Starting phenix.real_space_refine on Mon May 4 06:04:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e94_27955/05_2026/8e94_27955.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e94_27955/05_2026/8e94_27955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e94_27955/05_2026/8e94_27955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e94_27955/05_2026/8e94_27955.map" model { file = "/net/cci-nas-00/data/ceres_data/8e94_27955/05_2026/8e94_27955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e94_27955/05_2026/8e94_27955.cif" } resolution = 3.72 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= 0.010 sd= 0.740 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 12034 2.51 5 N 3235 2.21 5 O 3467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18816 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 4710 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 29, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 498 Unresolved non-hydrogen angles: 608 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'HIS:plan': 3, 'GLU:plan': 35, 'GLN:plan1': 8, 'ARG:plan': 11, 'ASP:plan': 15, 'PHE:plan': 1, 'ASN:plan1': 11, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 340 Chain: "B" Number of atoms: 4587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 4587 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 38, 'TRANS': 603} Chain breaks: 2 Unresolved non-hydrogen bonds: 402 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 334 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 10, 'PHE:plan': 4, 'ARG:plan': 15, 'ASP:plan': 11, 'GLU:plan': 17, 'HIS:plan': 5, 'ASN:plan1': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 292 Chain: "C" Number of atoms: 4620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 4620 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 29, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 595 Unresolved non-hydrogen angles: 726 Unresolved non-hydrogen dihedrals: 496 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 16, 'HIS:plan': 5, 'GLU:plan': 31, 'GLN:plan1': 6, 'PHE:plan': 3, 'ASN:plan1': 15, 'TRP:plan': 1, 'ASP:plan': 16, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 394 Chain: "D" Number of atoms: 4512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4512 Classifications: {'peptide': 638} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 39, 'TRANS': 598} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 547 Unresolved non-hydrogen dihedrals: 367 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 11, 'PHE:plan': 3, 'ARG:plan': 15, 'ASP:plan': 12, 'GLU:plan': 20, 'ASN:plan1': 5, 'HIS:plan': 7, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 310 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'IWB': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.37, per 1000 atoms: 0.23 Number of scatterers: 18816 At special positions: 0 Unit cell: (131.824, 147.232, 134.392, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 3467 8.00 N 3235 7.00 C 12034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=1.90 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 317 " distance=2.03 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 453 " distance=2.05 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.05 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.04 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 317 " distance=2.03 Simple disulfide: pdb=" SG CYS D 426 " - pdb=" SG CYS D 453 " distance=2.03 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 454 " distance=1.88 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 798 " 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 Atom "HETATM18684 O5 NAG A 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM18469 O5 NAG F 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " BMA F 3 " - " NAG F 4 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A 902 " - " ASN A 276 " " NAG A 903 " - " ASN A 771 " " NAG C 901 " - " ASN C 350 " " NAG C 902 " - " ASN C 203 " " NAG C 903 " - " ASN C 368 " " NAG D 901 " - " ASN D 337 " " NAG E 1 " - " ASN A 61 " " NAG F 1 " - " ASN A 368 " " NAG G 1 " - " ASN B 685 " " NAG H 1 " - " ASN B 337 " " NAG I 1 " - " ASN C 276 " " NAG J 1 " - " ASN C 61 " " NAG K 1 " - " ASN C 771 " Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 913.4 milliseconds 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4798 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 32 sheets defined 36.8% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 37 through 53 removed outlier: 3.700A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.878A pdb=" N SER A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.636A pdb=" N THR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 159 removed outlier: 4.054A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 204 through 213 removed outlier: 4.056A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.735A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 261' Processing helix chain 'A' and resid 278 through 296 removed outlier: 4.227A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.640A pdb=" N GLY A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.077A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.706A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 699 through 709 removed outlier: 3.944A pdb=" N HIS A 709 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 723 removed outlier: 3.880A pdb=" N ILE A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.546A pdb=" N GLU A 739 " --> pdb=" O VAL A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 783 Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 73 through 89 removed outlier: 3.721A pdb=" N HIS B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.590A pdb=" N GLN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.921A pdb=" N ARG B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 229 through 241 removed outlier: 4.134A pdb=" N GLU B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 305 Processing helix chain 'B' and resid 328 through 335 removed outlier: 3.939A pdb=" N TYR B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.609A pdb=" N GLY B 378 " --> pdb=" O TRP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 470 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 696 through 703 removed outlier: 3.688A pdb=" N HIS B 700 " --> pdb=" O TYR B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 721 removed outlier: 3.621A pdb=" N THR B 716 " --> pdb=" O GLU B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 739 Processing helix chain 'B' and resid 748 through 752 Processing helix chain 'B' and resid 768 through 784 removed outlier: 4.150A pdb=" N ALA B 772 " --> pdb=" O HIS B 768 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP B 774 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 775 " --> pdb=" O ARG B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 794 removed outlier: 3.806A pdb=" N LEU B 789 " --> pdb=" O GLU B 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 53 Processing helix chain 'C' and resid 70 through 84 Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.774A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 146 through 158 removed outlier: 4.162A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 204 through 213 removed outlier: 4.203A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 removed outlier: 4.231A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.573A