Starting phenix.real_space_refine on Fri Jun 5 19:30:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iyq_61001/06_2026/9iyq_61001_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iyq_61001/06_2026/9iyq_61001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iyq_61001/06_2026/9iyq_61001_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iyq_61001/06_2026/9iyq_61001_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iyq_61001/06_2026/9iyq_61001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iyq_61001/06_2026/9iyq_61001.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 135 5.16 5 C 15013 2.51 5 N 3953 2.21 5 O 4343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23446 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 5851 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 32, 'TRANS': 748} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ARG:plan': 7, 'HIS:plan': 2, 'GLU:plan': 15, 'GLN:plan1': 4, 'ASP:plan': 9, 'ASN:plan1': 3, 'TYR:plan': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 190 Chain: "B" Number of atoms: 5783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5783 Classifications: {'peptide': 768} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 27, 'TRANS': 740} Chain breaks: 3 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 11, 'GLU:plan': 12, 'HIS:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 5, 'TYR:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 188 Chain: "C" Number of atoms: 5894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 5894 Classifications: {'peptide': 786} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 34, 'TRANS': 751} Chain breaks: 2 Unresolved non-hydrogen bonds: 311 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 8, 'HIS:plan': 2, 'GLU:plan': 14, 'GLN:plan1': 4, 'ASP:plan': 14, 'PHE:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 199 Chain: "D" Number of atoms: 5764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5764 Classifications: {'peptide': 768} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 27, 'TRANS': 740} Chain breaks: 3 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 11, 'HIS:plan': 4, 'PHE:plan': 5, 'GLN:plan1': 2, 'TYR:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 194 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'7RC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'7RC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.65, per 1000 atoms: 0.24 Number of scatterers: 23446 At special positions: 0 Unit cell: (167.24, 149.48, 156.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 2 15.00 O 4343 8.00 N 3953 7.00 C 15013 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG A 902 " - " ASN A 61 " " NAG A 903 " - " ASN A 368 " " NAG A 904 " - " ASN A 203 " " NAG C 902 " - " ASN C 61 " " NAG C 903 " - " ASN C 276 " " NAG C 904 " - " ASN C 368 " " NAG C 905 " - " ASN C 471 " " NAG C 906 " - " ASN C 771 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 962.1 milliseconds 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5786 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 31 sheets defined 44.6% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.606A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.632A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.631A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N MET A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N MET A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.881A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 211 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.670A pdb=" N ILE A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 256' Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.654A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 298 Processing helix chain 'A' and resid 317 through 326 Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.723A pdb=" N GLN A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 582 removed outlier: 3.943A pdb=" N ARG A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'A' and resid 626 through 657 removed outlier: 4.403A pdb=" N ILE A 631 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.811A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 783 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 809 through 812 Processing helix chain 'A' and resid 813 through 837 removed outlier: 4.415A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 removed outlier: 3.723A pdb=" N HIS B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 89 Processing helix chain 'B' and resid 106 through 120 removed outlier: 3.689A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.630A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.765A pdb=" N GLN B 217 " --> pdb=" O ASP B 213 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.796A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 310 Processing helix chain 'B' and resid 323 through 330 removed outlier: 4.338A pdb=" N GLU B 326 " --> pdb=" O ASN B 323 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 330 " --> pdb=" O LYS B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 340 removed outlier: 3.651A pdb=" N LEU B 335 " --> pdb=" O GLN B 331 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 546 through 552 removed outlier: 4.425A pdb=" N PHE B 550 " --> pdb=" O PRO B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 579 removed outlier: 3.564A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.603A pdb=" N ILE B 606 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 654 removed outlier: 3.734A pdb=" N ILE B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 674 through 677 removed outlier: 4.128A pdb=" N PHE B 677 " --> pdb=" O PRO B 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 674 through 677' Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 699 through 706 Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 714 through 724 removed outlier: 3.528A pdb=" N LEU B 718 " --> pdb=" O VAL B 714 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 719 " --> pdb=" O ASP B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.566A pdb=" N ARG B 742 " --> pdb=" O TYR B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 787 removed outlier: 4.644A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.553A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 795 " --> pdb=" O GLU B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 838 removed outlier: 3.516A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 removed outlier: 3.722A pdb=" N ARG C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 85 Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.667A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.821A pdb=" N SER C 129 