Starting phenix.real_space_refine on Thu Jun 19 16:35:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b38_44131/06_2025/9b38_44131.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b38_44131/06_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_44131/06_2025/9b38_44131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b38_44131/06_2025/9b38_44131.map" model { file = "/net/cci-nas-00/data/ceres_data/9b38_44131/06_2025/9b38_44131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b38_44131/06_2025/9b38_44131.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.78, per 1000 atoms: 0.78 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: 6.50 Conformation dependent library (CDL) restraints added in 4.2 seconds 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: 2.41 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: 6.79 Time building geometry restraints manager: 7.55 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 805 or resid 1001 or resid 1002 through 1003)) selection = (chain 'B' and (resid 34 through 470 or resid 472 through 534 or resid 536 throu \ gh 805 or resid 1001 or resid 1002 through 1003)) selection = (chain 'C' and (resid 34 through 470 or resid 472 through 534 or resid 536 throu \ gh 805 or resid 1001 or resid 1002 through 1003)) selection = (chain 'D' and (resid 34 through 470 or resid 472 through 534 or resid 536 throu \ gh 805 or resid 1001 or resid 1002 through 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: 1.200 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: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.210 Process input model: 57.260 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.160 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.190 ------------------------------------------------------------------------------- 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 : 4.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.032 0.003 TRP D 134 HIS 0.018 0.002 HIS B 253 PHE 0.037 0.003 PHE B 228 TYR 0.038 0.003 TYR B 86 ARG 0.011 0.001 ARG D 712 Details of bonding type rmsd link_NAG-ASN : bond 0.01068 ( 32) link_NAG-ASN : angle 6.72667 ( 96) 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_ALPHA1-3 : bond 0.01140 ( 6) link_ALPHA1-3 : angle 2.71560 ( 18) hydrogen bonds : bond 0.30483 ( 712) hydrogen bonds : angle 9.72799 ( 2044) SS BOND : bond 0.00379 ( 6) SS BOND : angle 0.89152 ( 12) covalent geometry : bond 0.00764 (23146) covalent geometry : angle 1.29598 (31314) *********************** 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 : 2.392 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: 0.4218 time to fit residues: 320.5037 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 : 2.632 ------------------------------------------------------------------------------- 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 226 optimal weight: 0.7980 chunk 203 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 243 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 381 ASN B 677 GLN B 714 GLN C 98 GLN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.141086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.100942 restraints weight = 80113.788| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.72 r_work: 0.3080 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2573 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= 0.180 Angle : 0.950 11.786 31536 Z= 0.435 Chirality : 0.055 0.594 3704 Planarity : 0.006 0.071 3858 Dihedral : 20.473 116.964 4456 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.78 % Favored : 91.