pdb=" N ILE C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 4.225A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 297 removed outlier: 4.383A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 327 removed outlier: 3.878A pdb=" N SER C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 471 removed outlier: 3.701A pdb=" N THR C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 508 removed outlier: 3.741A pdb=" N GLY C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.800A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 695 removed outlier: 4.084A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 707 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 768 through 783 removed outlier: 3.846A pdb=" N LEU C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'D' and resid 73 through 89 Processing helix chain 'D' and resid 104 through 116 removed outlier: 3.701A pdb=" N LEU D 108 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 161 removed outlier: 3.926A pdb=" N VAL D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 153 " --> pdb=" O GLN D 149 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 187 removed outlier: 3.744A pdb=" N ARG D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 218 removed outlier: 3.907A pdb=" N THR D 212 " --> pdb=" O PRO D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 284 through 305 Processing helix chain 'D' and resid 325 through 336 Processing helix chain 'D' and resid 457 through 470 removed outlier: 3.550A pdb=" N LYS D 470 " --> pdb=" O ALA D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.622A pdb=" N GLU D 518 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 686 through 696 removed outlier: 4.412A pdb=" N ARG D 690 " --> pdb=" O GLY D 686 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN D 691 " --> pdb=" O SER D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 703 Processing helix chain 'D' and resid 712 through 721 removed outlier: 3.669A pdb=" N THR D 716 " --> pdb=" O GLU D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 737 removed outlier: 3.701A pdb=" N TYR D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 783 removed outlier: 3.934A pdb=" N ALA D 772 " --> pdb=" O HIS D 768 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 775 " --> pdb=" O ARG D 771 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA D 776 " --> pdb=" O ALA D 772 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP D 783 " --> pdb=" O GLN D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 794 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.489A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 197 Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.793A pdb=" N GLY A 268 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 402 removed outlier: 3.614A pdb=" N ILE A 400 " --> pdb=" O GLU A 475 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA8, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.898A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.898A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 64 through 68 removed outlier: 6.180A pdb=" N VAL B 32 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL B 67 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 34 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.380A pdb=" N ALA B 166 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N TYR B 227 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE B 168 " --> pdb=" O TYR B 227 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.568A pdb=" N VAL B 360 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 414 through 417 removed outlier: 3.508A pdb=" N GLU B 417 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS B 453 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 452 " --> pdb=" O CYS B 433 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 521 through 522 Processing sheet with id=AB6, first strand: chain 'B' and resid 725 through 729 removed outlier: 4.585A pdb=" N ILE B 531 " --> pdb=" O ALA B 755 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ALA B 755 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 26 through 33 removed outlier: 6.167A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N THR C 63 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE C 29 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.567A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 194 through 197 removed outlier: 6.718A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 222 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C 248 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 221 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.680A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 330 through 333 removed outlier: 5.793A pdb=" N ALA C 331 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL C 338 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 397 through 400 Processing sheet with id=AC4, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AC5, first strand: chain 'C' and resid 486 through 489 Processing sheet with id=AC6, first strand: chain 'C' and resid 534 through 536 removed outlier: 4.488A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 536 " --> pdb=" O SER C 756 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 729 through 732 removed outlier: 3.990A pdb=" N PHE C 729 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 67 through 68 removed outlier: 7.825A pdb=" N VAL D 67 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL D 34 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA D 33 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE D 93 " --> pdb=" O LEU D 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 197 through 201 removed outlier: 3.714A pdb=" N LEU D 201 " --> pdb=" O THR D 169 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA D 166 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N TYR D 227 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE D 168 " --> pdb=" O TYR D 227 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 274 through 277 removed outlier: 3.659A pdb=" N GLY D 373 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA D 362 " --> pdb=" O MET D 371 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N MET D 371 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AD3, first strand: chain 'D' and resid 346 through 347 removed outlier: 4.498A pdb=" N SER D 346 " --> pdb=" O VAL D 354 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 414 through 417 removed outlier: 8.046A pdb=" N LEU D 477 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARG D 434 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET D 505 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 406 " --> pdb=" O MET D 505 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET D 763 " --> pdb=" O ASP D 521 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 726 through 729 removed outlier: 4.929A pdb=" N ILE D 531 " --> pdb=" O ALA D 755 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA D 755 " --> pdb=" O ILE D 531 " (cutoff:3.500A) 706 hydrogen bonds defined for protein. 