Starting phenix.real_space_refine on Fri Sep 19 03:18:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b38_44131/09_2025/9b38_44131.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b38_44131/09_2025/9b38_44131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b38_44131/09_2025/9b38_44131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b38_44131/09_2025/9b38_44131.map" model { file = "/net/cci-nas-00/data/ceres_data/9b38_44131/09_2025/9b38_44131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b38_44131/09_2025/9b38_44131.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 120 5.16 5 C 14414 2.51 5 N 3690 2.21 5 O 4446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22670 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 5416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5416 Classifications: {'peptide': 679} Link IDs: {'PTRANS': 25, 'TRANS': 653} Chain breaks: 1 Chain: "B" Number of atoms: 5423 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 679, 5416 Classifications: {'peptide': 679} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 653} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 679, 5416 Classifications: {'peptide': 679} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 653} Chain breaks: 1 bond proxies already assigned to first conformer: 5526 Chain: "C" Number of atoms: 5416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5416 Classifications: {'peptide': 679} Link IDs: {'PTRANS': 25, 'TRANS': 653} Chain breaks: 1 Chain: "D" Number of atoms: 5423 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 679, 5416 Classifications: {'peptide': 679} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 653} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 679, 5416 Classifications: {'peptide': 679} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 653} Chain breaks: 1 bond proxies already assigned to first conformer: 5526 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" 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: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" 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: "N" 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: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" 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: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" 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: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 92 Unusual residues: {'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" 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: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 92 Unusual residues: {'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" 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 Time building chain proxies: 7.62, per 1000 atoms: 0.34 Number of scatterers: 22670 At special positions: 0 Unit cell: (122.732, 163.193, 171.285, 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 120 16.00 O 4446 8.00 N 3690 7.00 C 14414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA H 3 " - " MAN H 4 " " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA H 3 " - " MAN H 5 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " " BMA O 3 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " 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 K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A1002 " - " ASN A 67 " " NAG A1003 " - " ASN A 73 " " NAG A1006 " - " ASN A 423 " " NAG A1007 " - " ASN A 546 " " NAG A1008 " - " ASN A 751 " " NAG B1002 " - " ASN B 67 " " NAG B1003 " - " ASN B 73 " " NAG B1004 " - " ASN B 546 " " NAG B1005 " - " ASN B 751 " " NAG C1002 " - " ASN C 67 " " NAG C1003 " - " ASN C 73 " " NAG C1006 " - " ASN C 423 " " NAG C1007 " - " ASN C 546 " " NAG C1008 " - " ASN C 751 " " NAG D1002 " - " ASN D 67 " " NAG D1003 " - " ASN D 73 " " NAG D1004 " - " ASN D 546 " " NAG D1005 " - " ASN D 751 " " NAG E 1 " - " ASN A 275 " " NAG F 1 " - " ASN A 378 " " NAG G 1 " - " ASN A 412 " " NAG H 1 " - " ASN A 430 " " NAG I 1 " - " ASN B 275 " " NAG J 1 " - " ASN B 378 " " NAG K 1 " - " ASN B 412 " " NAG L 1 " - " ASN C 275 " " NAG M 1 " - " ASN C 378 " " NAG N 1 " - " ASN C 412 " " NAG O 1 " - " ASN C 430 " " NAG P 1 " - " ASN D 275 " " NAG Q 1 " - " ASN D 378 " " NAG R 1 " - " ASN D 412 " Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.2 microseconds 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5104 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 36 sheets defined 41.8% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 removed outlier: 3.616A pdb=" N VAL A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 102 removed outlier: 3.515A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.856A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 removed outlier: 4.291A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 211 through 220 removed outlier: 3.514A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 244 removed outlier: 3.517A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 286 through 300 removed outlier: 3.625A pdb=" N SER A 291 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 336 removed outlier: 3.594A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 423 through 427 removed outlier: 4.321A pdb=" N ASP A 426 " --> pdb=" O ASN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.580A pdb=" N GLU A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 508 removed outlier: 4.380A pdb=" N HIS A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 662 removed outlier: 3.812A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 676 removed outlier: 4.064A pdb=" N LYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.575A pdb=" N LYS A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 708 " --> pdb=" O LYS A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 717 removed outlier: 3.754A pdb=" N LEU A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 730 Processing helix chain 'A' and resid 738 through 749 removed outlier: 3.576A pdb=" N ILE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU A 743 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 745 " --> pdb=" O THR A 741 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 784 removed outlier: 3.923A pdb=" N ILE A 780 " --> pdb=" O ASP A 776 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.729A pdb=" N LYS A 797 " --> pdb=" O MET A 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 66 removed outlier: 3.695A pdb=" N ILE B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 102 removed outlier: 3.523A pdb=" N ALA B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 removed outlier: 4.082A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.620A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.725A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.560A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.800A pdb=" N SER B 309 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 306 through 310' Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.676A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 333 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.565A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 removed outlier: 3.681A pdb=" N GLU B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 527 removed outlier: 4.124A pdb=" N VAL B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B 527 " --> pdb=" O ARG B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 665 removed outlier: 3.736A pdb=" N ILE B 647 