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.14), residues: 2704 helix: -2.25 (0.12), residues: 1100 sheet: -3.70 (0.23), residues: 378 loop : -2.70 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 798 HIS 0.008 0.001 HIS A 111 PHE 0.023 0.002 PHE B 446 TYR 0.025 0.002 TYR D 774 ARG 0.010 0.001 ARG C 481 Details of bonding type rmsd link_NAG-ASN : bond 0.00820 ( 32) link_NAG-ASN : angle 4.19876 ( 96) link_ALPHA1-6 : bond 0.01585 ( 6) link_ALPHA1-6 : angle 3.32537 ( 18) link_BETA1-4 : bond 0.01091 ( 26) link_BETA1-4 : angle 4.06266 ( 78) link_ALPHA1-3 : bond 0.01665 ( 6) link_ALPHA1-3 : angle 2.76915 ( 18) hydrogen bonds : bond 0.04991 ( 712) hydrogen bonds : angle 5.27032 ( 2044) SS BOND : bond 0.00245 ( 6) SS BOND : angle 1.89047 ( 12) covalent geometry : bond 0.00398 (23146) covalent geometry : angle 0.89501 (31314) *********************** 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 360 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 315 time to evaluate : 2.643 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: symmetry clash REVERT: A 64 ILE cc_start: 0.8770 (mm) cc_final: 0.8535 (mt) REVERT: A 292 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8492 (mm) REVERT: A 298 MET cc_start: 0.8910 (ttp) cc_final: 0.8691 (tmm) REVERT: A 342 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8161 (m) REVERT: A 465 ASP cc_start: 0.8787 (t70) cc_final: 0.8410 (t0) REVERT: A 651 TYR cc_start: 0.7525 (t80) cc_final: 0.6933 (t80) REVERT: A 655 LEU cc_start: 0.9233 (tp) cc_final: 0.8891 (mm) REVERT: A 672 ASP cc_start: 0.7958 (t0) cc_final: 0.7255 (p0) REVERT: A 784 GLN cc_start: 0.8320 (mt0) cc_final: 0.7978 (mt0) REVERT: B 316 MET cc_start: 0.9086 (ttt) cc_final: 0.8661 (ttm) REVERT: B 484 GLU cc_start: 0.6102 (mp0) cc_final: 0.5702 (pm20) REVERT: B 534 MET cc_start: 0.7485 (ttp) cc_final: 0.7258 (ttp) REVERT: B 687 ASP cc_start: 0.7029 (m-30) cc_final: 0.6811 (m-30) REVERT: B 703 ASP cc_start: 0.7914 (t70) cc_final: 0.7484 (m-30) REVERT: B 770 MET cc_start: 0.7929 (tmt) cc_final: 0.7495 (tmm) REVERT: C 78 TYR cc_start: 0.7884 (p90) cc_final: 0.7647 (p90) REVERT: C 147 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8596 (m) REVERT: C 517 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8499 (tt) REVERT: C 645 LEU cc_start: 0.8106 (tp) cc_final: 0.7816 (mt) REVERT: C 651 TYR cc_start: 0.7136 (t80) cc_final: 0.6454 (t80) REVERT: C 655 LEU cc_start: 0.8821 (tt) cc_final: 0.8195 (mm) REVERT: C 723 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7869 (tt0) REVERT: D 447 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7163 (ttmm) REVERT: D 501 MET cc_start: 0.7537 (mtt) cc_final: 0.6781 (mmp) REVERT: D 534 MET cc_start: 0.7097 (ttp) cc_final: 0.6747 (ptm) REVERT: D 665 GLU cc_start: 0.7924 (tt0) cc_final: 0.7562 (tm-30) REVERT: D 666 SER cc_start: 0.8750 (m) cc_final: 0.8360 (t) REVERT: D 691 MET cc_start: 0.8255 (ppp) cc_final: 0.8012 (tmm) REVERT: D 696 LYS cc_start: 0.9101 (mtpt) cc_final: 0.8535 (pttm) REVERT: D 774 TYR cc_start: 0.6236 (t80) cc_final: 0.5909 (t80) REVERT: D 790 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8217 (mmtt) outliers start: 45 outliers final: 17 residues processed: 344 average time/residue: 0.3224 time to fit residues: 174.7660 Evaluate side-chains 280 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 258 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 292 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 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 147 VAL 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 138 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 219 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 495 ASN B 196 ASN C 129 HIS C 141 ASN C 495 ASN D 111 HIS D 714 