2034 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2971 1.29 - 1.43: 5205 1.43 - 1.58: 10949 1.58 - 1.72: 0 1.72 - 1.86: 124 Bond restraints: 19249 Sorted by residual: bond pdb=" C7 IWB B 901 " pdb=" C8 IWB B 901 " ideal model delta sigma weight residual 1.514 1.357 0.157 2.00e-02 2.50e+03 6.19e+01 bond pdb=" C PRO D 388 " pdb=" O PRO D 388 " ideal model delta sigma weight residual 1.233 1.150 0.083 1.23e-02 6.61e+03 4.53e+01 bond pdb=" C11 IWB B 901 " pdb=" C12 IWB B 901 " ideal model delta sigma weight residual 1.486 1.357 0.129 2.00e-02 2.50e+03 4.15e+01 bond pdb=" C PRO D 396 " pdb=" O PRO D 396 " ideal model delta sigma weight residual 1.234 1.166 0.067 1.08e-02 8.57e+03 3.88e+01 bond pdb=" C7 IWB B 901 " pdb=" N6 IWB B 901 " ideal model delta sigma weight residual 1.452 1.331 0.121 2.00e-02 2.50e+03 3.65e+01 ... (remaining 19244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 25920 3.09 - 6.18: 400 6.18 - 9.28: 55 9.28 - 12.37: 7 12.37 - 15.46: 1 Bond angle restraints: 26383 Sorted by residual: angle pdb=" C GLY D 260 " pdb=" N SER D 261 " pdb=" CA SER D 261 " ideal model delta sigma weight residual 120.28 130.71 -10.43 1.34e+00 5.57e-01 6.06e+01 angle pdb=" CA ARG B 411 " pdb=" C ARG B 411 " pdb=" N PRO B 412 " ideal model delta sigma weight residual 120.77 128.29 -7.52 9.70e-01 1.06e+00 6.01e+01 angle pdb=" C PRO D 396 " pdb=" CA PRO D 396 " pdb=" CB PRO D 396 " ideal model delta sigma weight residual 110.85 100.12 10.73 1.41e+00 5.03e-01 5.79e+01 angle pdb=" C ILE A 133 " pdb=" CA ILE A 133 " pdb=" CB ILE A 133 " ideal model delta sigma weight residual 111.80 120.57 -8.77 1.18e+00 7.18e-01 5.52e+01 angle pdb=" CA VAL A 246 " pdb=" C VAL A 246 " pdb=" O VAL A 246 " ideal model delta sigma weight residual 120.22 113.74 6.48 8.90e-01 1.26e+00 5.30e+01 ... (remaining 26378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.35: 10748 23.35 - 46.71: 746 46.71 - 70.06: 105 70.06 - 93.41: 27 93.41 - 116.76: 15 Dihedral angle restraints: 11641 sinusoidal: 4190 harmonic: 7451 Sorted by residual: dihedral pdb=" C ARG B 411 " pdb=" N ARG B 411 " pdb=" CA ARG B 411 " pdb=" CB ARG B 411 " ideal model delta harmonic sigma weight residual -122.60 -150.21 27.61 0 2.50e+00 1.60e-01 1.22e+02 dihedral pdb=" N ARG B 411 " pdb=" C ARG B 411 " pdb=" CA ARG B 411 " pdb=" CB ARG B 411 " ideal model delta harmonic sigma weight residual 122.80 149.13 -26.33 0 2.50e+00 1.60e-01 1.11e+02 dihedral pdb=" CB CYS C 420 " pdb=" SG CYS C 420 " pdb=" SG CYS C 454 " pdb=" CB CYS C 454 " ideal model delta sinusoidal sigma weight residual 93.00 28.63 64.37 1 1.00e+01 1.00e-02 5.45e+01 ... (remaining 11638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.785: 3213 0.785 - 1.570: 3 1.570 - 2.356: 0 2.356 - 3.141: 1 3.141 - 3.926: 1 Chirality restraints: 3218 Sorted by residual: chirality pdb=" C1 NAG F 4 " pdb=" O4 BMA F 3 " pdb=" C2 NAG F 4 " pdb=" O5 NAG F 4 " both_signs ideal model delta sigma weight residual False -2.40 -1.29 -1.11 2.00e-02 2.50e+03 3.09e+03 chirality pdb=" C7 IWB B 901 " pdb=" C18 IWB B 901 " pdb=" C8 IWB B 901 " pdb=" N6 IWB B 901 " both_signs ideal model delta sigma weight residual False -2.54 1.38 -3.93 2.00e-01 2.50e+01 3.85e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-02 2.50e+03 3.14e+02 ... (remaining 3215 not shown) Planarity restraints: 3354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 4 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG F 4 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG F 4 " 0.108 2.00e-02 2.50e+03 pdb=" N2 NAG F 4 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG F 4 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.318 2.00e-02 2.50e+03 2.76e-01 9.54e+02 pdb=" C7 NAG J 1 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.485 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " 0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 901 " 0.322 2.00e-02 2.50e+03 2.74e-01 9.36e+02 pdb=" C7 NAG A 901 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A 901 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG A 901 " -0.478 2.00e-02 2.50e+03 pdb=" O7 NAG A 901 " 0.054 2.00e-02 2.50e+03 ... (remaining 3351 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 19 2.23 - 2.89: 7728 2.89 - 3.56: 24854 3.56 - 4.23: 36806 4.23 - 4.90: 64166 Nonbonded interactions: 133573 Sorted by model distance: nonbonded pdb=" NE1 TRP D 304 " pdb=" O GLY D 308 " model vdw 1.557 3.120 nonbonded pdb=" ND2 ASN A 350 " pdb=" O5 NAG A 901 " model vdw 1.761 3.120 nonbonded pdb=" OD1 ASP B 97 " pdb=" N ASN B 98 " model vdw 1.845 3.120 nonbonded pdb=" NE1 TRP D 304 " pdb=" C GLY D 308 " model vdw 1.968 3.350 nonbonded pdb=" CD1 ILE A 220 " pdb=" CD1 LEU A 248 " model vdw 1.992 3.880 ... (remaining 133568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 25 through 26 and (name N or name CA or name C or name O \ or name CB )) or resid 27 through 34 or (resid 35 through 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 45 and (n \ ame N or name CA or name C or name O or name CB )) or resid 46 or (resid 47 thro \ ugh 52 and (name N or name CA or name C or name O or name CB )) or resid 53 thro \ ugh 55 or (resid 56 through 57 and (name N or name CA or name C or name O or nam \ e CB )) or resid 58 through 82 or (resid 83 and (name N or name CA or name C or \ name O or name CB )) or resid 84 through 98 or (resid 99 through 100 and (name N \ or name CA or name C or name O or name CB )) or resid 101 through 129 or (resid \ 130 through 131 and (name N or name CA or name C or name O or name CB )) or res \ id 132 through 158 or (resid 159 and (name N or name CA or name C or name O or n \ ame CB )) or resid 160 through 192 or (resid 193 and (name N or name CA or name \ C or name O or name CB )) or resid 194 through 211 or (resid 212 through 213 and \ (name N or name CA or name C or name O or name CB )) or resid 214 through 236 o \ r (resid 237 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 38 through 239 or (resid 240 and (name N or name CA or name C or name O or name \ CB )) or resid 241 through 250 or (resid 251 through 253 and (name N or name CA \ or name C or name O or name CB )) or resid 254 through 272 or (resid 273 and (na \ me N or name CA or name C or name O or name CB )) or resid 274 through 292 or (r \ esid 293 through 294 and (name N or name CA or name C or name O or name CB )) or \ resid 295 through 305 or (resid 306 and (name N or name CA or name C or name O \ or name CB )) or resid 307 through 322 or (resid 323 and (name N or name CA or n \ ame C or name O or name CB )) or resid 324 through 325 or (resid 326 and (name N \ or name CA or name C or name O or name CB )) or resid 327 through 342 or (resid \ 343 and (name N or name CA or name C or name O or name CB )) or (resid 344 thro \ ugh 347 and (name N or name CA or name C or name O or name CB )) or resid 348 th \ rough 359 or (resid 360 and (name N or name CA or name C or name O or name CB )) \ or resid 361 through 370 or (resid 371 and (name N or name CA or name C or name \ O or name CB )) or resid 372 through 376 or (resid 377 through 379 and (name N \ or name CA or name C or name O or name CB )) or resid 380 through 387 or (resid \ 388 and (name N or name CA or name C or name O or name CB )) or resid 389 or (re \ sid 390 and (name N or name CA or name C or name O or name CB )) or resid 391 th \ rough 414 or (resid 415 and (name N or name CA or name C or name O or name CB )) \ or resid 416 through 418 or (resid 419 and (name N or name CA or name C or name \ O or name CB )) or resid 420 through 421 or (resid 422 through 423 and (name N \ or name CA or name C or name O or name CB )) or resid 424 through 441 or (resid \ 442 through 443 and (name N or name CA or name C or name O or name CB )) or resi \ d 444 through 445 or (resid 446 and (name N or name CA or name C or