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 126 through 130' Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 158 removed outlier: 3.681A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET C 154 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N MET C 155 " --> pdb=" O TRP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.737A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 4.020A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 235 through 239 Processing helix chain 'C' and resid 255 through 262 Processing helix chain 'C' and resid 277 through 298 removed outlier: 3.839A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 326 Processing helix chain 'C' and resid 457 through 470 Processing helix chain 'C' and resid 499 through 508 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.684A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 581 removed outlier: 3.565A pdb=" N ASP C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 616 Processing helix chain 'C' and resid 626 through 657 removed outlier: 3.952A pdb=" N ILE C 631 " --> pdb=" O PHE C 627 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 699 through 708 removed outlier: 4.063A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.951A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 810 through 813 Processing helix chain 'C' and resid 814 through 837 removed outlier: 3.854A pdb=" N MET C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 56 removed outlier: 3.549A pdb=" N ASP D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.595A pdb=" N HIS D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 106 through 120 removed outlier: 3.728A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.582A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 Processing helix chain 'D' and resid 212 through 220 removed outlier: 3.763A pdb=" N ILE D 216 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN D 217 " --> pdb=" O ASP D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.603A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 removed outlier: 3.701A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 310 Processing helix chain 'D' and resid 323 through 330 removed outlier: 4.206A pdb=" N GLU D 326 " --> pdb=" O ASN D 323 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 339 removed outlier: 4.286A pdb=" N LEU D 335 " --> pdb=" O GLN D 331 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 548 through 552 Processing helix chain 'D' and resid 555 through 579 Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.663A pdb=" N VAL D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 654 removed outlier: 3.634A pdb=" N ILE D 630 " --> pdb=" O THR D 626 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 708 through 710 No H-bonds generated for 'chain 'D' and resid 708 through 710' Processing helix chain 'D' and resid 714 through 724 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.520A pdb=" N ARG D 742 " --> pdb=" O TYR D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 786 removed outlier: 3.603A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D 778 " --> pdb=" O ARG D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.580A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 803 removed outlier: 3.599A pdb=" N HIS D 802 " --> pdb=" O GLY D 799 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN D 803 " --> pdb=" O ILE D 800 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 799 through 803' Processing helix chain 'D' and resid 818 through 838 removed outlier: 3.580A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 removed outlier: 6.601A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL A 65 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY A 30 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.409A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.586A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 476 through 478 Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 488 removed outlier: 3.683A pdb=" N GLU A 488 " --> pdb=" O GLU A 497 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA8, first strand: chain 'A' and resid 681 through 682 removed outlier: 7.065A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 11.515A pdb=" N LYS A 534 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N ARG A 755 " --> pdb=" O LYS A 534 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N GLN A 536 " --> pdb=" O PHE A 753 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N PHE A 753 " --> pdb=" O GLN A 536 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 67 through 68 removed outlier: 8.026A pdb=" N VAL B 71 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 67 through 68 removed outlier: 3.563A pdb=" N GLY B 96 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 126 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N PHE B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 202 through 203 removed outlier: 3.536A pdb=" N THR B 173 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 257 through 258 removed outlier: 3.724A pdb=" N VAL B 280 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 453 through 454 removed outlier: 3.646A pdb=" N ILE B 453 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N MET B 508 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER B 407 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL B 510 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL B 409 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N SER B 512 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N GLY B 511 " --> pdb=" O ALA B 765 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ALA B 765 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU B 513 " --> pdb=" O GLY B 763 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 524 through 525 removed outlier: 5.754A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 418 through 419 Processing sheet with id=AB7, first strand: chain 'C' and resid 62 through 66 removed outlier: 6.222A pdb=" N ILE C 29 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 193 through 194 removed outlier: 3.888A pdb=" N LYS C 193 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER C 222 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 267 through 271 removed outlier: 3.828A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLN C 357 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU C 361 " --> pdb=" O GLN C 357 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 330 through 333 removed outlier: 6.223A pdb=" N ALA C 331 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL C 338 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 473 through 478 Processing sheet with