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.137787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.097518 restraints weight = 83101.236| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 4.71 r_work: 0.3005 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 23222 Z= 0.214 Angle : 0.905 15.174 31536 Z= 0.410 Chirality : 0.053 0.493 3704 Planarity : 0.005 0.068 3858 Dihedral : 17.024 111.575 4456 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.33 % Favored : 90.52 % Rotamer: Outliers : 2.14 % Allowed : 12.29 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.15), residues: 2704 helix: -1.23 (0.14), residues: 1108 sheet: -3.60 (0.22), residues: 406 loop : -2.47 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 353 HIS 0.031 0.002 HIS A 367 PHE 0.032 0.002 PHE D 359 TYR 0.019 0.002 TYR D 252 ARG 0.012 0.001 ARG D 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00667 ( 32) link_NAG-ASN : angle 3.84843 ( 96) link_ALPHA1-6 : bond 0.02164 ( 6) link_ALPHA1-6 : angle 3.16843 ( 18) link_BETA1-4 : bond 0.00946 ( 26) link_BETA1-4 : angle 3.69537 ( 78) link_ALPHA1-3 : bond 0.01888 ( 6) link_ALPHA1-3 : angle 2.67293 ( 18) hydrogen bonds : bond 0.04295 ( 712) hydrogen bonds : angle 4.89717 ( 2044) SS BOND : bond 0.00236 ( 6) SS BOND : angle 0.96779 ( 12) covalent geometry : bond 0.00491 (23146) covalent geometry : angle 0.85693 (31314) *********************** 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 317 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 274 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8162 (m) REVERT: A 651 TYR cc_start: 0.7479 (t80) cc_final: 0.6873 (t80) REVERT: A 655 LEU cc_start: 0.9208 (tp) cc_final: 0.8828 (mm) REVERT: A 672 ASP cc_start: 0.8257 (t0) cc_final: 0.7680 (p0) REVERT: B 484 GLU cc_start: 0.6301 (mp0) cc_final: 0.5926 (pm20) REVERT: B 534 MET cc_start: 0.7694 (ttp) cc_final: 0.7185 (ttp) REVERT: B 687 ASP cc_start: 0.7244 (m-30) cc_final: 0.6999 (m-30) REVERT: B 744 PHE cc_start: 0.8533 (t80) cc_final: 0.8134 (t80) REVERT: C 43 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7746 (tm-30) REVERT: C 78 TYR cc_start: 0.8070 (p90) cc_final: 0.7755 (p90) REVERT: C 141 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8495 (m110) REVERT: C 651 TYR cc_start: 0.6843 (t80) cc_final: 0.6244 (t80) REVERT: C 655 LEU cc_start: 0.8826 (tt) cc_final: 0.8180 (mm) REVERT: C 682 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7768 (m-10) REVERT: D 447 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6989 (ttmm) REVERT: D 501 MET cc_start: 0.7746 (mtt) cc_final: 0.7002 (mmp) REVERT: D 534 MET cc_start: 0.7343 (ttp) cc_final: 0.6679 (ptm) REVERT: D 665 GLU cc_start: 0.8023 (tt0) cc_final: 0.7626 (tm-30) REVERT: D 666 SER cc_start: 0.8725 (m) cc_final: 0.8386 (t) REVERT: D 691 MET cc_start: 0.8237 (ppp) cc_final: 0.7931 (tmm) REVERT: D 696 LYS cc_start: 0.9100 (mtpt) cc_final: 0.8599 (pttt) REVERT: D 735 PHE cc_start: 0.8718 (t80) cc_final: 0.8469 (t80) REVERT: D 794 MET cc_start: 0.4956 (ttp) cc_final: 0.4642 (ttp) outliers start: 43 outliers final: 26 residues processed: 303 average time/residue: 0.3085 time to fit residues: 151.1079 Evaluate side-chains 279 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 249 time to evaluate : 2.721 ------------------------------------------------------------------------------- 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 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 A residue 794 MET Chi-restraints excluded: chain B residue 199 LEU 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 141 ASN 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 C residue 745 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 207 ASP 