name O or na \ me CB )) or resid 447 through 666 or (resid 667 through 669 and (name N or name \ CA or name C or name O or name CB )) or resid 670 through 672 or (resid 673 thro \ ugh 674 and (name N or name CA or name C or name O or name CB )) or resid 675 th \ rough 678 or (resid 679 and (name N or name CA or name C or name O or name CB )) \ or resid 680 or (resid 681 through 682 and (name N or name CA or name C or name \ O or name CB )) or resid 683 through 684 or (resid 685 and (name N or name CA o \ r name C or name O or name CB )) or resid 686 through 693 or (resid 694 and (nam \ e N or name CA or name C or name O or name CB )) or resid 695 through 702 or (re \ sid 703 through 704 and (name N or name CA or name C or name O or name CB )) or \ resid 705 through 718 or (resid 719 through 721 and (name N or name CA or name C \ or name O or name CB )) or resid 722 through 723 or (resid 724 through 728 and \ (name N or name CA or name C or name O or name CB )) or resid 729 through 751 or \ (resid 752 and (name N or name CA or name C or name O or name CB )) or resid 75 \ 3 through 788 or (resid 789 through 790 and (name N or name CA or name C or name \ O or name CB )) or resid 791 through 903)) selection = (chain 'C' and (resid 25 through 47 or (resid 48 through 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 155 or (resid 156 and ( \ name N or name CA or name C or name O or name CB )) or resid 157 through 177 or \ (resid 178 and (name N or name CA or name C or name O or name CB )) or resid 179 \ through 189 or (resid 190 through 193 and (name N or name CA or name C or name \ O or name CB )) or resid 194 through 214 or (resid 215 through 216 and (name N o \ r name CA or name C or name O or name CB )) or resid 217 through 224 or (resid 2 \ 25 and (name N or name CA or name C or name O or name CB )) or resid 226 through \ 259 or (resid 260 and (name N or name CA or name C or name O or name CB )) or r \ esid 261 through 271 or (resid 272 through 273 and (name N or name CA or name C \ or name O or name CB )) or resid 274 through 289 or (resid 290 through 291 and ( \ name N or name CA or name C or name O or name CB )) or resid 292 through 296 or \ (resid 297 through 303 and (name N or name CA or name C or name O or name CB )) \ or resid 304 through 336 or (resid 337 and (name N or name CA or name C or name \ O or name CB )) or resid 338 or (resid 339 and (name N or name CA or name C or n \ ame O or name CB )) or resid 340 or (resid 341 through 343 and (name N or name C \ A or name C or name O or name CB )) or (resid 344 through 347 and (name N or nam \ e CA or name C or name O or name CB )) or resid 348 through 366 or (resid 367 an \ d (name N or name CA or name C or name O or name CB )) or resid 368 through 378 \ or (resid 379 and (name N or name CA or name C or name O or name CB )) or resid \ 380 through 425 or (resid 426 through 427 and (name N or name CA or name C or na \ me O or name CB )) or resid 428 through 503 or (resid 504 and (name N or name CA \ or name C or name O or name CB )) or resid 505 through 519 or (resid 520 and (n \ ame N or name CA or name C or name O or name CB )) or resid 521 through 540 or ( \ resid 541 and (name N or name CA or name C or name O or name CB )) or resid 542 \ through 663 or (resid 664 through 665 and (name N or name CA or name C or name O \ or name CB )) or (resid 666 through 669 and (name N or name CA or name C or nam \ e O or name CB )) or resid 670 through 696 or (resid 697 through 699 and (name N \ or name CA or name C or name O or name CB )) or resid 700 through 701 or (resid \ 702 through 704 and (name N or name CA or name C or name O or name CB )) or res \ id 705 through 741 or (resid 742 through 743 and (name N or name CA or name C or \ name O or name CB )) or resid 744 through 786 or (resid 787 and (name N or name \ CA or name C or name O or name CB )) or resid 788 through 903)) } ncs_group { reference = (chain 'B' and (resid 31 through 53 or (resid 54 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 72 or (resid 73 and (na \ me N or name CA or name C or name O or name CB )) or resid 74 through 88 or (res \ id 89 and (name N or name CA or name C or name O or name CB )) or resid 90 throu \ gh 96 or (resid 97 through 103 and (name N or name CA or name C or name O or nam \ e CB )) or resid 104 through 132 or (resid 133 through 134 and (name N or name C \ A or name C or name O or name CB )) or resid 135 through 157 or (resid 158 and ( \ name N or name CA or name C or name O or name CB )) or resid 159 through 160 or \ (resid 161 and (name N or name CA or name C or name O or name CB )) or resid 162 \ through 179 or (resid 180 and (name N or name CA or name C or name O or name CB \ )) or resid 181 through 182 or (resid 183 through 184 and (name N or name CA or \ name C or name O or name CB )) or resid 185 through 186 or (resid 187 through 1 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 189 or (res \ id 190 and (name N or name CA or name C or name O or name CB )) or resid 191 thr \ ough 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) \ or resid 204 through 216 or (resid 217 and (name N or name CA or name C or name \ O or name CB )) or resid 218 through 219 or (resid 220 through 221 and (name N o \ r name CA or name C or name O or name CB )) or resid 222 through 231 or (resid 2 \ 32 through 233 and (name N or name CA or name C or name O or name CB )) or resid \ 234 through 241 or (resid 242 through 243 and (name N or name CA or name C or n \ ame O or name CB )) or resid 244 through 256 or (resid 257 through 258 and (name \ N or name CA or name C or name O or name CB )) or resid 259 through 281 or (res \ id 282 and (name N or name CA or name C or name O or name CB )) or resid 283 thr \ ough 284 or (resid 285 through 287 and (name N or name CA or name C or name O or \ name CB )) or resid 288 through 305 or (resid 306 through 307 and (name N or na \ me CA or name C or name O or name CB )) or resid 308 through 327 or (resid 328 t \ hrough 330 and (name N or name CA or name C or name O or name CB )) or resid 331 \ through 343 or (resid 344 and (name N or name CA or name C or name O or name CB \ )) or resid 345 through 363 or (resid 364 through 365 and (name N or name CA or \ name C or name O or name CB )) or resid 366 through 408 or (resid 409 through 4 \ 10 and (name N or name CA or name C or name O or name CB )) or resid 411 through \ 416 or (resid 417 and (name N or name CA or name C or name O or name CB )) or r \ esid 418 through 435 or (resid 436 and (name N or name CA or name C or name O or \ name CB )) or resid 437 or (resid 447 through 449 and (name N or name CA or nam \ e C or name O or name CB )) or resid 450 or (resid 451 and (name N or name CA or \ name C or name O or name CB )) or resid 452 through 481 or (resid 482 and (name \ N or name CA or name C or name O or name CB )) or resid 483 through 496 or (res \ id 497 and (name N or name CA or name C or name O or name CB )) or resid 498 thr \ ough 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) \ or resid 502 through 537 or resid 659 through 667 or (resid 668 through 670 and \ (name N or name CA or name C or name O or name CB )) or resid 671 through 696 or \ (resid 697 and (name N or name CA or name C or name O or name CB )) or resid 69 \ 8 or (resid 699 through 700 and (name N or name CA or name C or name O or name C \ B )) or resid 701 or (resid 702 through 703 and (name N or name CA or name C or \ name O or name CB )) or resid 