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 676 Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.538A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 Processing helix chain 'B' and resid 738 through 749 removed outlier: 3.564A pdb=" N GLU B 743 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 745 " --> pdb=" O THR B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 788 removed outlier: 3.969A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.615A pdb=" N VAL C 61 " --> pdb=" O PHE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 102 removed outlier: 3.515A pdb=" N ALA C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.855A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 168 removed outlier: 4.291A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 161 " --> pdb=" O SER C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 211 through 220 removed outlier: 3.514A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 244 removed outlier: 3.518A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 238 " --> pdb=" O MET C 234 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 286 through 300 removed outlier: 3.626A pdb=" N SER C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 336 removed outlier: 3.595A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 364 Processing helix chain 'C' and resid 423 through 427 removed outlier: 4.322A pdb=" N ASP C 426 " --> pdb=" O ASN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.580A pdb=" N GLU C 469 " --> pdb=" O ASP C 465 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 508 removed outlier: 4.379A pdb=" N HIS C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 662 removed outlier: 3.812A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 676 removed outlier: 4.064A pdb=" N LYS C 676 " --> pdb=" O ASP C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 696 Processing helix chain 'C' and resid 699 through 712 removed outlier: 3.575A pdb=" N LYS C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 708 " --> pdb=" O LYS C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 717 removed outlier: 3.754A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 730 Processing helix chain 'C' and resid 738 through 749 removed outlier: 3.576A pdb=" N ILE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU C 743 " --> pdb=" O SER C 739 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 745 " --> pdb=" O THR C 741 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 784 removed outlier: 3.924A pdb=" N ILE C 780 " --> pdb=" O ASP C 776 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 781 " --> pdb=" O LYS C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 798 removed outlier: 3.728A pdb=" N LYS C 797 " --> pdb=" O MET C 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 66 removed outlier: 3.695A pdb=" N ILE D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 102 removed outlier: 3.523A pdb=" N ALA D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 removed outlier: 4.083A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 3.621A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 211 through 220 Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.724A pdb=" N LEU D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.559A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 310 removed outlier: 3.801A pdb=" N SER D 309 " --> pdb=" O LYS D 306 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY D 310 " --> pdb=" O PRO D 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 306 through 310' Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.676A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.565A pdb=" N ILE D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 removed outlier: 3.681A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 527 removed outlier: 4.125A pdb=" N VAL D 526 " --> pdb=" O VAL D 522 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D 527 " --> pdb=" O ARG D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 665 removed outlier: 3.737A pdb=" N ILE D 647 " --> pdb=" O PHE D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 676 Processing helix chain 'D' and resid 688 through 696 Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.538A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 Processing helix chain 'D' and resid 738 through 749 removed outlier: 3.565A pdb=" N GLU D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 745 " --> pdb=" O THR D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 788 removed outlier: 3.969A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 794 through 799 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42 removed outlier: 4.166A pdb=" N GLY A 40 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 107 removed outlier: 6.307A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS A 129 " --> pdb=" O VAL A 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.566A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASP A 229 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE A 228 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 406 Processing sheet with id=AA5, first strand: chain 'A' and resid 432 through 437 removed outlier: 6.937A pdb=" N LEU A 433 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ARG A 481 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 446 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 534 through 537 removed outlier: 4.150A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 543 removed outlier: 3.981A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 681 through 683 removed outlier: 6.548A pdb=" N GLU A 681 " --> pdb=" O ALA A 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'B' and resid 77 through 78 removed outlier: 4.503A pdb=" N ALA B 105 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 129 through 131 Processing sheet with id=AB5, first strand: chain 'B' and resid 175 through 176 Processing sheet with id=AB6, first strand: chain 'B' and resid 225 through 226 Processing sheet with id=AB7, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.753A pdb=" N LEU B 389 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR B 404 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 391 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 402 " --> pdb=" O VAL B 391 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 433 through 436 removed outlier: 3.769A pdb=" N GLU B 479 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 517 through 518 removed outlier: 4.105A pdb=" N LEU B 517 " --> pdb=" O GLY B 765 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 39 through 42 removed outlier: 4.166A pdb=" N GLY C 40 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 106 through 107 removed outlier: 6.308A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS C 129 " --> pdb=" O VAL C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.566A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE C 228 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TYR C 254 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N MET C 276 " --> pdb=" O LEU C 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 403 through 406 Processing sheet with id=AC5, first strand: chain 'C' and resid 432 through 437 removed outlier: 6.938A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ARG C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AC7, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AC8, first strand: chain 'C' and resid 534 through 537 removed