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 491 GLN Chi-restraints excluded: chain D residue 679 LYS 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 120 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 153 optimal weight: 0.7980 chunk 267 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 238 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 784 GLN B 196 ASN B 350 HIS C 141 ASN D 98 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.139283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.100886 restraints weight = 88583.775| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 4.91 r_work: 0.3025 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23222 Z= 0.154 Angle : 0.850 11.687 31536 Z= 0.381 Chirality : 0.051 0.425 3704 Planarity : 0.005 0.064 3858 Dihedral : 15.667 109.416 4454 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.67 % Favored : 91.19 % Rotamer: Outliers : 1.97 % Allowed : 13.72 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.16), residues: 2704 helix: -0.67 (0.15), residues: 1102 sheet: -3.48 (0.22), residues: 422 loop : -2.29 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 640 HIS 0.014 0.001 HIS A 350 PHE 0.026 0.002 PHE B 446 TYR 0.014 0.001 TYR B 86 ARG 0.006 0.000 ARG D 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00699 ( 32) link_NAG-ASN : angle 3.67845 ( 96) link_ALPHA1-6 : bond 0.01969 ( 6) link_ALPHA1-6 : angle 2.74123 ( 18) link_BETA1-4 : bond 0.00844 ( 26) link_BETA1-4 : angle 3.61763 ( 78) link_ALPHA1-3 : bond 0.01937 ( 6) link_ALPHA1-3 : angle 2.71362 ( 18) hydrogen bonds : bond 0.03606 ( 712) hydrogen bonds : angle 4.62293 ( 2044) SS BOND : bond 0.00324 ( 6) SS BOND : angle 2.74056 ( 12) covalent geometry : bond 0.00342 (23146) covalent geometry : angle 0.80152 (31314) *********************** 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 302 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 263 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.7008 (t80) REVERT: A 342 VAL cc_start: 0.8374 (OUTLIER) cc_final: 0.8118 (m) REVERT: A 508 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.7162 (m90) REVERT: A 651 TYR cc_start: 0.7441 (t80) cc_final: 0.6841 (t80) REVERT: A 655 LEU cc_start: 0.9196 (tp) cc_final: 0.8824 (mm) REVERT: A 672 ASP cc_start: 0.8218 (t0) cc_final: 0.7643 (p0) REVERT: B 138 VAL cc_start: 0.8825 (t) cc_final: 0.8612 (m) REVERT: B 251 TYR cc_start: 0.8772 (m-80) cc_final: 0.8564 (m-80) REVERT: B 484 GLU cc_start: 0.6284 (mp0) cc_final: 0.5937 (pm20) REVERT: B 534 MET cc_start: 0.7687 (ttp) cc_final: 0.7152 (ttp) REVERT: B 641 TRP cc_start: 0.6249 (t-100) cc_final: 0.6033 (t-100) REVERT: B 687 ASP cc_start: 0.7261 (m-30) cc_final: 0.7031 (m-30) REVERT: B 735 PHE cc_start: 0.8392 (t80) cc_final: 0.8097 (t80) REVERT: B 737 MET cc_start: 0.8320 (ptp) cc_final: 0.7858 (pmm) REVERT: B 744 PHE cc_start: 0.8526 (t80) cc_final: 0.8306 (t80) REVERT: B 790 LYS cc_start: 0.8733 (mtpp) cc_final: 0.8281 (mmtt) REVERT: B 793 MET cc_start: 0.8645 (tpp) cc_final: 0.8439 (mtp) REVERT: C 43 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7686 (tm-30) REVERT: C 79 ASP cc_start: 0.8219 (t0) cc_final: 0.7581 (t70) REVERT: C 141 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8318 (m110) REVERT: C 645 LEU cc_start: 0.8052 (tp) cc_final: 0.7725 (mt) REVERT: C 651 TYR cc_start: 0.6899 (t80) cc_final: 0.6332 (t80) REVERT: C 655 LEU cc_start: 0.8888 (tt) cc_final: 0.8296 (mm) REVERT: C 682 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.7687 (m-10) REVERT: D 501 MET cc_start: 0.7811 (mtt) cc_final: 0.7094 (mmp) REVERT: D 534 MET cc_start: 0.7472 (ttp) cc_final: 0.7143 (ttm) REVERT: D 665 GLU cc_start: 0.7970 (tt0) cc_final: 