704 through 705 or (resid 706 through 709 and (nam \ e N or name CA or name C or name O or name CB )) or resid 710 through 723 or (re \ sid 724 through 725 and (name N or name CA or name C or name O or name CB )) or \ resid 726 through 773 or (resid 774 and (name N or name CA or name C or name O o \ r name CB )) or resid 775 through 798)) selection = (chain 'D' and (resid 31 through 54 or (resid 55 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 262 or (resid 263 throu \ gh 264 and (name N or name CA or name C or name O or name CB )) or resid 265 thr \ ough 278 or (resid 279 and (name N or name CA or name C or name O or name CB )) \ or resid 280 through 285 or (resid 286 through 287 and (name N or name CA or nam \ e C or name O or name CB )) or resid 288 through 297 or (resid 298 and (name N o \ r name CA or name C or name O or name CB )) or resid 299 through 304 or (resid 3 \ 05 through 307 and (name N or name CA or name C or name O or name CB )) or resid \ 308 through 364 or (resid 365 and (name N or name CA or name C or name O or nam \ e CB )) or resid 366 through 373 or (resid 374 and (name N or name CA or name C \ or name O or name CB )) or resid 375 or (resid 376 and (name N or name CA or nam \ e C or name O or name CB )) or resid 377 through 389 or (resid 390 and (name N o \ r name CA or name C or name O or name CB )) or resid 391 or (resid 399 and (name \ N or name CA or name C or name O or name CB )) or resid 400 through 433 or (res \ id 434 and (name N or name CA or name C or name O or name CB )) or resid 435 thr \ ough 448 or (resid 449 and (name N or name CA or name C or name O or name CB )) \ or resid 450 through 454 or (resid 455 and (name N or name CA or name C or name \ O or name CB )) or resid 456 through 514 or (resid 515 and (name N or name CA or \ name C or name O or name CB )) or resid 516 through 527 or (resid 528 and (name \ N or name CA or name C or name O or name CB )) or resid 529 through 664 or (res \ id 665 through 670 and (name N or name CA or name C or name O or name CB )) or r \ esid 671 through 672 or (resid 673 through 675 and (name N or name CA or name C \ or name O or name CB )) or resid 676 through 679 or (resid 680 and (name N or na \ me CA or name C or name O or name CB )) or resid 681 through 712 or (resid 713 t \ hrough 714 and (name N or name CA or name C or name O or name CB )) or resid 715 \ through 796 or (resid 797 and (name N or name CA or name C or name O or name CB \ )) or resid 798)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'G' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.140 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: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.425 19285 Z= 0.404 Angle : 1.090 51.357 26479 Z= 0.579 Chirality : 0.108 3.926 3218 Planarity : 0.016 0.304 3341 Dihedral : 16.610 116.764 6807 Min Nonbonded Distance : 1.557 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.48 % Favored : 91.32 % Rotamer: Outliers : 1.27 % Allowed : 20.66 % Favored : 78.08 % Cbeta Deviations : 0.50 % 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: -2.58 (0.16), residues: 2570 helix: -0.07 (0.18), residues: 829 sheet: -2.09 (0.24), residues: 411 loop : -2.76 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 194 TYR 0.058 0.001 TYR D 390 PHE 0.032 0.001 PHE C 458 TRP 0.026 0.002 TRP D 387 HIS 0.011 0.001 HIS A 705 Details of bonding type rmsd covalent geometry : bond 0.00536 (19249) covalent geometry : angle 0.91122 (26383) SS BOND : bond 0.05798 ( 12) SS BOND : angle 11.45115 ( 24) hydrogen bonds : bond 0.18156 ( 702) hydrogen bonds : angle 7.63829 ( 2034) link_BETA1-4 : bond 0.01124 ( 11) link_BETA1-4 : angle 6.27432 ( 33) link_NAG-ASN : bond 0.17889 ( 13) link_NAG-ASN : angle 11.45614 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 185 average time/residue: 0.1265 time to fit residues: 37.8485 Evaluate side-chains 172 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 392 TYR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 0.0060 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 705 HIS ** D 334 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 = 0.3596 r_free = 0.3596 target = 0.125703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105149 restraints weight = 42532.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.107088 restraints weight = 26889.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108230 restraints weight = 19988.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109230 restraints weight = 16712.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.109706 restraints weight = 14663.533| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19285 Z= 0.180 Angle : 0.753 12.105 26479 Z= 0.369 Chirality : 0.049 0.443 3218 Planarity : 0.005 0.070 3341 Dihedral : 10.732 103.601 3341 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 4.60 % Allowed : 20.66 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.31 (0.16), residues: 2570 helix: 0.24 (0.18), residues: 848 sheet: -1.97 (0.25), residues: 392 loop : -2.69 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 411 TYR 0.035 0.001 TYR A 703 PHE 0.027 0.002 PHE C 458 TRP 0.011 0.001 TRP C 731 HIS 0.006 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00417 (19249) covalent geometry : angle 0.72829 (26383) SS BOND : bond 0.00548 ( 12) SS BOND : angle 1.68533 ( 24) hydrogen bonds : bond 0.05042 ( 702) hydrogen bonds : angle 5.81594 ( 2034) link_BETA1-4 : bond 0.00871 ( 11) link_BETA1-4 : angle 3.78071 ( 33) link_NAG-ASN : bond 0.00663 ( 13) link_NAG-ASN : angle 3.49279 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 170 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 SER cc_start: 0.9272 (m) cc_final: 0.9047 (p) REVERT: A 277 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7833 (tm-30) REVERT: A 366 ILE cc_start: 0.8678 (mm) cc_final: 0.8235 (mt) REVERT: A 542 VAL cc_start: 0.7212 (p) cc_final: 0.6910 (m) REVERT: B 685 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8734 (p0) REVERT: C 712 GLU cc_start: 0.7329 (tp30) cc_final: 0.6921 (tp30) REVERT: D 337 ASN cc_start: 0.6270 (p0) cc_final: 0.6022 (p0) outliers start: 80 outliers final: 46 residues processed: 232 average time/residue: 0.1169 time to fit residues: 44.6281 Evaluate side-chains 205 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 685 ASN Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 768 HIS Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 98 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 136 optimal weight: 20.0000 chunk 215 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 206 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106364 restraints weight = 42462.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108327 restraints weight = 26694.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109700 restraints weight = 19840.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.110473 restraints weight = 16267.