id=AC3, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AC4, first strand: chain 'C' and resid 527 through 529 Processing sheet with id=AC5, first strand: chain 'C' and resid 681 through 682 removed outlier: 7.037A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.475A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU C 538 " --> pdb=" O PHE C 754 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N PHE C 754 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ILE C 540 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N LEU C 752 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 10.228A pdb=" N VAL C 542 " --> pdb=" O GLY C 750 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N GLY C 750 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 67 through 68 Processing sheet with id=AC7, first strand: chain 'D' and resid 67 through 68 removed outlier: 3.950A pdb=" N GLY D 96 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE D 123 " --> pdb=" O PHE D 144 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 202 through 203 removed outlier: 6.916A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 257 through 258 removed outlier: 3.666A pdb=" N VAL D 280 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 437 through 438 removed outlier: 3.627A pdb=" N ASP D 477 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 408 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET D 508 " --> pdb=" O SER D 407 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 418 through 419 Processing sheet with id=AD3, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.839A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.839A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE D 530 " --> pdb=" O TYR D 762 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 1019 hydrogen bonds defined for protein. 2961 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.36 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7595 1.35 - 1.48: 5923 1.48 - 1.61: 10185 1.61 - 1.73: 0 1.73 - 1.86: 234 Bond restraints: 23937 Sorted by residual: bond pdb=" C MET D 561 " pdb=" N MET D 562 " ideal model delta sigma weight residual 1.335 1.309 0.026 1.31e-02 5.83e+03 4.06e+00 bond pdb=" C ILE D 534 " pdb=" N SER D 535 " ideal model delta sigma weight residual 1.331 1.302 0.028 1.41e-02 5.03e+03 4.02e+00 bond pdb=" C1 NAG A 904 " pdb=" O5 NAG A 904 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.95e+00 bond pdb=" O02 7RC D 901 " pdb=" P01 7RC D 901 " ideal model delta sigma weight residual 1.537 1.509 0.028 2.00e-02 2.50e+03 1.94e+00 bond pdb=" O02 7RC B 901 " pdb=" P01 7RC B 901 " ideal model delta sigma weight residual 1.537 1.510 0.027 2.00e-02 2.50e+03 1.84e+00 ... (remaining 23932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 32114 1.34 - 2.68: 318 2.68 - 4.01: 109 4.01 - 5.35: 8 5.35 - 6.69: 4 Bond angle restraints: 32553 Sorted by residual: angle pdb=" N ASP B 557 " pdb=" CA ASP B 557 " pdb=" C ASP B 557 " ideal model delta sigma weight residual 111.33 107.67 3.66 1.21e+00 6.83e-01 9.14e+00 angle pdb=" CA GLY B 543 " pdb=" C GLY B 543 " pdb=" O GLY B 543 " ideal model delta sigma weight residual 122.23 120.18 2.05 6.90e-01 2.10e+00 8.82e+00 angle pdb=" N TYR B 389 " pdb=" CA TYR B 389 " pdb=" C TYR B 389 " ideal model delta sigma weight residual 113.30 109.41 3.89 1.34e+00 5.57e-01 8.45e+00 angle pdb=" C VAL B 558 " pdb=" CA VAL B 558 " pdb=" CB VAL B 558 " ideal model delta sigma weight residual 111.97 108.44 3.53 1.28e+00 6.10e-01 7.59e+00 angle pdb=" N LYS B 382 " pdb=" CA LYS B 382 " pdb=" C LYS B 382 " ideal model delta sigma weight residual 114.56 111.64 2.92 1.27e+00 6.20e-01 5.28e+00 ... (remaining 32548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.60: 13948 33.60 - 67.19: 356 67.19 - 100.79: 28 100.79 - 134.38: 4 134.38 - 167.98: 2 Dihedral angle restraints: 14338 sinusoidal: 5367 harmonic: 8971 Sorted by residual: dihedral pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" SG CYS A 455 " pdb=" CB CYS A 455 " ideal model delta sinusoidal sigma weight residual 93.00 176.05 -83.05 1 1.00e+01 1.00e-02 8.44e+01 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 -160.19 74.19 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" CB CYS A 420 " pdb=" SG CYS A 420 " pdb=" SG CYS A 454 " pdb=" CB CYS A 454 " ideal model delta sinusoidal sigma weight residual 93.00 162.41 -69.41 1 1.00e+01 1.00e-02 6.22e+01 ... (remaining 14335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3111 0.049 - 0.098: 520 0.098 - 0.146: 144 0.146 - 0.195: 2 0.195 - 0.244: 2 Chirality restraints: 3779 Sorted by residual: chirality pdb=" C1 NAG C 902 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C 902 " pdb=" O5 NAG C 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C01 7RC B 901 " pdb=" C02 7RC B 901 " pdb=" C08 7RC B 901 " pdb=" N02 7RC B 901 " both_signs ideal model delta sigma weight residual False 2.45 2.61 -0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 3776 not shown) Planarity restraints: 4149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 669 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO A 670 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 550 " 0.010 2.00e-02 2.50e+03 1.14e-02 2.29e+00 pdb=" CG PHE D 550 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE D 550 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 550 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE D 550 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 550 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 550 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 77 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 78 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 78 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 78 " 0.020 5.00e-02 4.00e+02 ... (remaining 4146 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 230 2.63 - 3.20: 21937 3.20 - 3.77: 34372 3.77 - 4.33: 46454 4.33 - 4.90: 78803 Nonbonded interactions: 181796 Sorted by model distance: nonbonded pdb=" OG SER D 555 " pdb=" OD1 ASP D 557 " model vdw 2.066 3.040 nonbonded pdb=" OG1 THR D 691 " pdb=" O03 7RC D 901 " model vdw 2.167 3.040 nonbonded pdb=" O ARG C 260 " pdb=" NH2 ARG C 359 " model vdw 2.199 3.120 nonbonded pdb=" O ASN C 492 " pdb=" OG SER C 493 " model vdw 2.217 3.040 nonbonded pdb=" N SER D 690 " pdb=" O04 7RC D 901 " model vdw 2.231 3.120 ... (remaining 181791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB )) or resid 87 through 101 or (resid 102 through 103 and \ (name N or name CA or name C or name O or name CB )) or resid 104 through 192 or \ (resid 193 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 4 through 274 or (resid 275 and (name N or name CA or name C or name O or name C \ B )) or resid 276 