D 702 MET cc_start: 0.8326 (tmm) cc_final: 0.8086 (tpp) REVERT: D 715 ASP cc_start: 0.8888 (p0) cc_final: 0.8583 (p0) REVERT: D 732 ASP cc_start: 0.8532 (m-30) cc_final: 0.7782 (t0) REVERT: D 743 ASP cc_start: 0.6865 (t70) cc_final: 0.6586 (t70) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.1205 time to fit residues: 95.9904 Evaluate side-chains 384 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 130 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 295 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 11 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN B 145 GLN C 161 ASN C 162 HIS ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.120336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.087336 restraints weight = 66050.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.090198 restraints weight = 39351.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.092159 restraints weight = 28005.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.093453 restraints weight = 22216.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094379 restraints weight = 18980.575| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 24049 Z= 0.213 Angle : 0.710 17.731 32891 Z= 0.361 Chirality : 0.045 0.387 3910 Planarity : 0.004 0.088 4184 Dihedral : 5.869 111.904 3583 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.35 % Favored : 91.52 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.15), residues: 3136 helix: 0.44 (0.15), residues: 1136 sheet: -0.89 (0.28), residues: 380 loop : -1.76 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 84 TYR 0.025 0.002 TYR D 389 PHE 0.028 0.002 PHE B 176 TRP 0.026 0.002 TRP D 635 HIS 0.006 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00484 (24026) covalent geometry : angle 0.70201 (32838) SS BOND : bond 0.00652 ( 16) SS BOND : angle 2.09945 ( 32) hydrogen bonds : bond 0.04612 ( 857) hydrogen bonds : angle 4.97889 ( 2457) link_BETA1-4 : bond 0.00172 ( 2) link_BETA1-4 : angle 1.51349 ( 6) link_NAG-ASN : bond 0.00917 ( 5) link_NAG-ASN : angle 3.98160 ( 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 444 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8956 (mtp-110) cc_final: 0.8236 (ttp80) REVERT: A 240 MET cc_start: 0.8677 (mpp) cc_final: 0.8446 (mpp) REVERT: A 354 MET cc_start: 0.8459 (mmp) cc_final: 0.8117 (mmm) REVERT: A 461 ASP cc_start: 0.9085 (m-30) cc_final: 0.8821 (t70) REVERT: A 565 LEU cc_start: 0.9255 (pp) cc_final: 0.8809 (tt) REVERT: A 577 LEU cc_start: 0.9454 (mm) cc_final: 0.9244 (mm) REVERT: A 669 ASP cc_start: 0.9486 (t0) cc_final: 0.9283 (t0) REVERT: A 706 MET cc_start: 0.8836 (tmm) cc_final: 0.8475 (tmm) REVERT: B 105 GLN cc_start: 0.8381 (mp10) cc_final: 0.8101 (pm20) REVERT: B 142 MET cc_start: 0.7651 (tpp) cc_final: 0.7087 (mmt) REVERT: B 158 LEU cc_start: 0.8707 (tp) cc_final: 0.8274 (tp) REVERT: B 192 ASN cc_start: 0.8765 (t0) cc_final: 0.8423 (m110) REVERT: B 477 ASP cc_start: 0.8740 (t70) cc_final: 0.8493 (t0) REVERT: B 562 MET cc_start: 0.8548 (tmm) cc_final: 0.8306 (tmm) REVERT: C 61 GLN cc_start: 0.6848 (tp-100) cc_final: 0.6362 (tp-100) REVERT: C 109 TYR cc_start: 0.7965 (p90) cc_final: 0.7694 (p90) REVERT: C 154 MET cc_start: 0.8234 (tpt) cc_final: 0.8012 (tpt) REVERT: C 354 MET cc_start: 0.8456 (mmp) cc_final: 0.8045 (mmm) REVERT: C 502 MET cc_start: 0.9233 (tpp) cc_final: 0.8988 (tpp) REVERT: C 520 ASN cc_start: 0.8921 (t0) cc_final: 0.8627 (t0) REVERT: C 641 MET cc_start: 0.8945 (tmm) cc_final: 0.8464 (tmm) REVERT: C 642 ILE cc_start: 0.9620 (mm) cc_final: 0.9275 (mm) REVERT: C 643 ILE cc_start: 0.9610 (mm) cc_final: 0.9392 (mm) REVERT: C 669 ASP cc_start: 0.9326 (t0) cc_final: 0.8944 (t0) REVERT: C 817 PHE cc_start: 0.9262 (m-80) cc_final: 0.8848 (m-80) REVERT: D 101 ASP cc_start: 0.8812 (t0) cc_final: 0.8271 (t0) REVERT: D 142 MET cc_start: 0.8642 (tpp) cc_final: 0.8059 (ttm) REVERT: D 168 ILE cc_start: 0.8930 (pt) cc_final: 0.8521 (mt) REVERT: D 358 MET cc_start: 0.8594 (mmt) cc_final: 0.8260 (mmp) REVERT: D 457 CYS cc_start: 0.7411 (m) cc_final: 0.7167 (m) REVERT: D 554 PHE cc_start: 0.8397 (t80) cc_final: 0.7834 (t80) REVERT: D 565 MET cc_start: 0.9276 (tpt) cc_final: 0.8941 (tpt) REVERT: D 654 MET cc_start: 0.8988 (tpp) cc_final: 0.8557 (tpp) REVERT: D 702 MET cc_start: 0.8436 (tmm) cc_final: 0.8181 (tpp) REVERT: D 715 ASP cc_start: 0.8888 (p0) cc_final: 0.8571 (p0) REVERT: D 732 ASP cc_start: 0.8652 (m-30) cc_final: 0.7780 (t0) REVERT: D 743 ASP cc_start: 0.6948 (t70) cc_final: 0.6696 (t70) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.1182 time to fit residues: 91.0814 Evaluate side-chains 367 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 208 optimal weight: 4.9990 chunk 300 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 246 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 157 optimal weight: 30.0000 chunk 176 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN A 710 ASN A 812 ASN B 145 GLN C 161 ASN C 162 HIS ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 ASN D 615 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.123862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090900 restraints weight = 65212.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.093903 restraints weight = 38539.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.095938 restraints weight = 27186.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.097305 restraints weight = 21468.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098270 restraints weight = 18241.542| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 24049 Z= 0.115 Angle : 0.642 16.852 32891 Z= 0.321 Chirality : 0.044 0.367 3910 Planarity : 0.004 0.088 4184 Dihedral : 5.608 112.890 3583 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.35 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.15), residues: 3136 helix: 0.57 (0.16), residues: 1144 sheet: -0.60 (0.29), residues: 362 loop : -1.70 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 704 TYR 0.023 0.001 TYR A 526 PHE 0.042 0.001 PHE B 554 TRP 0.024 0.001 TRP B 197 HIS 0.007 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00261 (24026) covalent geometry : angle 0.63421 (32838) SS BOND : bond 0.00538 ( 16) SS BOND : angle 1.72729 ( 32) hydrogen bonds : bond 0.03837 ( 857) hydrogen bonds : angle 4.58459 ( 2457) link_BETA1-4 : bond 0.00579 ( 2) link_BETA1-4 : angle 1.65051 ( 6) link_NAG-ASN : bond 0.01035 ( 5) link_NAG-ASN : angle 4.00544 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3842.03 seconds wall clock time: 66 minutes 53.40 seconds (4013.40 seconds total)