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111160 restraints weight = 14418.559| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19285 Z= 0.142 Angle : 0.690 13.423 26479 Z= 0.337 Chirality : 0.047 0.532 3218 Planarity : 0.005 0.086 3341 Dihedral : 9.323 96.498 3337 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 5.12 % Allowed : 21.35 % Favored : 73.53 % 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: -2.00 (0.16), residues: 2570 helix: 0.57 (0.18), residues: 846 sheet: -1.84 (0.25), residues: 392 loop : -2.53 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 290 TYR 0.022 0.001 TYR A 392 PHE 0.024 0.001 PHE C 458 TRP 0.039 0.001 TRP D 304 HIS 0.005 0.001 HIS C 705 Details of bonding type rmsd covalent geometry : bond 0.00326 (19249) covalent geometry : angle 0.66282 (26383) SS BOND : bond 0.00377 ( 12) SS BOND : angle 1.68374 ( 24) hydrogen bonds : bond 0.04252 ( 702) hydrogen bonds : angle 5.28223 ( 2034) link_BETA1-4 : bond 0.00805 ( 11) link_BETA1-4 : angle 3.50664 ( 33) link_NAG-ASN : bond 0.00706 ( 13) link_NAG-ASN : angle 3.68023 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 181 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8723 (tpp) cc_final: 0.8409 (tpp) REVERT: A 277 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7664 (tm-30) REVERT: A 502 MET cc_start: 0.8483 (tpp) cc_final: 0.8221 (tpp) REVERT: A 542 VAL cc_start: 0.7213 (p) cc_final: 0.6817 (m) REVERT: B 161 ASP cc_start: 0.6942 (t0) cc_final: 0.6674 (t0) REVERT: C 712 GLU cc_start: 0.7352 (tp30) cc_final: 0.6935 (tp30) REVERT: D 159 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: D 269 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7874 (m-10) REVERT: D 337 ASN cc_start: 0.6124 (p0) cc_final: 0.5805 (p0) outliers start: 89 outliers final: 56 residues processed: 252 average time/residue: 0.1130 time to fit residues: 47.7673 Evaluate side-chains 223 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 768 HIS Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 28 optimal weight: 8.9990 chunk 156 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 178 optimal weight: 0.0980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS D 366 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.127473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107575 restraints weight = 42447.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109341 restraints weight = 28003.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110561 restraints weight = 21362.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111412 restraints weight = 17889.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111770 restraints weight = 15870.687| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19285 Z= 0.126 Angle : 0.652 10.399 26479 Z= 0.319 Chirality : 0.046 0.380 3218 Planarity : 0.004 0.070 3341 Dihedral : 8.710 87.100 3335 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 5.35 % Allowed : 22.15 % Favored : 72.50 % 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: -1.73 (0.17), residues: 2570 helix: 0.78 (0.18), residues: 854 sheet: -1.65 (0.25), residues: 392 loop : -2.38 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 694 TYR 0.020 0.001 TYR A 392 PHE 0.020 0.001 PHE C 458 TRP 0.023 0.001 TRP D 304 HIS 0.005 0.001 HIS C 705 Details of bonding type rmsd covalent geometry : bond 0.00288 (19249) covalent geometry : angle 0.63183 (26383) SS BOND : bond 0.00370 ( 12) SS BOND : angle 1.49096 ( 24) hydrogen bonds : bond 0.03799 ( 702) hydrogen bonds : angle 5.01120 ( 2034) link_BETA1-4 : bond 0.00652 ( 11) link_BETA1-4 : angle 3.24095 ( 33) link_NAG-ASN : bond 0.00520 ( 13) link_NAG-ASN : angle 2.93426 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 172 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7610 (tt) REVERT: A 261 TYR cc_start: 0.6507 (OUTLIER) cc_final: 0.3942 (p90) REVERT: A 277 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 502 MET cc_start: 0.8280 (tpp) cc_final: 0.8058 (tpp) REVERT: A 542 VAL cc_start: 0.7165 (p) cc_final: 0.6745 (m) REVERT: B 161 ASP cc_start: 0.6888 (t0) cc_final: 0.6608 (t0) REVERT: B 685 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8523 (p0) REVERT: D 269 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7883 (m-10) REVERT: D 337 ASN cc_start: 0.6229 (p0) cc_final: 0.5932 (p0) outliers start: 93 outliers final: 67 residues processed: 246 average time/residue: 0.1151 time to fit residues: 47.2304 Evaluate side-chains 237 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 166 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 685 ASN Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 768 HIS Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 89 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 254 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 239 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS B 513 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108234 restraints weight = 42234.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110028 restraints weight = 27832.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111264 restraints weight = 21160.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111990 restraints weight = 17659.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.112633 restraints weight = 15771.315| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19285 Z= 0.123 Angle : 0.638 11.614 26479 Z= 0.311 Chirality : 0.046 0.317 3218 Planarity : 0.004 0.070 3341 Dihedral : 8.256 75.949 3335 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 5.70 % Allowed : 22.21 % Favored : 72.09 % 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: -1.56 (0.17), residues: 2570 helix: 0.90 (0.18), residues: 858 sheet: -1.58 (0.25), residues: 398 loop : -2.26 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 290 TYR 0.020 0.001 TYR A 392 PHE 0.018 0.001 PHE C 458 TRP 0.015 0.001 TRP A 56 HIS 0.005 0.001 HIS C 705 Details of bonding type rmsd covalent geometry : bond 0.00284 (19249) covalent geometry : angle 0.61901 (26383) SS BOND : bond 0.00325 ( 12) SS BOND : angle 1.46563 ( 24) hydrogen bonds : bond 0.03631 ( 702) hydrogen bonds : angle 4.86475 ( 2034) link_BETA1-4 : bond 0.00651 ( 11) link_BETA1-4 : angle 3.05752 ( 33) link_NAG-ASN : bond 0.00508 ( 13) link_NAG-ASN : angle 2.85215 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 180 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8644 (tpp) cc_final: 0.8424 (tpp) REVERT: A 261 TYR cc_start: 0.6452 (OUTLIER) cc_final: 0.4333 (p90) REVERT: A 442 THR cc_start: 0.6188 (OUTLIER) cc_final: 0.5918 (p) REVERT: A 542 VAL cc_start: 0.7117 (p) cc_final: 0.6631 (m) REVERT: B 161 ASP cc_start: 0.7052 (t0) cc_final: 0.6824 (t0) REVERT: B 685 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8502 (p0) REVERT: C 711 TYR cc_start: 0.6904 (m-10) cc_final: 0.6608 (m-10) REVERT: D 269 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7809 (m-10) outliers start: 99 outliers final: 71 residues processed: 259 average time/residue: 0.1087 time to fit residues: 46.8989 Evaluate side-chains 249 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 174 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 247 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 685 ASN Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 768 HIS Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 186 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 40.0000 chunk 256 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 chunk 253 optimal weight: 0.4980 chunk 226 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS D 141 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.126528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106297 restraints weight = 42129.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.108355 restraints weight = 26015.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109769 restraints weight = 18991.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110564 restraints weight = 15427.