outlier: 4.150A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 540 through 543 removed outlier: 3.980A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 681 through 683 removed outlier: 6.548A pdb=" N GLU C 681 " --> pdb=" O ALA C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 77 through 78 Processing sheet with id=AD3, first strand: chain 'D' and resid 77 through 78 removed outlier: 4.504A pdb=" N ALA D 105 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=AD5, first strand: chain 'D' and resid 175 through 176 Processing sheet with id=AD6, first strand: chain 'D' and resid 225 through 226 Processing sheet with id=AD7, first strand: chain 'D' and resid 389 through 395 removed outlier: 6.754A pdb=" N LEU D 389 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR D 404 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL D 391 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE D 402 " --> pdb=" O VAL D 391 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 433 through 436 removed outlier: 3.768A pdb=" N GLU D 479 " --> pdb=" O LEU D 433 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 517 through 518 removed outlier: 4.104A pdb=" N LEU D 517 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 2044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.54 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6921 1.34 - 1.46: 4429 1.46 - 1.57: 11572 1.57 - 1.69: 12 1.69 - 1.81: 212 Bond restraints: 23146 Sorted by residual: bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.574 -0.168 2.00e-02 2.50e+03 7.02e+01 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.570 -0.164 2.00e-02 2.50e+03 6.75e+01 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.538 -0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.535 -0.129 2.00e-02 2.50e+03 4.15e+01 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.528 -0.122 2.00e-02 2.50e+03 3.74e+01 ... (remaining 23141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 30281 3.18 - 6.36: 899 6.36 - 9.53: 111 9.53 - 12.71: 21 12.71 - 15.89: 2 Bond angle restraints: 31314 Sorted by residual: angle pdb=" C GLU B 440 " pdb=" N GLU B 441 " pdb=" CA GLU B 441 " ideal model delta sigma weight residual 121.80 137.69 -15.89 2.44e+00 1.68e-01 4.24e+01 angle pdb=" C GLU D 440 " pdb=" N GLU D 441 " pdb=" CA GLU D 441 " ideal model delta sigma weight residual 121.80 137.67 -15.87 2.44e+00 1.68e-01 4.23e+01 angle pdb=" N LYS A 797 " pdb=" CA LYS A 797 " pdb=" C LYS A 797 " ideal model delta sigma weight residual 114.56 106.44 8.12 1.27e+00 6.20e-01 4.09e+01 angle pdb=" N LYS C 797 " pdb=" CA LYS C 797 " pdb=" C LYS C 797 " ideal model delta sigma weight residual 114.56 106.46 8.10 1.27e+00 6.20e-01 4.07e+01 angle pdb=" C GLN C 417 " pdb=" N LYS C 418 " pdb=" CA LYS C 418 " ideal model delta sigma weight residual 121.54 132.50 -10.96 1.91e+00 2.74e-01 3.29e+01 ... (remaining 31309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.20: 13876 24.20 - 48.40: 517 48.40 - 72.59: 191 72.59 - 96.79: 163 96.79 - 120.99: 85 Dihedral angle restraints: 14832 sinusoidal: 6908 harmonic: 7924 Sorted by residual: dihedral pdb=" CA ASP C 507 " pdb=" C ASP C 507 " pdb=" N HIS C 508 " pdb=" CA HIS C 508 " ideal model delta harmonic sigma weight residual 180.00 122.94 57.06 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA ASP A 507 " pdb=" C ASP A 507 " pdb=" N HIS A 508 " pdb=" CA HIS A 508 " ideal model delta harmonic sigma weight residual 180.00 122.97 57.03 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA GLN A 417 " pdb=" C GLN A 417 " pdb=" N LYS A 418 " pdb=" CA LYS A 418 " ideal model delta harmonic sigma weight residual 180.00 126.51 53.49 0 5.00e+00 4.00e-02 1.14e+02 ... (remaining 14829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.304: 3687 0.304 - 0.607: 11 0.607 - 0.911: 4 0.911 - 1.215: 0 1.215 - 1.518: 2 Chirality restraints: 3704 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN D 378 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.88 -1.52 2.00e-01 2.50e+01 5.76e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 378 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.08 -1.32 2.00e-01 2.50e+01 4.38e+01 chirality pdb=" C1 NAG A1003 " pdb=" ND2 ASN A 73 " pdb=" C2 NAG A1003 " pdb=" O5 NAG A1003 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.16e+01 ... (remaining 3701 not shown) Planarity restraints: 3890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 227 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.63e+01 pdb=" C ILE C 227 " 0.070 2.00e-02 2.50e+03 pdb=" O ILE C 227 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE C 228 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 227 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C ILE A 227 " -0.070 2.00e-02 2.50e+03 pdb=" O ILE A 227 " 0.026 2.00e-02 2.50e+03 pdb=" N PHE A 228 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 255 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C ILE C 255 " 0.067 2.00e-02 2.50e+03 pdb=" O ILE C 255 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE C 256 " -0.022 2.00e-02 2.50e+03 ... (remaining 3887 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5849 2.80 - 3.32: 20074 3.32 - 3.85: 36877 3.85 - 4.37: 43213 4.37 - 4.90: 73151 Nonbonded interactions: 179164 Sorted by model distance: nonbonded pdb=" OE1 GLU C 53 " pdb=" OG SER C 110 " model vdw 2.270 3.040 nonbonded pdb=" OE1 GLU A 53 " pdb=" OG SER A 110 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR D 443 " pdb=" OG1 THR D 740 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR B 443 " pdb=" OG1 THR B 740 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR C 251 " pdb=" OD1 ASP C 511 " model vdw 2.294 3.040 ... (remaining 179159 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 470 or resid 472 through 534 or resid 536 throu \ gh 1003)) selection = (chain 'B' and (resid 34 through 470 or resid 472 through 534 or resid 536 throu \ gh 1003)) selection = (chain 'C' and (resid 34 through 470 or resid 472 through 534 or resid 536 throu \ gh 1003)) selection = (chain 'D' and (resid 34 through 470 or resid 472 through 534 or resid 536 throu \ gh 1003)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'I' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 25.440 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 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 : 0.008 0.168 23222 Z= 0.372 Angle : 1.380 19.318 31536 Z= 0.737 Chirality : 0.076 1.518 3704 Planarity : 0.007 0.086 3858 Dihedral : 20.143 120.990 9710 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.04 % Favored : 90.59 % Rotamer: Outliers : 0.76 % Allowed : 4.70 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.38 % 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 aren not related in a simple way. whole: -5.67 (0.12), residues: 2704 helix: -4.30 (0.07), residues: 1052 sheet: -4.07 (0.19), residues: 398 loop : -3.02 (0.15), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 712 TYR 0.038 0.003 TYR B 86 PHE 0.037 0.003 PHE B 228 TRP 0.032 0.003 TRP D 134 HIS 0.018 0.002 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00764 (23146) covalent geometry : angle 1.29598 (31314) SS BOND : bond 0.00379 ( 6) SS BOND : angle 0.89152 ( 12) hydrogen bonds : bond 0.30483 ( 712) hydrogen bonds : angle 9.72799 ( 2044) link_ALPHA1-3 : bond 0.01140 ( 6) link_ALPHA1-3 : angle 2.71560 ( 18) link_ALPHA1-6 : bond 0.01801 ( 6) link_ALPHA1-6 : angle 3.39951 ( 18) link_BETA1-4 : bond 0.01816 ( 26) link_BETA1-4 : angle 5.94025 ( 78) link_NAG-ASN : bond 