through 295 or (resid 296 through 299 and (name N or name CA o \ r name C or name O or name CB )) or resid 300 through 302 or (resid 303 and (nam \ e N or name CA or name C or name O or name CB )) or resid 304 through 305 or (re \ sid 306 and (name N or name CA or name C or name O or name CB )) or resid 307 th \ rough 413 or (resid 414 and (name N or name CA or name C or name O or name CB )) \ or resid 415 through 416 or (resid 417 and (name N or name CA or name C or name \ O or name CB )) or resid 418 or (resid 419 and (name N or name CA or name C or \ name O or name CB )) or resid 420 through 448 or (resid 449 and (name N or name \ CA or name C or name O or name CB )) or resid 450 through 493 or (resid 494 thro \ ugh 495 and (name N or name CA or name C or name O or name CB )) or resid 496 th \ rough 664 or (resid 665 and (name N or name CA or name C or name O or name CB )) \ or resid 666 through 668 or (resid 669 and (name N or name CA or name C or name \ O or name CB )) or resid 670 through 698 or (resid 699 and (name N or name CA o \ r name C or name O or name CB )) or resid 700 through 797 or (resid 798 through \ 799 and (name N or name CA or name C or name O or name CB )) or resid 800 throug \ h 904)) selection = (chain 'C' and (resid 27 through 92 or (resid 93 through 94 and (name N or name \ CA or name C or name O or name CB )) or resid 95 or resid 101 through 109 or (re \ sid 110 through 111 and (name N or name CA or name C or name O or name CB )) or \ resid 112 through 121 or (resid 122 and (name N or name CA or name C or name O o \ r name CB )) or resid 123 through 156 or (resid 157 and (name N or name CA or na \ me C or name O or name CB )) or resid 158 through 207 or (resid 208 through 209 \ and (name N or name CA or name C or name O or name CB )) or resid 210 through 23 \ 8 or (resid 239 and (name N or name CA or name C or name O or name CB )) or resi \ d 240 through 242 or (resid 243 and (name N or name CA or name C or name O or na \ me CB )) or resid 244 through 280 or (resid 281 and (name N or name CA or name C \ or name O or name CB )) or resid 282 through 287 or (resid 288 through 289 and \ (name N or name CA or name C or name O or name CB )) or resid 290 through 294 or \ (resid 295 through 299 and (name N or name CA or name C or name O or name CB )) \ or resid 300 through 321 or (resid 322 and (name N or name CA or name C or name \ O or name CB )) or resid 323 or (resid 324 and (name N or name CA or name C or \ name O or name CB )) or resid 325 through 334 or (resid 335 and (name N or name \ CA or name C or name O or name CB )) or resid 336 through 353 or (resid 354 and \ (name N or name CA or name C or name O or name CB )) or resid 355 through 436 or \ (resid 437 and (name N or name CA or name C or name O or name CB )) or resid 43 \ 8 through 489 or (resid 490 and (name N or name CA or name C or name O or name C \ B )) or resid 491 or (resid 492 through 495 and (name N or name CA or name C or \ name O or name CB )) or resid 496 through 579 or (resid 580 through 603 and (nam \ e N or name CA or name C or name O or name CB )) or resid 604 through 634 or (re \ sid 635 and (name N or name CA or name C or name O or name CB )) or resid 636 th \ rough 700 or (resid 701 and (name N or name CA or name C or name O or name CB )) \ or resid 702 through 723 or (resid 724 and (name N or name CA or name C or name \ O or name CB )) or resid 725 through 732 or (resid 733 through 734 and (name N \ or name CA or name C or name O or name CB )) or resid 735 through 736 or (resid \ 737 and (name N or name CA or name C or name O or name CB )) or resid 738 or (re \ sid 739 through 740 and (name N or name CA or name C or name O or name CB )) or \ resid 741 through 768 or (resid 769 through 770 and (name N or name CA or name C \ or name O or name CB )) or resid 771 through 785 or (resid 786 through 787 and \ (name N or name CA or name C or name O or name CB )) or resid 788 through 794 or \ (resid 795 and (name N or name CA or name C or name O or name CB )) or resid 79 \ 6 through 804 or (resid 805 through 806 and (name N or name CA or name C or name \ O or name CB )) or resid 807 through 904)) } ncs_group { reference = (chain 'B' and (resid 35 through 49 or (resid 50 through 62 and (name N or name \ CA or name C or name O or name CB )) or resid 63 or (resid 64 and (name N or nam \ e CA or name C or name O or name CB )) or resid 65 through 85 or (resid 86 and ( \ name N or name CA or name C or name O or name CB )) or resid 87 through 94 or (r \ esid 95 and (name N or name CA or name C or name O or name CB )) or resid 96 thr \ ough 154 or (resid 155 and (name N or name CA or name C or name O or name CB )) \ or resid 156 through 224 or (resid 225 and (name N or name CA or name C or name \ O or name CB )) or resid 226 through 315 or (resid 316 and (name N or name CA or \ name C or name O or name CB )) or resid 317 through 333 or (resid 334 and (name \ N or name CA or name C or name O or name CB )) or resid 335 through 452 or (res \ id 453 and (name N or name CA or name C or name O or name CB )) or resid 454 thr \ ough 481 or (resid 482 and (name N or name CA or name C or name O or name CB )) \ or resid 483 through 497 or (resid 498 and (name N or name CA or name C or name \ O or name CB )) or resid 499 through 672 or (resid 673 and (name N or name CA or \ name C or name O or name CB )) or resid 674 through 675 or (resid 676 through 6 \ 77 and (name N or name CA or name C or name O or name CB )) or resid 678 through \ 704 or (resid 705 and (name N or name CA or name C or name O or name CB )) or r \ esid 706 through 724 or (resid 725 and (name N or name CA or name C or name O or \ name CB )) or resid 726 through 742 or (resid 743 and (name N or name CA or nam \ e C or name O or name CB )) or resid 744 through 804 or (resid 805 through 806 a \ nd (name N or name CA or name C or name O or name CB )) or resid 807 through 901 \ )) selection = (chain 'D' and (resid 35 through 61 or (resid 62 and (name N or name CA or name \ C or name O or name CB )) or resid 63 through 72 or (resid 73 through 76 and (na \ me N or name CA or name C or name O or name CB )) or resid 77 through 87 or (res \ id 88 through 89 and (name N or name CA or name C or name O or name CB )) or res \ id 90 through 205 or (resid 206 and (name N or name CA or name C or name O or na \ me CB )) or resid 207 through 223 or (resid 224 through 225 and (name N or name \ CA or name C or name O or name CB )) or resid 226 through 337 or (resid 338 and \ (name N or name CA or name C or name O or name CB )) or resid 339 through 433 or \ (resid 434 and (name N or name CA or name C or name O or name CB )) or resid 43 \ 5 through 465 or (resid 466 and (name N or name CA or name C or name O or name