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111272 restraints weight = 13581.645| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19285 Z= 0.153 Angle : 0.660 11.282 26479 Z= 0.323 Chirality : 0.046 0.352 3218 Planarity : 0.004 0.071 3341 Dihedral : 8.123 67.484 3329 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 6.27 % Allowed : 22.21 % Favored : 71.52 % 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: -1.56 (0.17), residues: 2570 helix: 0.91 (0.18), residues: 856 sheet: -1.66 (0.25), residues: 394 loop : -2.24 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.021 0.001 TYR A 392 PHE 0.017 0.001 PHE C 458 TRP 0.015 0.001 TRP A 56 HIS 0.004 0.001 HIS C 705 Details of bonding type rmsd covalent geometry : bond 0.00363 (19249) covalent geometry : angle 0.64031 (26383) SS BOND : bond 0.00435 ( 12) SS BOND : angle 1.86430 ( 24) hydrogen bonds : bond 0.03931 ( 702) hydrogen bonds : angle 4.91018 ( 2034) link_BETA1-4 : bond 0.00621 ( 11) link_BETA1-4 : angle 3.03070 ( 33) link_NAG-ASN : bond 0.00506 ( 13) link_NAG-ASN : angle 2.89000 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 170 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8707 (tpp) cc_final: 0.8369 (tpp) REVERT: A 261 TYR cc_start: 0.6572 (OUTLIER) cc_final: 0.4943 (p90) REVERT: A 442 THR cc_start: 0.6299 (OUTLIER) cc_final: 0.6010 (p) REVERT: A 542 VAL cc_start: 0.7166 (p) cc_final: 0.6653 (m) REVERT: B 161 ASP cc_start: 0.7166 (t0) cc_final: 0.6952 (t0) REVERT: B 203 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8003 (pp) REVERT: B 217 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7094 (ttt90) REVERT: B 685 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8495 (p0) REVERT: C 711 TYR cc_start: 0.7087 (m-10) cc_final: 0.6797 (m-10) REVERT: D 262 THR cc_start: 0.8426 (p) cc_final: 0.7642 (m) REVERT: D 269 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7813 (m-10) outliers start: 109 outliers final: 79 residues processed: 254 average time/residue: 0.1129 time to fit residues: 47.5185 Evaluate side-chains 251 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 166 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 685 ASN Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 768 HIS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 29 optimal weight: 1.9990 chunk 253 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.126275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106466 restraints weight = 42506.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108198 restraints weight = 28106.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109433 restraints weight = 21547.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110071 restraints weight = 18001.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110641 restraints weight = 16160.302| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19285 Z= 0.164 Angle : 0.668 11.459 26479 Z= 0.328 Chirality : 0.047 0.373 3218 Planarity : 0.004 0.070 3341 Dihedral : 7.974 64.260 3327 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 6.33 % Allowed : 22.38 % Favored : 71.29 % 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: -1.56 (0.17), residues: 2570 helix: 0.85 (0.18), residues: 863 sheet: -1.61 (0.25), residues: 393 loop : -2.23 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.021 0.001 TYR A 392 PHE 0.017 0.002 PHE C 458 TRP 0.018 0.001 TRP A 56 HIS 0.005 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00387 (19249) covalent geometry : angle 0.64837 (26383) SS BOND : bond 0.00409 ( 12) SS BOND : angle 1.61834 ( 24) hydrogen bonds : bond 0.04019 ( 702) hydrogen bonds : angle 4.93148 ( 2034) link_BETA1-4 : bond 0.00636 ( 11) link_BETA1-4 : angle 3.00285 ( 33) link_NAG-ASN : bond 0.00529 ( 13) link_NAG-ASN : angle 3.04621 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 168 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 TYR cc_start: 0.6566 (OUTLIER) cc_final: 0.5065 (p90) REVERT: A 442 THR cc_start: 0.6320 (OUTLIER) cc_final: 0.6018 (p) REVERT: A 542 VAL cc_start: 0.7139 (p) cc_final: 0.6641 (m) REVERT: B 203 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8005 (pp) REVERT: B 217 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7012 (ttt90) REVERT: B 685 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8404 (p0) REVERT: B 723 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7820 (mp) REVERT: C 711 TYR cc_start: 0.7096 (m-10) cc_final: 0.6860 (m-10) REVERT: D 269 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7825 (m-10) outliers start: 110 outliers final: 89 residues processed: 252 average time/residue: 0.1121 time to fit residues: 46.8116 Evaluate side-chains 261 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 165 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 247 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 685 ASN Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 768 HIS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 114 optimal weight: 10.0000 chunk 196 optimal weight: 0.0870 chunk 229 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 195 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106081 restraints weight = 42395.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107804 restraints weight = 28137.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109051 restraints weight = 21548.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.109855 restraints weight = 17979.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.110412 restraints weight = 15919.099| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19285 Z= 0.165 Angle : 0.670 11.195 26479 Z= 0.330 Chirality : 0.047 0.387 3218 Planarity : 0.005 0.073 3341 Dihedral : 7.813 63.616 3327 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 6.27 % Allowed : 22.96 % Favored : 70.77 % 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: -1.57 (0.17), residues: 2570 helix: 0.84 (0.18), residues: 860 sheet: -1.62 (0.25), residues: 387 loop : -2.23 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.022 0.001 TYR A 392 PHE 0.016 0.002 PHE C 458 TRP 0.021 0.001 TRP A 56 HIS 0.005 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00390 (19249) covalent geometry : angle 0.64967 (26383) SS BOND : bond 0.00395 ( 12) SS BOND : angle 1.61733 ( 24) hydrogen bonds : bond 0.04024 ( 702) hydrogen bonds : angle 4.94928 ( 2034) link_BETA1-4 : bond 0.00639 ( 11) link_BETA1-4 : angle 2.93276 ( 33) link_NAG-ASN : bond 0.00515 ( 13) link_NAG-ASN : angle 3.20000 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 164 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 TYR cc_start: 0.6673 (OUTLIER) cc_final: 0.5443 (p90) REVERT: A 442 THR cc_start: 0.6347 (OUTLIER) cc_final: 0.6046 (p) REVERT: A 542 VAL cc_start: 0.7103 (p) cc_final: 0.6594 (m) REVERT: B 203 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7977 (pp) REVERT: B 217 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7019 (ttt90) REVERT: B 685 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8339 (p0) REVERT: B 723 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7794 (mp) REVERT: C 711 TYR cc_start: 0.7119 (m-10) cc_final: 0.6894 (m-10) REVERT: D 269 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7845 (m-10) outliers start: 109 outliers final: 90 residues processed: 245 average time/residue: 0.1098 time to fit residues: 44.6464 Evaluate side-chains 254 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 157 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 247 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 685 ASN Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 768 HIS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 216 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 240 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 189 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 230 optimal weight: 0.4980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107574 restraints weight = 42047.