0.01068 ( 32) link_NAG-ASN : angle 6.72667 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 506 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 TYR cc_start: 0.6659 (m-80) cc_final: 0.6226 (m-80) REVERT: A 140 ASP cc_start: 0.7674 (m-30) cc_final: 0.7018 (m-30) REVERT: A 185 LEU cc_start: 0.8727 (mt) cc_final: 0.8415 (mp) REVERT: A 312 LEU cc_start: 0.8109 (mt) cc_final: 0.7459 (mt) REVERT: A 651 TYR cc_start: 0.7433 (t80) cc_final: 0.6867 (t80) REVERT: A 655 LEU cc_start: 0.9062 (tp) cc_final: 0.8697 (mm) REVERT: A 672 ASP cc_start: 0.7831 (t0) cc_final: 0.6954 (p0) REVERT: B 316 MET cc_start: 0.8997 (ttt) cc_final: 0.8625 (ttm) REVERT: B 323 MET cc_start: 0.8500 (tpp) cc_final: 0.8297 (tpt) REVERT: B 484 GLU cc_start: 0.6089 (mp0) cc_final: 0.5396 (pm20) REVERT: B 534 MET cc_start: 0.6959 (ttp) cc_final: 0.6650 (ttm) REVERT: B 677 GLN cc_start: 0.7960 (tp40) cc_final: 0.7552 (pp30) REVERT: B 702 TYR cc_start: 0.7708 (m-10) cc_final: 0.7484 (m-10) REVERT: B 703 ASP cc_start: 0.7541 (t70) cc_final: 0.7258 (m-30) REVERT: B 709 MET cc_start: 0.8735 (mtm) cc_final: 0.8508 (mtp) REVERT: B 770 MET cc_start: 0.7608 (tmt) cc_final: 0.7289 (tmm) REVERT: B 794 MET cc_start: 0.5702 (ptp) cc_final: 0.4830 (ptm) REVERT: C 130 ILE cc_start: 0.9078 (mt) cc_final: 0.8805 (mp) REVERT: C 154 SER cc_start: 0.8473 (p) cc_final: 0.8057 (p) REVERT: C 170 LYS cc_start: 0.8738 (mttm) cc_final: 0.8524 (mtmm) REVERT: C 312 LEU cc_start: 0.7812 (mt) cc_final: 0.7355 (mt) REVERT: C 331 SER cc_start: 0.8912 (m) cc_final: 0.8565 (p) REVERT: C 402 ILE cc_start: 0.8205 (tt) cc_final: 0.7859 (tp) REVERT: C 501 MET cc_start: 0.7118 (mtm) cc_final: 0.6904 (mtp) REVERT: C 645 LEU cc_start: 0.8012 (tp) cc_final: 0.7612 (mt) REVERT: C 651 TYR cc_start: 0.6667 (t80) cc_final: 0.6297 (t80) REVERT: C 723 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7620 (tt0) REVERT: C 737 MET cc_start: 0.8497 (mtp) cc_final: 0.8053 (mtp) REVERT: C 792 HIS cc_start: 0.8144 (m170) cc_final: 0.7622 (m170) REVERT: D 86 TYR cc_start: 0.7111 (m-10) cc_final: 0.6900 (m-80) REVERT: D 251 TYR cc_start: 0.8079 (m-80) cc_final: 0.7865 (m-10) REVERT: D 501 MET cc_start: 0.7338 (mtt) cc_final: 0.6927 (mmt) REVERT: D 534 MET cc_start: 0.6348 (ttp) cc_final: 0.5901 (ptm) REVERT: D 544 LYS cc_start: 0.7509 (tmtt) cc_final: 0.7234 (tmtt) REVERT: D 665 GLU cc_start: 0.7903 (tt0) cc_final: 0.7438 (tm-30) REVERT: D 666 SER cc_start: 0.8774 (m) cc_final: 0.8381 (t) REVERT: D 677 GLN cc_start: 0.7743 (tp40) cc_final: 0.7398 (pp30) REVERT: D 687 ASP cc_start: 0.6397 (m-30) cc_final: 0.6057 (m-30) REVERT: D 702 TYR cc_start: 0.7834 (m-10) cc_final: 0.7561 (m-10) REVERT: D 794 MET cc_start: 0.5402 (ptp) cc_final: 0.3566 (ttp) outliers start: 10 outliers final: 1 residues processed: 516 average time/residue: 0.1963 time to fit residues: 148.9533 Evaluate side-chains 275 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS A 123 ASN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 283 ASN A 350 HIS A 367 HIS A 456 ASN A 749 ASN A 792 HIS B 98 GLN B 336 GLN B 381 ASN B 677 GLN B 714 GLN C 98 GLN C 129 HIS C 141 ASN C 283 ASN C 456 ASN ** C 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN D 350 HIS D 381 ASN D 677 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.141720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.102487 restraints weight = 97769.543| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 5.19 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23222 Z= 0.171 Angle : 0.941 11.706 31536 Z= 0.430 Chirality : 0.055 0.574 3704 Planarity : 0.006 0.071 3858 Dihedral : 20.240 116.900 4456 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.67 % Favored : 91.19 % Rotamer: Outliers : 2.22 % Allowed : 10.36 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -4.08 (0.14), residues: 2704 helix: -2.25 (0.12), residues: 1100 sheet: -3.74 (0.22), residues: 380 loop : -2.68 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 481 TYR 0.025 0.002 TYR D 774 PHE 0.022 0.002 PHE B 446 TRP 0.038 0.002 TRP D 798 HIS 0.007 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00374 (23146) covalent geometry : angle 0.88820 (31314) SS BOND : bond 0.00479 ( 6) SS BOND : angle 1.72622 ( 12) hydrogen bonds : bond 0.04691 ( 712) hydrogen bonds : angle 5.23601 ( 2044) link_ALPHA1-3 : bond 0.01733 ( 6) link_ALPHA1-3 : angle 2.74088 ( 18) link_ALPHA1-6 : bond 0.01695 ( 6) link_ALPHA1-6 : angle 3.26905 ( 18) link_BETA1-4 : bond 0.01081 ( 26) link_BETA1-4 : angle 4.02009 ( 78) link_NAG-ASN : bond 0.00774 ( 32) link_NAG-ASN : angle 4.11618 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 324 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8618 (mm) cc_final: 0.8354 (mt) REVERT: A 342 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8108 (m) REVERT: A 465 ASP cc_start: 0.8349 (t70) cc_final: 0.8028 (t0) REVERT: A 651 TYR cc_start: 0.7192 (t80) cc_final: 0.6816 (t80) REVERT: A 655 LEU cc_start: 0.9100 (tp) cc_final: 0.8854 (mm) REVERT: A 672 ASP cc_start: 0.7615 (t0) cc_final: 0.7065 (p0) REVERT: A 784 GLN cc_start: 0.8241 (mt0) cc_final: 0.7995 (mt0) REVERT: B 316 MET cc_start: 0.9075 (ttt) cc_final: 0.8595 (ttm) REVERT: B 319 ASP cc_start: 0.7835 (t0) cc_final: 0.7605 (t0) REVERT: B 703 ASP cc_start: 0.7591 (t70) cc_final: 0.7275 (m-30) REVERT: C 481 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7819 (mmt90) REVERT: C 517 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8285 (tt) REVERT: C 651 TYR cc_start: 0.6904 (t80) cc_final: 0.6437 (t80) REVERT: C 655 LEU cc_start: 0.8510 (tt) cc_final: 0.8054 (mm) REVERT: C 723 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7696 (tt0) REVERT: D 447 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6962 (ttmm) REVERT: D 501 MET cc_start: 0.7597 (mtt) cc_final: 0.7003 (mmp) REVERT: D 666 SER cc_start: 0.8696 (m) cc_final: 0.8399 (t) REVERT: D 691 MET cc_start: 0.8181 (ppp) cc_final: 0.7958 (tmm) REVERT: D 696 LYS cc_start: 0.8950 (mtpt) cc_final: 0.8513 (pttm) REVERT: D 774 TYR cc_start: 0.5652 (t80) cc_final: 0.5303 (t80) REVERT: D 790 LYS cc_start: 0.7963 (mmtt) cc_final: 0.6652 (mmtt) outliers start: 45 outliers final: 17 residues processed: 353 average time/residue: 0.1582 time to fit residues: 88.6385 Evaluate side-chains 276 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 256 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 367 HIS Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 447 LYS Chi-restraints excluded: chain D residue 679 LYS Chi-restraints excluded: chain D residue 758 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 94 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 104 optimal weight: 0.4980 chunk 42 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 111 HIS A 129 HIS A 350 HIS A 495 ASN B 196 ASN C 141 ASN C 495 ASN D 111 HIS D 350 HIS D 721 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.140477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.100157 restraints weight = 90134.823| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 4.97 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23222 Z= 0.166 Angle : 0.878 14.432 31536 Z= 0.395 Chirality : 0.052 0.488 3704 Planarity : 0.005 0.069 3858 Dihedral : 17.327 112.347 4456 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.74 % Favored : 91.11 % Rotamer: Outliers : 1.93 % Allowed : 12.16 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -3.27 (0.15), residues: 2704 helix: -1.24 (0.14), residues: 1108 sheet: -3.55 (0.22), residues: 402 loop : -2.48 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 