C \ B )) or resid 467 through 484 or (resid 485 and (name N or name CA or name C or \ name O or name CB )) or resid 486 through 556 or (resid 557 and (name N or name \ CA or name C or name O or name CB )) or resid 558 through 676 or (resid 677 and \ (name N or name CA or name C or name O or name CB )) or resid 678 through 691 or \ (resid 692 and (name N or name CA or name C or name O or name CB )) or resid 69 \ 3 through 805 or (resid 806 and (name N or name CA or name C or name O or name C \ B )) or resid 807 through 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.900 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 : 0.002 0.037 23956 Z= 0.089 Angle : 0.378 6.689 32597 Z= 0.198 Chirality : 0.039 0.244 3779 Planarity : 0.002 0.060 4141 Dihedral : 14.763 167.979 8522 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.25 % Allowed : 17.67 % Favored : 82.07 % 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 (0.17), residues: 3073 helix: 3.24 (0.16), residues: 1257 sheet: -1.10 (0.26), residues: 423 loop : -1.20 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 323 TYR 0.005 0.000 TYR B 389 PHE 0.027 0.001 PHE D 550 TRP 0.006 0.000 TRP D 607 HIS 0.003 0.000 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00175 / 0.09 (23937) covalent geometry : angle 0.37475 / 0.20 (32553) SS BOND : bond 0.00125 / 0.05 ( 10) SS BOND : angle 0.44077 / 0.34 ( 20) hydrogen bonds : bond 0.13464 / 8.98 ( 1010) hydrogen bonds : angle 5.55765 / 3.89 ( 2961) Misc. bond : bond 0.00100 / 0.05 ( 1) link_NAG-ASN : bond 0.00384 / 0.20 ( 8) link_NAG-ASN : angle 1.76309 / 1.22 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 218 time to evaluate : 0.850 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 220 average time/residue: 0.1372 time to fit residues: 50.2088 Evaluate side-chains 217 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 214 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 813 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN B 437 GLN B 802 HIS C 50 ASN C 67 HIS C 363 GLN C 812 ASN D 698 ASN D 711 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.108940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.080022 restraints weight = 47437.713| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.00 r_work: 0.2911 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23956 Z= 0.155 Angle : 0.520 9.214 32597 Z= 0.271 Chirality : 0.044 0.351 3779 Planarity : 0.004 0.064 4141 Dihedral : 7.783 171.057 3511 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.16 % Allowed : 16.74 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.16), residues: 3073 helix: 2.45 (0.15), residues: 1293 sheet: -1.04 (0.26), residues: 411 loop : -1.36 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 252 TYR 0.018 0.001 TYR B 388 PHE 0.019 0.001 PHE C 472 TRP 0.014 0.001 TRP C 151 HIS 0.004 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (23937) covalent geometry : angle 0.51195 / 0.27 (32553) SS BOND : bond 0.00162 / 0.09 ( 10) SS BOND : angle 0.86742 / 0.54 ( 20) hydrogen bonds : bond 0.04234 / 2.89 ( 1010) hydrogen bonds : angle 4.40413 / 3.13 ( 2961) Misc. bond : bond 0.00259 / 0.14 ( 1) link_NAG-ASN : bond 0.00609 / 0.32 ( 8) link_NAG-ASN : angle 3.37586 / 2.30 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 1.123 Fit side-chains REVERT: A 363 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: A 400 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8852 (mt) REVERT: A 555 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8784 (mtt) REVERT: B 608 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8672 (tp) REVERT: D 84 ARG cc_start: 0.8370 (tpm170) cc_final: 0.8142 (tpp80) REVERT: D 204 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7873 (tt) REVERT: D 227 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8330 (mm) REVERT: D 286 ASP cc_start: 0.7740 (t0) cc_final: 0.7403 (t0) REVERT: D 711 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6824 (tt0) outliers start: 51 outliers final: 24 residues processed: 257 average time/residue: 0.1434 time to fit residues: 61.6636 Evaluate side-chains 240 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 711 GLN Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 85 optimal weight: 0.9990 chunk 186 optimal weight: 8.9990 chunk 216 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 69 optimal weight: 0.0020 chunk 105 optimal weight: 20.0000 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 219 GLN B 437 GLN B 802 HIS ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 710 ASN D 711 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.107127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.078447 restraints weight = 47522.685| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.93 r_work: 0.2881 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23956 Z= 0.174 Angle : 0.535 9.652 32597 Z= 0.280 Chirality : 0.044 0.384 3779 Planarity : 0.004 0.063 4141 Dihedral : 7.615 175.660 3505 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.96 % Allowed : 16.91 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.16), residues: 3073 helix: 2.16 (0.15), residues: 1282 sheet: -1.02 (0.26), residues: 393 loop : -1.49 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 337 TYR 0.020 0.001 TYR B 388 PHE 0.025 0.002 PHE D 550 TRP 0.012 0.001 TRP C 151 HIS 0.006 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (23937) covalent geometry : angle 0.52612 / 0.28 (32553) SS BOND : bond 0.00246 / 0.16 ( 10) SS BOND : angle 1.03532 / 0.63 ( 20) hydrogen bonds : bond 0.04461 / 3.04 ( 1010) hydrogen bonds : angle 4.30792 / 3.09 ( 2961) Misc. bond : bond 0.00189 / 0.10 ( 1) link_NAG-ASN : bond 0.00610 / 0.32 ( 8) link_NAG-ASN : angle 3.54068 / 2.46 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 207 time to evaluate : 0.990 Fit side-chains REVERT: A 68 LYS cc_start: 0.8227 (mmtm) cc_final: 0.7599 (mptt) REVERT: A 363 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: A 400 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8848 (mt) REVERT: C 240 MET cc_start: 0.8838 (tpp) cc_final: 0.8548 (mmm) REVERT: D 84 ARG cc_start: 0.8362 (tpm170) cc_final: 0.8130 (tpp80) REVERT: D 204 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8040 (tt) REVERT: D 227 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8482 (mm) REVERT: D 286 ASP cc_start: 0.7829 (t0) cc_final: 0.7526 (t0) outliers start: 70 outliers final: 38 residues processed: 263 average time/residue: 0.1428 time to fit residues: 62.0754 Evaluate side-chains 240 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 429 CYS Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 813 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 123 optimal weight: 8.9990 chunk 300 