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109637 restraints weight = 25966.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111051 restraints weight = 18937.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112001 restraints weight = 15382.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.112528 restraints weight = 13396.663| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19285 Z= 0.119 Angle : 0.634 13.060 26479 Z= 0.309 Chirality : 0.045 0.377 3218 Planarity : 0.004 0.072 3341 Dihedral : 7.457 65.125 3327 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 5.75 % Allowed : 23.30 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.17), residues: 2570 helix: 1.00 (0.18), residues: 862 sheet: -1.60 (0.26), residues: 371 loop : -2.13 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 771 TYR 0.019 0.001 TYR A 392 PHE 0.014 0.001 PHE C 458 TRP 0.024 0.001 TRP A 56 HIS 0.005 0.001 HIS C 705 Details of bonding type rmsd covalent geometry : bond 0.00276 (19249) covalent geometry : angle 0.61448 (26383) SS BOND : bond 0.00376 ( 12) SS BOND : angle 1.44380 ( 24) hydrogen bonds : bond 0.03433 ( 702) hydrogen bonds : angle 4.75416 ( 2034) link_BETA1-4 : bond 0.00631 ( 11) link_BETA1-4 : angle 2.76699 ( 33) link_NAG-ASN : bond 0.00482 ( 13) link_NAG-ASN : angle 3.16699 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 169 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 TYR cc_start: 0.6570 (OUTLIER) cc_final: 0.4995 (p90) REVERT: A 442 THR cc_start: 0.6360 (OUTLIER) cc_final: 0.6036 (p) REVERT: A 542 VAL cc_start: 0.7094 (p) cc_final: 0.6584 (m) REVERT: B 203 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7990 (pp) REVERT: B 217 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7045 (ttt90) REVERT: B 685 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8364 (p0) REVERT: B 723 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7834 (mp) REVERT: C 451 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8039 (m) REVERT: C 711 TYR cc_start: 0.7041 (m-10) cc_final: 0.6771 (m-10) REVERT: D 269 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7845 (m-10) outliers start: 100 outliers final: 80 residues processed: 245 average time/residue: 0.1102 time to fit residues: 44.7784 Evaluate side-chains 246 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 158 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 247 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 685 ASN Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 768 HIS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 207 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.125209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104926 restraints weight = 42138.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.106965 restraints weight = 26098.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108361 restraints weight = 19011.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109123 restraints weight = 15511.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109825 restraints weight = 13688.918| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19285 Z= 0.189 Angle : 0.691 12.135 26479 Z= 0.341 Chirality : 0.048 0.434 3218 Planarity : 0.005 0.102 3341 Dihedral : 7.656 61.993 3327 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 5.98 % Allowed : 23.19 % Favored : 70.83 % 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: -1.55 (0.17), residues: 2570 helix: 0.86 (0.18), residues: 859 sheet: -1.63 (0.26), residues: 386 loop : -2.21 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 290 TYR 0.026 0.001 TYR A 703 PHE 0.025 0.002 PHE D 154 TRP 0.065 0.002 TRP A 56 HIS 0.005 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00450 (19249) covalent geometry : angle 0.67060 (26383) SS BOND : bond 0.00438 ( 12) SS BOND : angle 1.60958 ( 24) hydrogen bonds : bond 0.04265 ( 702) hydrogen bonds : angle 4.95288 ( 2034) link_BETA1-4 : bond 0.00648 ( 11) link_BETA1-4 : angle 2.88260 ( 33) link_NAG-ASN : bond 0.00517 ( 13) link_NAG-ASN : angle 3.34019 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 155 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 TYR cc_start: 0.6758 (OUTLIER) cc_final: 0.5499 (p90) REVERT: A 442 THR cc_start: 0.6416 (OUTLIER) cc_final: 0.6101 (p) REVERT: A 542 VAL cc_start: 0.7115 (p) cc_final: 0.6586 (m) REVERT: B 203 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8081 (pp) REVERT: B 217 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7085 (ttt90) REVERT: B 685 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8362 (p0) REVERT: B 723 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7885 (mp) REVERT: B 774 ASP cc_start: 0.7517 (m-30) cc_final: 0.7270 (m-30) REVERT: C 711 TYR cc_start: 0.7216 (m-10) cc_final: 0.6994 (m-10) REVERT: D 269 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7904 (m-10) outliers start: 104 outliers final: 89 residues processed: 235 average time/residue: 0.1135 time to fit residues: 44.4364 Evaluate side-chains 253 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 157 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 685 ASN Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 528 GLU Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 768 HIS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 162 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 191 optimal weight: 0.8980 chunk 199 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.126036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105638 restraints weight = 42809.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107632 restraints weight = 26759.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.108981 restraints weight = 19748.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109891 restraints weight = 16174.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110529 restraints weight = 14185.058| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19285 Z= 0.162 Angle : 0.669 12.181 26479 Z= 0.329 Chirality : 0.047 0.413 3218 Planarity : 0.005 0.100 3341 Dihedral : 7.581 61.749 3327 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 5.70 % Allowed : 23.53 % Favored : 70.77 % 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: -1.52 (0.17), residues: 2570 helix: 0.90 (0.18), residues: 859 sheet: -1.61 (0.26), residues: 384 loop : -2.20 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.022 0.001 TYR A 703 PHE 0.016 0.002 PHE C 458 TRP 0.045 0.001 TRP A 56 HIS 0.005 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00383 (19249) covalent geometry : angle 0.64947 (26383) SS BOND : bond 0.00421 ( 12) SS BOND : angle 1.55050 ( 24) hydrogen bonds : bond 0.03975 ( 702) hydrogen bonds : angle 4.90304 ( 2034) link_BETA1-4 : bond 0.00640 ( 11) link_BETA1-4 : angle 2.82128 ( 33) link_NAG-ASN : bond 0.00492 ( 13) link_NAG-ASN : angle 3.26526 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2935.27 seconds wall clock time: 51 minutes 29.70 seconds (3089.70 seconds total)