354 TYR 0.018 0.002 TYR B 462 PHE 0.018 0.002 PHE D 359 TRP 0.021 0.002 TRP D 798 HIS 0.015 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00369 (23146) covalent geometry : angle 0.82813 (31314) SS BOND : bond 0.00958 ( 6) SS BOND : angle 1.25785 ( 12) hydrogen bonds : bond 0.04133 ( 712) hydrogen bonds : angle 4.84560 ( 2044) link_ALPHA1-3 : bond 0.01822 ( 6) link_ALPHA1-3 : angle 2.70556 ( 18) link_ALPHA1-6 : bond 0.02017 ( 6) link_ALPHA1-6 : angle 3.40299 ( 18) link_BETA1-4 : bond 0.00945 ( 26) link_BETA1-4 : angle 3.75989 ( 78) link_NAG-ASN : bond 0.00712 ( 32) link_NAG-ASN : angle 3.78735 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8080 (m) REVERT: A 651 TYR cc_start: 0.7214 (t80) cc_final: 0.6763 (t80) REVERT: A 655 LEU cc_start: 0.9120 (tp) cc_final: 0.8828 (mm) REVERT: A 672 ASP cc_start: 0.7709 (t0) cc_final: 0.7153 (p0) REVERT: B 316 MET cc_start: 0.9084 (ttt) cc_final: 0.8526 (ttm) REVERT: B 541 LEU cc_start: 0.8446 (tt) cc_final: 0.8205 (tp) REVERT: C 210 ASP cc_start: 0.7710 (t0) cc_final: 0.7469 (m-30) REVERT: C 645 LEU cc_start: 0.8112 (tp) cc_final: 0.7837 (mt) REVERT: C 651 TYR cc_start: 0.6724 (t80) cc_final: 0.6210 (t80) REVERT: C 655 LEU cc_start: 0.8572 (tt) cc_final: 0.8066 (mm) REVERT: C 682 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.7527 (m-10) REVERT: C 723 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7634 (tt0) REVERT: D 447 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.6974 (ttmm) REVERT: D 501 MET cc_start: 0.7668 (mtt) cc_final: 0.7036 (mmp) REVERT: D 666 SER cc_start: 0.8640 (m) cc_final: 0.8427 (t) REVERT: D 691 MET cc_start: 0.8147 (ppp) cc_final: 0.7862 (tmm) REVERT: D 696 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8552 (pttt) REVERT: D 787 GLU cc_start: 0.6509 (mm-30) cc_final: 0.5701 (pp20) REVERT: D 794 MET cc_start: 0.5581 (ttp) cc_final: 0.5268 (ttp) outliers start: 38 outliers final: 20 residues processed: 303 average time/residue: 0.1469 time to fit residues: 72.3557 Evaluate side-chains 269 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 682 TYR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 447 LYS Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 758 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 258 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 350 HIS D 350 HIS D 714 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.136035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096304 restraints weight = 80824.985| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 4.46 r_work: 0.2990 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 23222 Z= 0.256 Angle : 0.909 14.459 31536 Z= 0.414 Chirality : 0.053 0.445 3704 Planarity : 0.005 0.066 3858 Dihedral : 15.510 108.358 4456 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.89 % Favored : 89.96 % Rotamer: Outliers : 2.39 % Allowed : 13.51 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.23 % 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 aren not related in a simple way. whole: -2.80 (0.16), residues: 2704 helix: -0.71 (0.15), residues: 1084 sheet: -3.47 (0.22), residues: 406 loop : -2.27 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 58 TYR 0.027 0.002 TYR D 252 PHE 0.029 0.002 PHE B 446 TRP 0.025 0.002 TRP D 353 HIS 0.041 0.002 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00599 (23146) covalent geometry : angle 0.86458 (31314) SS BOND : bond 0.00646 ( 6) SS BOND : angle 1.19245 ( 12) hydrogen bonds : bond 0.04009 ( 712) hydrogen bonds : angle 4.76249 ( 2044) link_ALPHA1-3 : bond 0.02000 ( 6) link_ALPHA1-3 : angle 2.68718 ( 18) link_ALPHA1-6 : bond 0.01907 ( 6) link_ALPHA1-6 : angle 2.80930 ( 18) link_BETA1-4 : bond 0.00870 ( 26) link_BETA1-4 : angle 3.64468 ( 78) link_NAG-ASN : bond 0.00631 ( 32) link_NAG-ASN : angle 3.69833 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 260 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 TYR cc_start: 0.6836 (m-80) cc_final: 0.6561 (m-80) REVERT: A 315 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7094 (t80) REVERT: A 342 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8236 (m) REVERT: A 651 TYR cc_start: 0.7466 (t80) cc_final: 0.6849 (t80) REVERT: A 655 LEU cc_start: 0.9220 (tp) cc_final: 0.8879 (mm) REVERT: B 316 MET cc_start: 0.9074 (ttt) cc_final: 0.8863 (ttt) REVERT: B 323 MET cc_start: 0.9190 (tpt) cc_final: 0.8793 (tpt) REVERT: B 541 LEU cc_start: 0.8685 (tt) cc_final: 0.8392 (tp) REVERT: B 735 PHE cc_start: 0.8561 (t80) cc_final: 0.8152 (t80) REVERT: B 737 MET cc_start: 0.8356 (ptp) cc_final: 0.7442 (pmm) REVERT: B 792 HIS cc_start: 0.6015 (p-80) cc_final: 0.5333 (p90) REVERT: B 793 MET cc_start: 0.8521 (tpp) cc_final: 0.8281 (tmm) REVERT: C 43 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7705 (tm-30) REVERT: C 517 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8593 (tt) REVERT: C 645 LEU cc_start: 0.8049 (tp) cc_final: 0.7749 (mt) REVERT: C 651 TYR cc_start: 0.6943 (t80) cc_final: 0.6464 (t80) REVERT: C 655 LEU cc_start: 0.8844 (tt) cc_final: 0.8250 (mm) REVERT: C 682 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7741 (m-10) REVERT: C 723 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7904 (tt0) REVERT: D 501 MET cc_start: 0.7783 (mtt) cc_final: 0.7071 (mmp) REVERT: D 666 SER cc_start: 0.8675 (m) cc_final: 0.8339 (t) REVERT: D 691 MET cc_start: 0.8247 (ppp) cc_final: 0.7877 (tmm) REVERT: D 696 LYS cc_start: 0.9083 (mtpt) cc_final: 0.8576 (pttt) REVERT: D 787 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6036 (pp20) REVERT: D 794 MET cc_start: 0.5813 (ttp) cc_final: 0.4076 (ttp) outliers start: 49 outliers final: 28 residues processed: 291 average time/residue: 0.1513 time to fit residues: 71.2980 Evaluate side-chains 271 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 682 TYR Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 679 LYS Chi-restraints excluded: chain D residue 758 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 37 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 178 optimal weight: 0.1980 chunk 140 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 220 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS A 350 HIS A 497 GLN B 196 ASN B 328 HIS B 350 HIS D 350 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.139492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100738 restraints weight = 80970.616| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.66 r_work: 0.3049 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23222 Z= 0.142 Angle : 0.819 12.749 31536 Z= 0.367 Chirality : 0.049 0.407 3704 Planarity : 0.005 0.064 3858 Dihedral : 14.542 106.746 4454 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.19 % Favored : 91.63 % Rotamer: Outliers : 1.97 % Allowed : 14.51 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -2.42 (0.16), residues: 2704 helix: -0.30 (0.16), residues: 1088 sheet: -3.38 (0.23), residues: 408 loop : -2.11 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 800 TYR 0.029 0.001 TYR B 86 PHE 0.019 0.002 PHE B 446 TRP 0.022 0.001 TRP C 640 HIS 0.007 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00313 (23146) covalent geometry : angle 0.77418 (31314) SS BOND : bond 0.00421 ( 6) SS BOND : angle 1.34400 ( 12) hydrogen bonds : bond 0.03291 ( 712) hydrogen bonds : angle 4.43814 ( 2044) link_ALPHA1-3 : bond 0.01889 ( 6) link_ALPHA1-3 : angle 2.68579 ( 18) link_ALPHA1-6 : bond 0.01874 ( 6) link_ALPHA1-6 : angle 2.75560 ( 18) link_BETA1-4 : bond 0.00849 ( 26) link_BETA1-4 : angle 3.42131 ( 78) link_NAG-ASN : bond 0.00728 ( 32) link_NAG-ASN : angle 3.48609 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 262 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.8288 (t0) cc_final: 0.7490 (t70) REVERT: A 82 LYS cc_start: 0.7516 (tttp) cc_final: 0.7188 (tptm) REVERT: A 86 TYR cc_start: 0.6932 (m-80) cc_final: 0.6515 (m-80) REVERT: A 298 MET cc_start: 0.8729 (ptp) cc_final: 0.8290 (ppp) REVERT: A 315 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7250 (t80) REVERT: A 342 VAL cc_start: 0.8374 (OUTLIER) cc_final: 0.8126 (m) REVERT: A 508 HIS cc_start: 0.7799 (OUTLIER) cc_final: 0.7029 (m90) REVERT: A 651 TYR cc_start: 0.7478 (t80) cc_final: 0.6846 (t80) REVERT: A 655 LEU cc_start: 0.9198 (tp) cc_final: 0.8821 (mm) REVERT: B 316 MET cc_start: 0.9090 (ttt) cc_final: 0.8882 (ttt) REVERT: B 323 MET cc_start: 0.9162 (tpt) cc_final: 0.8849 (tpt) REVERT: B 665 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6758 (tm-30) REVERT: B 702 TYR cc_start: 0.8454 (m-10) cc_final: 0.8108 (m-10) REVERT: B 735 PHE cc_start: 0.8248 (t80) cc_final: 0.7995 (t80) REVERT: B 737 MET cc_start: 0.8517 (ptp) cc_final: 0.7952 (pmm) REVERT: B 790 LYS cc_start: 0.9048 (mmtt) cc_final: 0.8483 (tptp) REVERT: B 793 MET cc_start: 0.8634 (tpp) cc_final: 0.8229 (mtp) REVERT: C 43 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7510 (tm-30) REVERT: C 70 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8339 (tt) REVERT: C 79 ASP cc_start: 0.8246 (t0) cc_final: 0.7562 (t70) REVERT: C 517 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8494 (tt) REVERT: C 655 LEU cc_start: 0.8942 (tt) cc_final: 0.8491 (mm) REVERT: C 674 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8084 (tp) REVERT: C 682 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.7748 (m-10) REVERT: C 723 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7717 (tt0) REVERT: D 501 MET cc_start: 0.7845 (mtt) cc_final: 0.7054 (mmp) REVERT: D 529 PHE cc_start: 0.5408 (p90) cc_final: 0.5119 (p90) REVERT: D 666 SER cc_start: 0.8624 (m) cc_final: 0.8315 (t) REVERT: D 691 MET cc_start: 0.8202 (ppp) cc_final: 0.7843 (tmm) REVERT: D 696 LYS cc_start: 0.9060 (mtpt) cc_final: 0.8576 (pttt) REVERT: D 787 GLU cc_start: 0.6907 (mm-30) cc_final: 0.5860 (pp20) REVERT: D 790 LYS cc_start: 0.8684 (mmtt) cc_final: 0.7944 (mmtt) outliers start: 39 outliers final: 17 residues processed: 289 average time/residue: 0.1433 time to fit residues: 67.1323 Evaluate side-chains 276 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 682 TYR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 758 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 54 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 chunk 143 optimal weight: 0.5980 chunk 17 optimal weight: 0.0870 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS B 350 HIS D 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.138480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.099565 restraints weight = 84170.713| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 4.81 r_work: 0.3020 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23222 Z= 0.164 Angle : 0.804 10.379 31536 Z= 0.363 Chirality : 0.049 0.401 3704 Planarity : 0.004 0.061 3858 Dihedral : 13.765 105.863 4454 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.81 % Favored : 91.04 % Rotamer: Outliers : 2.22 % Allowed : 14.60 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -2.28 (0.16), residues: 2704 helix: -0.15 (0.16), residues: 1092 sheet: -3.26 (0.23), residues: 410 loop : -2.10 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 349 TYR 0.018 0.001 TYR B 86 PHE 0.021 0.002 PHE C 228 TRP 0.024 0.001 TRP C 640 HIS 0.031 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00375 (23146) covalent geometry : angle 0.76078 (31314) SS BOND : bond 0.00492 ( 6) SS BOND : angle 0.71874 ( 12) hydrogen bonds : bond 0.03366 ( 712) hydrogen bonds : angle 4.39009 ( 2044) link_ALPHA1-3 : bond 0.01966 ( 6) link_ALPHA1-3 : angle 2.76466 ( 18) link_ALPHA1-6 : bond 0.01960 ( 6) link_ALPHA1-6 : angle 2.84359 ( 18) link_BETA1-4 : bond 0.00837 ( 26) link_BETA1-4 : angle 3.37841 ( 78) link_NAG-ASN : bond 0.00666 ( 32) link_NAG-ASN : angle 3.34238 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7656 (tttp) cc_final: 0.7191 (tptm) REVERT: A 86 TYR cc_start: 0.7054 (m-80) cc_final: 0.5614 (m-80) REVERT: A 298 MET cc_start: 0.8766 (ptp) cc_final: 0.8320 (ppp) REVERT: A 315 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7345 (t80) REVERT: A 342 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8172 (m) REVERT: A 508 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7031 (m90) REVERT: A 651 TYR cc_start: 0.7474 (t80) cc_final: 0.6825 (t80) REVERT: A 655 LEU cc_start: 0.9197 (tp) cc_final: 0.8819 (mm) REVERT: B 316 MET cc_start: 0.9077 (ttt) cc_final: 0.8861 (ttt) REVERT: B 323 MET cc_start: 0.9213 (tpt) cc_final: 0.8938 (tpt) REVERT: B 665 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6822 (tm-30) REVERT: B 666 SER cc_start: 0.8614 (m) cc_final: 0.8317 (p) REVERT: B 702 TYR cc_start: 0.8448 (m-10) cc_final: 0.8137 (m-10) REVERT: B 735 PHE cc_start: 0.8195 (t80) cc_final: 0.7952 (t80) REVERT: B 737 MET cc_start: 0.8454 (ptp) cc_final: 0.7977 (pmm) REVERT: B 793 MET cc_start: 0.8563 (tpp) cc_final: 0.8217 (tmm) REVERT: C 79 ASP cc_start: 0.8120 (t0) cc_final: 0.7094 (t70) REVERT: C 517 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8515 (tt) REVERT: C 655 LEU cc_start: 0.9011 (tt) cc_final: 0.8543 (mm) REVERT: C 669 ASP cc_start: 0.8230 (t70) cc_final: 0.8003 (t0) REVERT: C 674 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8060 (tp) REVERT: C 682 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7722 (m-10) REVERT: C 723 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7741 (tt0) REVERT: D 319 ASP cc_start: 0.8413 (t0) cc_final: 0.7623 (t0) REVERT: D 501 MET cc_start: 0.7862 (mtt) cc_final: 0.7044 (mmt) REVERT: D 529 PHE cc_start: 0.5419 (p90) cc_final: 0.5177 (p90) REVERT: D 666 SER cc_start: 0.8657 (m) cc_final: 0.8322 (t) REVERT: D 691 MET cc_start: 0.8228 (ppp) cc_final: 0.7840 (tmm) REVERT: D 696 LYS cc_start: 0.9053 (mtpt) cc_final: 0.8583 (pttt) REVERT: D 787 GLU cc_start: 0.6985 (mm-30) cc_final: 0.6037 (pp20) outliers start: 45 outliers final: 22 residues processed: 285 average time/residue: 0.1353 time to fit residues: 62.4449 Evaluate side-chains 265 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 682 TYR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 794 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 170 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS B 136 HIS B 196 ASN B 350 HIS D 196 ASN D 328 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.134723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.093847 restraints weight = 78110.456| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 4.30 r_work: 0.2998 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 23222 Z= 0.251 Angle : 0.866 10.484 31536 Z= 0.395 Chirality : 0.052 0.394 3704 Planarity : 0.005 0.059 3858 Dihedral : 13.039 106.485 4454 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.19 % Favored : 89.67 % Rotamer: Outliers : 2.27 % Allowed : 14.97 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -2.29 (0.16), residues: 2704 helix: -0.15 (0.16), residues: 1090 sheet: -3.19 (0.23), residues: 408 loop : -2.15 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 800 TYR 0.030 0.002 TYR B 252 PHE 0.020 0.002 PHE D 446 TRP 0.028 0.002 TRP C 640 HIS 0.009 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00590 (23146) covalent geometry : angle 0.82673 (31314) SS BOND : bond 0.00261 ( 6) SS BOND : angle 0.54774 ( 12) hydrogen bonds : bond 0.03737 ( 712) hydrogen bonds : angle 4.54946 ( 2044) link_ALPHA1-3 : bond 0.01988 ( 6) link_ALPHA1-3 : angle 2.74232 ( 18) link_ALPHA1-6 : bond 0.02215 ( 6) link_ALPHA1-6 : angle 3.06699 ( 18) link_BETA1-4 : bond 0.00834 ( 26) link_BETA1-4 : angle 3.30732 ( 78) link_NAG-ASN : bond 0.00621 ( 32) link_NAG-ASN : angle 3.34750 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7519 (tttp) cc_final: 0.7182 (tptm) REVERT: A 86 TYR cc_start: 0.6939 (m-80) cc_final: 0.6542 (m-80) REVERT: A 298 MET cc_start: 0.8515 (ptp) cc_final: 0.8235 (ppp) REVERT: A 315 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7515 (t80) REVERT: A 508 HIS cc_start: 0.8186 (OUTLIER) cc_final: 0.7581 (m90) REVERT: A 651 TYR cc_start: 0.7565 (t80) cc_final: 0.6931 (t80) REVERT: A 655 LEU cc_start: 0.9223 (tp) cc_final: 0.8881 (mm) REVERT: A 674 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8540 (tp) REVERT: B 86 TYR cc_start: 0.7758 (m-80) cc_final: 0.7267 (m-80) REVERT: B 316 MET cc_start: 0.9010 (ttt) cc_final: 0.8809 (ttt) REVERT: B 665 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6772 (tm-30) REVERT: B 666 SER cc_start: 0.8660 (m) cc_final: 0.8328 (t) REVERT: B 735 PHE cc_start: 0.8317 (t80) cc_final: 0.8037 (t80) REVERT: B 737 MET cc_start: 0.8532 (ptp) cc_final: 0.8036 (pmm) REVERT: B 793 MET cc_start: 0.8498 (tpp) cc_final: 0.8138 (tmm) REVERT: C 508 HIS cc_start: 0.8156 (OUTLIER) cc_final: 0.7611 (m90) REVERT: C 517 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8528 (tt) REVERT: C 655 LEU cc_start: 0.9073 (tt) cc_final: 0.8605 (mm) REVERT: C 669 ASP cc_start: 0.8250 (t70) cc_final: 0.8014 (t0) REVERT: C 674 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8301 (tp) REVERT: C 682 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7819 (m-10) REVERT: C 723 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7851 (tt0) REVERT: D 501 MET cc_start: 0.7800 (mtt) cc_final: 0.7001 (mmp) REVERT: D 666 SER cc_start: 0.8770 (m) cc_final: 0.8430 (t) REVERT: D 691 MET cc_start: 0.8318 (ppp) cc_final: 0.7921 (tmm) REVERT: D 696 LYS cc_start: 0.9021 (mtpt) cc_final: 0.8565 (pttt) REVERT: D 787 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6694 (pp20) outliers start: 46 outliers final: 25 residues processed: 272 average time/residue: 0.1501 time to fit residues: 66.2109 Evaluate side-chains 266 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 682 TYR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 794 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 17 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 250 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 195 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 222 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS B 350 HIS D 196 ASN D 350 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.137453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.096737 restraints weight = 75906.633| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 4.33 r_work: 0.3042 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23222 Z= 0.157 Angle : 0.794 10.295 31536 Z= 0.359 Chirality : 0.048 0.385 3704 Planarity : 0.004 0.059 3858 Dihedral : 12.429 105.855 4454 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.78 % Favored : 91.15 % Rotamer: Outliers : 1.97 % Allowed : 15.60 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -2.07 (0.16), residues: 2704 helix: 0.08 (0.16), residues: 1094 sheet: -3.13 (0.23), residues: 422 loop : -2.04 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 800 TYR 0.022 0.001 TYR D 764 PHE 0.019 0.002 PHE C 228 TRP 0.028 0.001 TRP C 640 HIS 0.004 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00356 (23146) covalent geometry : angle 0.75439 (31314) SS BOND : bond 0.00240 ( 6) SS BOND : angle 0.48885 ( 12) hydrogen bonds : bond 0.03278 ( 712) hydrogen bonds : angle 4.33375 ( 2044) link_ALPHA1-3 : bond 0.02028 ( 6) link_ALPHA1-3 : angle 2.71786 ( 18) link_ALPHA1-6 : bond 0.02339 ( 6) link_ALPHA1-6 : angle 3.00383 ( 18) link_BETA1-4 : bond 0.00845 ( 26) link_BETA1-4 : angle 3.17863 ( 78) link_NAG-ASN : bond 0.00672 ( 32) link_NAG-ASN : angle 3.19887 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 TYR cc_start: 0.6931 (m-80) cc_final: 0.6491 (m-80) REVERT: A 315 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7437 (t80) REVERT: A 342 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8216 (m) REVERT: A 508 HIS cc_start: 0.7765 (OUTLIER) cc_final: 0.7045 (m90) REVERT: A 651 TYR cc_start: 0.7465 (t80) cc_final: 0.6775 (t80) REVERT: A 655 LEU cc_start: 0.9190 (tp) cc_final: 0.8812 (mm) REVERT: B 665 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6731 (tm-30) REVERT: B 666 SER cc_start: 0.8634 (m) cc_final: 0.8306 (t) REVERT: B 691 MET cc_start: 0.8076 (ppp) cc_final: 0.7703 (tmm) REVERT: B 702 TYR cc_start: 0.8481 (m-10) cc_final: 0.8170 (m-10) REVERT: B 735 PHE cc_start: 0.8119 (t80) cc_final: 0.7817 (t80) REVERT: B 737 MET cc_start: 0.8499 (ptp) cc_final: 0.8068 (pmm) REVERT: B 793 MET cc_start: 0.8518 (tpp) cc_final: 0.8179 (tmm) REVERT: C 185 LEU cc_start: 0.8901 (mt) cc_final: 0.8487 (mp) REVERT: C 508 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.7069 (m90) REVERT: C 517 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8516 (tt) REVERT: C 655 LEU cc_start: 0.9050 (tt) cc_final: 0.8591 (mm) REVERT: C 669 ASP cc_start: 0.8188 (t70) cc_final: 0.7969 (t0) REVERT: C 674 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8008 (tp) REVERT: C 682 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7629 (m-10) REVERT: C 723 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7822 (tt0) REVERT: C 794 MET cc_start: 0.7237 (mtm) cc_final: 0.7017 (mtm) REVERT: D 501 MET cc_start: 0.7804 (mtt) cc_final: 0.7013 (mmp) REVERT: D 666 SER cc_start: 0.8734 (m) cc_final: 0.8385 (t) REVERT: D 691 MET cc_start: 0.8245 (ppp) cc_final: 0.7889 (tmm) REVERT: D 696 LYS cc_start: 0.9009 (mtpt) cc_final: 0.8554 (pttt) REVERT: D 737 MET cc_start: 0.8175 (ptt) cc_final: 0.7407 (ptt) REVERT: D 787 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6422 (pp20) REVERT: D 790 LYS cc_start: 0.8352 (mmtt) cc_final: 0.8104 (mtmm) outliers start: 39 outliers final: 26 residues processed: 268 average time/residue: 0.1429 time to fit residues: 62.3149 Evaluate side-chains 271 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 682 TYR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 794 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 212 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS B 196 ASN B 350 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.138384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.098320 restraints weight = 61519.650| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.82 r_work: 0.3091 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23222 Z= 0.160 Angle : 0.803 13.621 31536 Z= 0.361 Chirality : 0.049 0.384 3704 Planarity : 0.004 0.059 3858 Dihedral : 11.934 105.471 4454 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.30 % Favored : 90.63 % Rotamer: Outliers : 2.01 % Allowed : 15.48 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -1.91 (0.16), residues: 2704 helix: 0.24 (0.16), residues: 1092 sheet: -3.04 (0.24), residues: 422 loop : -1.98 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 349 TYR 0.028 0.001 TYR B 86 PHE 0.019 0.002 PHE C 228 TRP 0.032 0.001 TRP C 640 HIS 0.010 