optimal weight: 0.9980 chunk 273 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 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 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 HIS C 94 HIS C 101 HIS D 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.106739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.077989 restraints weight = 47340.450| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.07 r_work: 0.2869 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23956 Z= 0.165 Angle : 0.531 9.918 32597 Z= 0.278 Chirality : 0.044 0.395 3779 Planarity : 0.004 0.061 4141 Dihedral : 7.388 168.019 3505 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.26 % Allowed : 17.63 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.16), residues: 3073 helix: 2.01 (0.15), residues: 1283 sheet: -1.04 (0.26), residues: 388 loop : -1.57 (0.17), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 393 TYR 0.016 0.001 TYR B 388 PHE 0.019 0.002 PHE C 472 TRP 0.016 0.001 TRP B 391 HIS 0.005 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 (23937) covalent geometry : angle 0.52099 / 0.28 (32553) SS BOND : bond 0.00182 / 0.09 ( 10) SS BOND : angle 1.13988 / 0.72 ( 20) hydrogen bonds : bond 0.04321 / 2.95 ( 1010) hydrogen bonds : angle 4.22914 / 3.03 ( 2961) Misc. bond : bond 0.00181 / 0.10 ( 1) link_NAG-ASN : bond 0.00651 / 0.34 ( 8) link_NAG-ASN : angle 3.62715 / 2.50 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 205 time to evaluate : 0.784 Fit side-chains REVERT: A 68 LYS cc_start: 0.8234 (mmtm) cc_final: 0.7889 (mptt) REVERT: A 363 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: A 400 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8869 (mt) REVERT: C 217 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7916 (mmt180) REVERT: C 240 MET cc_start: 0.8866 (tpp) cc_final: 0.8601 (mmm) REVERT: D 84 ARG cc_start: 0.8379 (tpm170) cc_final: 0.8121 (tpp80) REVERT: D 204 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8106 (tt) REVERT: D 227 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8495 (mm) REVERT: D 286 ASP cc_start: 0.7885 (t0) cc_final: 0.7633 (t0) outliers start: 77 outliers final: 49 residues processed: 270 average time/residue: 0.1441 time to fit residues: 64.2948 Evaluate side-chains 249 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 813 MET Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain D residue 145 GLN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 429 CYS Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 747 LYS Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 813 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 76 optimal weight: 0.9980 chunk 203 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 106 optimal weight: 0.0270 chunk 85 optimal weight: 1.9990 chunk 211 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 802 HIS D 145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.108942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.080328 restraints weight = 47019.668| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.99 r_work: 0.2915 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23956 Z= 0.094 Angle : 0.474 9.389 32597 Z= 0.247 Chirality : 0.042 0.369 3779 Planarity : 0.003 0.055 4141 Dihedral : 7.127 173.224 3505 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.41 % Allowed : 19.15 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.16), residues: 3073 helix: 2.19 (0.15), residues: 1282 sheet: -0.88 (0.27), residues: 386 loop : -1.53 (0.17), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 673 TYR 0.012 0.001 TYR D 479 PHE 0.024 0.001 PHE B 550 TRP 0.013 0.001 TRP B 391 HIS 0.017 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (23937) covalent geometry : angle 0.46519 / 0.25 (32553) SS BOND : bond 0.00431 / 0.14 ( 10) SS BOND : angle 0.77652 / 0.54 ( 20) hydrogen bonds : bond 0.03340 / 2.29 ( 1010) hydrogen bonds : angle 4.06298 / 2.90 ( 2961) Misc. bond : bond 0.00125 / 0.07 ( 1) link_NAG-ASN : bond 0.00657 / 0.34 ( 8) link_NAG-ASN : angle 3.36756 / 2.32 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 221 time to evaluate : 0.986 Fit side-chains REVERT: A 68 LYS cc_start: 0.8215 (mmtm) cc_final: 0.7850 (mptt) REVERT: A 363 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: A 400 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8818 (mt) REVERT: B 425 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7560 (tt) REVERT: C 240 MET cc_start: 0.8868 (tpp) cc_final: 0.8610 (mmm) REVERT: D 84 ARG cc_start: 0.8355 (tpm170) cc_final: 0.8125 (tpp80) REVERT: D 227 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8273 (mm) REVERT: D 286 ASP cc_start: 0.7853 (t0) cc_final: 0.7603 (t0) outliers start: 57 outliers final: 42 residues processed: 265 average time/residue: 0.1460 time to fit residues: 63.6317 Evaluate side-chains 252 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 673 ARG Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 813 MET Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 747 LYS Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 146 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 206 optimal weight: 0.0470 chunk 30 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 275 optimal weight: 0.0770 chunk 175 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 286 optimal weight: 6.9990 overall best weight: 2.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 HIS C 94 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.078715 restraints weight = 47443.511| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.00 r_work: 0.2882 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23956 Z= 0.141 Angle : 0.504 9.486 32597 Z= 0.264 Chirality : 0.044 0.375 3779 Planarity : 0.004 0.055 4141 Dihedral : 7.182 177.587 3505 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.26 % Allowed : 18.39 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 3073 helix: 2.10 (0.15), residues: 1284 sheet: -0.92 (0.27), residues: 388 loop : -1.54 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 673 TYR 0.013 0.001 TYR D 479 PHE 0.031 0.001 PHE D 550 TRP 0.012 0.001 TRP B 391 HIS 0.004 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (23937) covalent geometry : angle 0.49510 / 0.26 (32553) SS BOND : bond 0.00180 / 0.09 ( 10) SS BOND : angle 0.94147 / 0.62 ( 20) hydrogen bonds : bond 0.03920 / 2.68 ( 1010) hydrogen bonds : angle 4.09938 / 2.94 ( 2961) Misc. bond : bond 0.00166 / 0.09 ( 1) link_NAG-ASN : bond 0.00616 / 0.32 ( 8) link_NAG-ASN : angle 3.44380 / 2.38 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 206 time to evaluate : 0.980 Fit side-chains REVERT: A 68 LYS cc_start: 0.8194 (mmtm) cc_final: 0.7839 (mptt) REVERT: A 363 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: A 400 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8841 (mt) REVERT: B 77 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7733 (t0) REVERT: B 425 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7603 (tt) REVERT: C 240 MET cc_start: 0.8901 (tpp) cc_final: 0.8651 (mmm) REVERT: D 84 ARG cc_start: 0.8349 (tpm170) cc_final: 0.8108 (tpp80) REVERT: D 204 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8034 (tt) REVERT: D 227 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8425 (mm) REVERT: D 286 ASP cc_start: 0.7916 (t0) cc_final: 0.7682 (t0) outliers start: 77 outliers final: 57 residues processed: 268 average time/residue: 0.1411 time to fit residues: 62.7729 Evaluate side-chains 267 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 204 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 673 ARG Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 813 MET Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 429 CYS Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 747 LYS Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 813 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 44 optimal weight: 1.9990 chunk 267 optimal weight: 0.0970 chunk 47 optimal weight: 8.9990 chunk 276 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 297 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN B 802 HIS ** C 94 HIS ** 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 = 0.3552 r_free = 0.3552 target = 0.108679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.080061 restraints weight = 46986.343| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.99 r_work: 0.2912 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23956 Z= 0.100 Angle : 0.474 9.235 32597 Z= 0.248 Chirality : 0.043 0.364 3779 Planarity : 0.003 0.053 4141 Dihedral : 7.112 175.874 3505 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.79 % Allowed : 18.94 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.16), residues: 3073 helix: 2.17 (0.15), residues: 1284 sheet: -0.73 (0.27), residues: 381 loop : -1.53 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 548 TYR 0.012 0.001 TYR D 479 PHE 0.016 0.001 PHE D 460 TRP 0.013 0.001 TRP B 391 HIS 0.005 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (23937) covalent geometry : angle 0.46544 / 0.25 (32553) SS BOND : bond 0.00291 / 0.15 ( 10) SS BOND : angle 0.78163 / 0.50 ( 20) hydrogen bonds : bond 0.03368 / 2.31 ( 1010) hydrogen bonds : angle 4.01637 / 2.87 ( 2961) Misc. bond : bond 0.00112 / 0.06 ( 1) link_NAG-ASN : bond 0.00632 / 0.33 ( 8) link_NAG-ASN : angle 3.31675 / 2.28 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 209 time to evaluate : 0.926 Fit side-chains REVERT: A 68 LYS cc_start: 0.8192 (mmtm) cc_final: 0.7827 (mptt) REVERT: A 363 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: A 400 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8825 (mt) REVERT: B 409 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.7997 (p) REVERT: B 425 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7572 (tt) REVERT: C 217 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7742 (mmt180) REVERT: C 240 MET cc_start: 0.8899 (tpp) cc_final: 0.8647 (mmm) REVERT: D 84 ARG cc_start: 0.8334 (tpm170) cc_final: 0.8109 (tpp80) REVERT: D 227 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8303 (mm) REVERT: D 286 ASP cc_start: 0.7933 (t0) cc_final: 0.7695 (t0) outliers start: 66 outliers final: 47 residues processed: 263 average time/residue: 0.1465 time to fit residues: 63.3869 Evaluate side-chains 259 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 206 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 673 ARG Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 813 MET Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 747 LYS Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 813 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 166 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 291 optimal weight: 20.0000 chunk 278 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 238 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN B 802 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.078383 restraints weight = 47132.002| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.08 r_work: 0.2875 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23956 Z= 0.148 Angle : 0.514 9.453 32597 Z= 0.270 Chirality : 0.044 0.378 3779 Planarity : 0.004 0.054 4141 Dihedral : 7.147 175.839 3505 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.21 % Allowed : 18.69 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.16), residues: 3073 helix: 2.08 (0.15), residues: 1284 sheet: -0.87 (0.27), residues: 388 loop : -1.56 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 393 TYR 0.013 0.001 TYR B 479 PHE 0.032 0.001 PHE D 550 TRP 0.012 0.001 TRP B 391 HIS 0.004 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (23937) covalent geometry : angle 0.50548 / 0.27 (32553) SS BOND : bond 0.00195 / 0.10 ( 10) SS BOND : angle 1.05255 / 0.66 ( 20) hydrogen bonds : bond 0.04013 / 2.75 ( 1010) hydrogen bonds : angle 4.09942 / 2.94 ( 2961) Misc. bond : bond 0.00144 / 0.08 ( 1) link_NAG-ASN : bond 0.00601 / 0.32 ( 8) link_NAG-ASN : angle 3.42773 / 2.37 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 205 time to evaluate : 0.985 Fit side-chains REVERT: A 68 LYS cc_start: 0.8208 (mmtm) cc_final: 0.7865 (mptt) REVERT: A 363 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: A 400 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8847 (mt) REVERT: B 425 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7594 (tt) REVERT: C 217 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8314 (mmt-90) REVERT: C 240 MET cc_start: 0.8901 (tpp) cc_final: 0.8647 (mmm) REVERT: D 84 ARG cc_start: 0.8355 (tpm170) cc_final: 0.8103 (tpp80) REVERT: D 204 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8052 (tt) REVERT: D 227 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8442 (mm) REVERT: D 286 ASP cc_start: 0.7931 (t0) cc_final: 0.7711 (t0) outliers start: 76 outliers final: 58 residues processed: 268 average time/residue: 0.1453 time to fit residues: 63.8618 Evaluate side-chains 263 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 199 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 673 ARG Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 813 MET Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain D residue 145 GLN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 747 LYS Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 813 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 67 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 17 optimal weight: 0.0870 chunk 189 optimal weight: 20.0000 chunk 