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00366 (23146) covalent geometry : angle 0.76453 (31314) SS BOND : bond 0.00220 ( 6) SS BOND : angle 0.40526 ( 12) hydrogen bonds : bond 0.03261 ( 712) hydrogen bonds : angle 4.27474 ( 2044) link_ALPHA1-3 : bond 0.02074 ( 6) link_ALPHA1-3 : angle 2.78616 ( 18) link_ALPHA1-6 : bond 0.02403 ( 6) link_ALPHA1-6 : angle 3.06833 ( 18) link_BETA1-4 : bond 0.00850 ( 26) link_BETA1-4 : angle 3.15899 ( 78) link_NAG-ASN : bond 0.00655 ( 32) link_NAG-ASN : angle 3.16902 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7787 (p90) REVERT: A 86 TYR cc_start: 0.6975 (m-80) cc_final: 0.6566 (m-80) REVERT: A 342 VAL cc_start: 0.8364 (OUTLIER) cc_final: 0.8127 (m) REVERT: A 360 MET cc_start: 0.8771 (tpt) cc_final: 0.8439 (tpp) REVERT: A 508 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.7114 (m90) REVERT: A 651 TYR cc_start: 0.7456 (t80) cc_final: 0.6785 (t80) REVERT: A 655 LEU cc_start: 0.9177 (tp) cc_final: 0.8807 (mm) REVERT: A 664 MET cc_start: 0.8393 (tpp) cc_final: 0.8155 (mmt) REVERT: B 665 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6750 (tm-30) REVERT: B 666 SER cc_start: 0.8644 (m) cc_final: 0.8327 (t) REVERT: B 691 MET cc_start: 0.8120 (ppp) cc_final: 0.7745 (tmm) REVERT: B 735 PHE cc_start: 0.8098 (t80) cc_final: 0.7868 (t80) REVERT: B 737 MET cc_start: 0.8492 (ptp) cc_final: 0.8120 (pmm) REVERT: C 185 LEU cc_start: 0.8941 (mt) cc_final: 0.8526 (mp) REVERT: C 508 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.7141 (m90) REVERT: C 517 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8468 (tt) REVERT: C 655 LEU cc_start: 0.9025 (tt) cc_final: 0.8587 (mm) REVERT: C 669 ASP cc_start: 0.8152 (t70) cc_final: 0.7942 (t0) REVERT: C 674 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8046 (tp) REVERT: C 682 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7627 (m-10) REVERT: C 794 MET cc_start: 0.7248 (mtm) cc_final: 0.6998 (mtm) REVERT: D 501 MET cc_start: 0.7786 (mtt) cc_final: 0.6853 (mmm) REVERT: D 666 SER cc_start: 0.8748 (m) cc_final: 0.8392 (t) REVERT: D 691 MET cc_start: 0.8255 (ppp) cc_final: 0.7894 (tmm) REVERT: D 737 MET cc_start: 0.8244 (ptt) cc_final: 0.8012 (ptt) REVERT: D 787 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6383 (pp20) outliers start: 40 outliers final: 26 residues processed: 260 average time/residue: 0.1409 time to fit residues: 59.3816 Evaluate side-chains 261 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 682 TYR Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 794 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 252 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 263 optimal weight: 0.0670 chunk 90 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 HIS B 111 HIS B 350 HIS D 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.139947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.100100 restraints weight = 71601.422| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 4.21 r_work: 0.3102 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23222 Z= 0.137 Angle : 0.788 14.834 31536 Z= 0.353 Chirality : 0.048 0.375 3704 Planarity : 0.004 0.056 3858 Dihedral : 11.384 105.382 4454 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.30 % Favored : 91.63 % Rotamer: Outliers : 1.72 % Allowed : 16.02 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -1.68 (0.17), residues: 2704 helix: 0.52 (0.16), residues: 1070 sheet: -2.94 (0.24), residues: 410 loop : -1.91 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 800 TYR 0.018 0.001 TYR D 764 PHE 0.021 0.001 PHE C 228 TRP 0.034 0.001 TRP C 640 HIS 0.005 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00303 (23146) covalent geometry : angle 0.74968 (31314) SS BOND : bond 0.00206 ( 6) SS BOND : angle 0.42146 ( 12) hydrogen bonds : bond 0.03072 ( 712) hydrogen bonds : angle 4.20015 ( 2044) link_ALPHA1-3 : bond 0.02153 ( 6) link_ALPHA1-3 : angle 2.87623 ( 18) link_ALPHA1-6 : bond 0.02466 ( 6) link_ALPHA1-6 : angle 3.13102 ( 18) link_BETA1-4 : bond 0.00855 ( 26) link_BETA1-4 : angle 3.03084 ( 78) link_NAG-ASN : bond 0.00711 ( 32) link_NAG-ASN : angle 3.10114 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7803 (p90) REVERT: A 86 TYR cc_start: 0.7005 (m-80) cc_final: 0.6648 (m-80) REVERT: A 342 VAL cc_start: 0.8238 (OUTLIER) cc_final: 0.7996 (m) REVERT: A 360 MET cc_start: 0.8795 (tpt) cc_final: 0.8426 (tpp) REVERT: A 508 HIS cc_start: 0.7492 (OUTLIER) cc_final: 0.6697 (m90) REVERT: A 651 TYR cc_start: 0.7472 (t80) cc_final: 0.6729 (t80) REVERT: A 655 LEU cc_start: 0.9168 (tp) cc_final: 0.8796 (mm) REVERT: B 665 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6741 (tm-30) REVERT: B 666 SER cc_start: 0.8648 (m) cc_final: 0.8332 (t) REVERT: B 691 MET cc_start: 0.8009 (ppp) cc_final: 0.7632 (tmm) REVERT: B 702 TYR cc_start: 0.8631 (m-10) cc_final: 0.8329 (m-10) REVERT: B 737 MET cc_start: 0.8464 (ptp) cc_final: 0.8121 (pmm) REVERT: C 508 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.6646 (m90) REVERT: C 517 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8457 (tt) REVERT: C 655 LEU cc_start: 0.9042 (tt) cc_final: 0.8598 (mm) REVERT: C 794 MET cc_start: 0.7106 (mtm) cc_final: 0.6867 (mtm) REVERT: D 501 MET cc_start: 0.7826 (mtt) cc_final: 0.6886 (mmm) REVERT: D 666 SER cc_start: 0.8748 (m) cc_final: 0.8389 (t) REVERT: D 691 MET cc_start: 0.8245 (ppp) cc_final: 0.7906 (tmm) REVERT: D 737 MET cc_start: 0.8150 (ptt) cc_final: 0.7623 (ptt) REVERT: D 787 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6632 (pp20) outliers start: 33 outliers final: 24 residues processed: 260 average time/residue: 0.1361 time to fit residues: 57.9310 Evaluate side-chains 264 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 679 LYS Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 794 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 212 optimal weight: 0.9980 chunk 241 optimal weight: 9.9990 chunk 157 optimal weight: 0.5980 chunk 220 optimal weight: 4.9990 chunk 31 optimal weight: 0.0270 chunk 50 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS B 350 HIS D 350 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.139748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.097813 restraints weight = 70230.871| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 4.20 r_work: 0.3080 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23222 Z= 0.140 Angle : 0.775 15.046 31536 Z= 0.348 Chirality : 0.048 0.369 3704 Planarity : 0.004 0.056 3858 Dihedral : 11.037 105.574 4454 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.70 % Favored : 91.22 % Rotamer: Outliers : 1.59 % Allowed : 16.36 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -1.55 (0.17), residues: 2704 helix: 0.63 (0.16), residues: 1072 sheet: -2.84 (0.25), residues: 406 loop : -1.86 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 800 TYR 0.018 0.001 TYR D 764 PHE 0.022 0.001 PHE A 228 TRP 0.034 0.001 TRP C 640 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00314 (23146) covalent geometry : angle 0.73706 (31314) SS BOND : bond 0.00204 ( 6) SS BOND : angle 0.41653 ( 12) hydrogen bonds : bond 0.03060 ( 712) hydrogen bonds : angle 4.18495 ( 2044) link_ALPHA1-3 : bond 0.02184 ( 6) link_ALPHA1-3 : angle 2.88874 ( 18) link_ALPHA1-6 : bond 0.02435 ( 6) link_ALPHA1-6 : angle 3.20381 ( 18) link_BETA1-4 : bond 0.00838 ( 26) link_BETA1-4 : angle 2.96375 ( 78) link_NAG-ASN : bond 0.00697 ( 32) link_NAG-ASN : angle 3.08355 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5875.05 seconds wall clock time: 101 minutes 38.44 seconds (6098.44 seconds total)