110 optimal weight: 8.9990 chunk 237 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN B 802 HIS C 94 HIS D 357 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.108338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.079813 restraints weight = 47391.211| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.10 r_work: 0.2910 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23956 Z= 0.102 Angle : 0.477 9.069 32597 Z= 0.251 Chirality : 0.043 0.358 3779 Planarity : 0.003 0.053 4141 Dihedral : 6.954 178.326 3505 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.83 % Allowed : 18.94 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.16), residues: 3073 helix: 2.15 (0.15), residues: 1285 sheet: -0.69 (0.27), residues: 381 loop : -1.54 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 468 TYR 0.012 0.001 TYR D 479 PHE 0.029 0.001 PHE D 550 TRP 0.014 0.001 TRP B 391 HIS 0.005 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (23937) covalent geometry : angle 0.46857 / 0.25 (32553) SS BOND : bond 0.00170 / 0.10 ( 10) SS BOND : angle 0.71003 / 0.44 ( 20) hydrogen bonds : bond 0.03335 / 2.29 ( 1010) hydrogen bonds : angle 4.00264 / 2.86 ( 2961) Misc. bond : bond 0.00087 / 0.05 ( 1) link_NAG-ASN : bond 0.00619 / 0.33 ( 8) link_NAG-ASN : angle 3.26832 / 2.24 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 206 time to evaluate : 0.933 Fit side-chains REVERT: A 68 LYS cc_start: 0.8184 (mmtm) cc_final: 0.7836 (mptt) REVERT: A 363 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: A 400 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8816 (mt) REVERT: B 425 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7581 (tt) REVERT: C 217 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7724 (mmt180) REVERT: C 240 MET cc_start: 0.8904 (tpp) cc_final: 0.8639 (mmm) REVERT: D 84 ARG cc_start: 0.8334 (tpm170) cc_final: 0.8099 (tpp80) REVERT: D 227 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8256 (mm) REVERT: D 286 ASP cc_start: 0.7928 (t0) cc_final: 0.7714 (t0) outliers start: 67 outliers final: 56 residues processed: 261 average time/residue: 0.1455 time to fit residues: 62.4507 Evaluate side-chains 260 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 199 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 673 ARG Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 813 MET Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain D residue 145 GLN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 747 LYS Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 813 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 51 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 262 optimal weight: 0.8980 chunk 257 optimal weight: 5.9990 chunk 286 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 HIS D 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.108085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.079551 restraints weight = 47284.022| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.10 r_work: 0.2905 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23956 Z= 0.110 Angle : 0.483 9.021 32597 Z= 0.253 Chirality : 0.043 0.356 3779 Planarity : 0.003 0.053 4141 Dihedral : 6.865 179.139 3505 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.62 % Allowed : 19.28 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.16), residues: 3073 helix: 2.14 (0.15), residues: 1286 sheet: -0.68 (0.27), residues: 383 loop : -1.53 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 548 TYR 0.012 0.001 TYR D 479 PHE 0.031 0.001 PHE D 550 TRP 0.011 0.001 TRP B 391 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (23937) covalent geometry : angle 0.47443 / 0.25 (32553) SS BOND : bond 0.00178 / 0.10 ( 10) SS BOND : angle 0.79736 / 0.50 ( 20) hydrogen bonds : bond 0.03439 / 2.36 ( 1010) hydrogen bonds : angle 3.99839 / 2.86 ( 2961) Misc. bond : bond 0.00098 / 0.05 ( 1) link_NAG-ASN : bond 0.00611 / 0.32 ( 8) link_NAG-ASN : angle 3.25439 / 2.24 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 202 time to evaluate : 0.889 Fit side-chains REVERT: A 68 LYS cc_start: 0.8191 (mmtm) cc_final: 0.7853 (mptt) REVERT: A 363 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: A 400 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8814 (mt) REVERT: B 425 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7583 (tt) REVERT: C 217 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7469 (mmt90) REVERT: C 240 MET cc_start: 0.8919 (tpp) cc_final: 0.8662 (mmm) REVERT: D 84 ARG cc_start: 0.8319 (tpm170) cc_final: 0.8085 (tpp80) REVERT: D 227 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8263 (mm) REVERT: D 286 ASP cc_start: 0.7929 (t0) cc_final: 0.7726 (t0) outliers start: 62 outliers final: 57 residues processed: 253 average time/residue: 0.1461 time to fit residues: 61.3390 Evaluate side-chains 261 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 199 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 673 ARG Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 813 MET Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain D residue 145 GLN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 720 SER Chi-restraints excluded: chain D residue 747 LYS Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 813 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 306 optimal weight: 0.0270 chunk 48 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 171 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN D 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.106380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.077249 restraints weight = 47179.403| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.80 r_work: 0.2882 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23956 Z= 0.166 Angle : 0.533 9.333 32597 Z= 0.281 Chirality : 0.044 0.380 3779 Planarity : 0.004 0.054 4141 Dihedral : 6.992 177.242 3505 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.04 % Allowed : 18.77 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 3073 helix: 2.04 (0.15), residues: 1284 sheet: -0.79 (0.27), residues: 383 loop : -1.60 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 673 TYR 0.014 0.001 TYR B 479 PHE 0.034 0.002 PHE D 550 TRP 0.014 0.001 TRP B 391 HIS 0.005 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (23937) covalent geometry : angle 0.52459 / 0.28 (32553) SS BOND : bond 0.00242 / 0.13 ( 10) SS BOND : angle 1.12120 / 0.71 ( 20) hydrogen bonds : bond 0.04240 / 2.90 ( 1010) hydrogen bonds : angle 4.11875 / 2.95 ( 2961) Misc. bond : bond 0.00148 / 0.08 ( 1) link_NAG-ASN : bond 0.00591 / 0.31 ( 8) link_NAG-ASN : angle 3.41446 / 2.36 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5677.24 seconds wall clock time: 97 minutes 51.37 seconds (5871.37 seconds total)