0.7447 (tm-30) REVERT: D 666 SER cc_start: 0.8653 (m) cc_final: 0.8316 (t) REVERT: D 691 MET cc_start: 0.8218 (ppp) cc_final: 0.7879 (tmm) REVERT: D 696 LYS cc_start: 0.9066 (mtpt) cc_final: 0.8575 (pttt) REVERT: D 735 PHE cc_start: 0.8611 (t80) cc_final: 0.8366 (t80) REVERT: D 794 MET cc_start: 0.4647 (ttp) cc_final: 0.4397 (ttp) outliers start: 39 outliers final: 21 residues processed: 287 average time/residue: 0.3137 time to fit residues: 145.7235 Evaluate side-chains 267 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 2.442 ------------------------------------------------------------------------------- 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 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 508 HIS Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 439 LEU 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 141 ASN 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 661 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 57 optimal weight: 1.9990 chunk 258 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 153 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS B 111 HIS B 196 ASN B 328 HIS B 350 HIS C 141 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.138220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.099895 restraints weight = 75213.673| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 4.49 r_work: 0.3050 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- 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 = 0.39 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 = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23222 Z= 0.168 Angle : 0.821 10.925 31536 Z= 0.369 Chirality : 0.050 0.412 3704 Planarity : 0.005 0.063 3858 Dihedral : 14.669 106.356 4454 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.04 % Favored : 90.81 % Rotamer: Outliers : 2.43 % Allowed : 13.34 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.16), residues: 2704 helix: -0.27 (0.16), residues: 1086 sheet: -3.44 (0.22), residues: 408 loop : -2.20 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 640 HIS 0.005 0.001 HIS D 253 PHE 0.019 0.002 PHE D 359 TYR 0.028 0.001 TYR B 86 ARG 0.007 0.000 ARG B 800 Details of bonding type rmsd link_NAG-ASN : bond 0.00671 ( 32) link_NAG-ASN : angle 3.49647 ( 96) link_ALPHA1-6 : bond 0.01881 ( 6) link_ALPHA1-6 : angle 2.78131 ( 18) link_BETA1-4 : bond 0.00843 ( 26) link_BETA1-4 : angle 3.48682 ( 78) link_ALPHA1-3 : bond 0.01924 ( 6) link_ALPHA1-3 : angle 2.72734 ( 18) hydrogen bonds : bond 0.03453 ( 712) hydrogen bonds : angle 4.47409 ( 2044) SS BOND : bond 0.00406 ( 6) SS BOND : angle 0.37861 ( 12) covalent geometry : bond 0.00383 (23146) covalent geometry : angle 0.77628 (31314) *********************** 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 306 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 256 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8394 (ppp) REVERT: A 342 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8061 (m) REVERT: A 508 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7120 (m90) REVERT: A 651 TYR cc_start: 0.7435 (t80) cc_final: 0.6844 (t80) REVERT: A 655 LEU cc_start: 0.9181 (tp) cc_final: 0.8820 (mm) REVERT: B 196 ASN cc_start: 0.7209 (t0) cc_final: 0.6971 (t0) REVERT: B 251 TYR cc_start: 0.8691 (m-80) cc_final: 0.8484 (m-80) REVERT: B 319 ASP cc_start: 0.8096 (t0) cc_final: 0.7803 (t0) REVERT: B 534 MET cc_start: 0.7649 (ttp) cc_final: 0.7130 (ttp) REVERT: B 665 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6776 (tm-30) REVERT: B 687 ASP cc_start: 0.7347 (m-30) cc_final: 0.7100 (m-30) REVERT: B 702 TYR cc_start: 0.8455 (m-10) cc_final: 0.8096 (m-10) REVERT: B 735 PHE cc_start: 0.8369 (t80) cc_final: 0.8095 (t80) REVERT: B 737 MET cc_start: 0.8413 (ptp) cc_final: 0.8042 (pmm) REVERT: B 744 PHE cc_start: 0.8336 (t80) cc_final: 0.8114 (t80) REVERT: B 793 MET cc_start: 0.8637 (tpp) cc_final: 0.8329 (mtp) REVERT: C 296 TRP cc_start: 0.6905 (m-10) cc_final: 0.6460 (m-10) REVERT: C 645 LEU cc_start: 0.8099 (tp) cc_final: 0.7772 (mt) REVERT: C 655 LEU cc_start: 0.8897 (tt) cc_final: 0.8454 (mm) REVERT: C 674 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8424 (tp) REVERT: C 682 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7746 (m-10) REVERT: D 298 MET cc_start: 0.8361 (mmp) cc_final: 0.8152 (mmp) REVERT: D 501 MET cc_start: 0.7841 (mtt) cc_final: 0.7034 (mmp) REVERT: D 534 MET cc_start: 0.7340 (ttp) cc_final: 0.6859 (ttp) REVERT: D 665 GLU cc_start: 0.7948 (tt0) cc_final: 0.7357 (tm-30) REVERT: D 666 SER cc_start: 0.8650 (m) cc_final: 0.8356 (t) REVERT: D 691 MET cc_start: 0.8302 (ppp) cc_final: 0.7928 (tmm) REVERT: D 696 LYS cc_start: 0.9025 (mtpt) cc_final: 0.8568 (pttt) REVERT: D 735 PHE cc_start: 0.8563 (t80) cc_final: 0.8303 (t80) outliers start: 50 outliers final: 24 residues processed: 285 average time/residue: 0.3166 time to fit residues: 146.6714 Evaluate side-chains 266 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 292 ILE 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 414 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain B residue 199 LEU 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 138 VAL Chi-restraints excluded: chain C residue 210 ASP 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 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 14 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 246 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 0.0970 chunk 260 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS C 141 ASN D 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.135018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.092046 restraints weight = 75885.806| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 4.45 r_work: 0.2960 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.128 23222 Z= 0.299 Angle : 0.904 10.555 31536 Z= 0.412 Chirality : 0.053 0.406 3704 Planarity : 0.005 0.082 3858 Dihedral : 14.055 106.939 4454 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.07 % Favored : 89.70 % Rotamer: Outliers : 2.31 % Allowed : 14.26 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.16), residues: 2704 helix: -0.37 (0.15), residues: 1092 sheet: -3.31 (0.23), residues: 396 loop : -2.20 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 353 HIS 0.039 0.002 HIS A 350 PHE 0.023 0.002 PHE D 359 TYR 0.033 0.002 TYR D 252 ARG 0.020 0.001 ARG A 349 Details of bonding type rmsd link_NAG-ASN : bond 0.00642 ( 32) link_NAG-ASN : angle 3.50839 ( 96) link_ALPHA1-6 : bond 0.02045 ( 6) link_ALPHA1-6 : angle 2.98172 ( 18) link_BETA1-4 : bond 0.00818 ( 26) link_BETA1-4 : angle 3.45647 ( 78) link_ALPHA1-3 : bond 0.01948 ( 6) link_ALPHA1-3 : angle 2.73701 ( 18) hydrogen bonds : bond 0.03938 ( 712) hydrogen bonds : angle 4.69289 ( 2044) SS BOND : bond 0.00675 ( 6) SS BOND : angle 1.37711 ( 12) covalent geometry : bond 0.00707 (23146) covalent geometry : angle 0.86325 (31314) *********************** 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: 47 poor density : 251 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7840 (tttp) cc_final: 0.7187 (tptm) REVERT: A 298 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8465 (ppp) REVERT: A 508 HIS cc_start: 0.8226 (OUTLIER) cc_final: 0.7647 (m90) REVERT: A 651 TYR cc_start: 0.7550 (t80) cc_final: 0.6929 (t80) REVERT: A 655 LEU cc_start: 0.9244 (tp) cc_final: 0.8909 (mm) REVERT: B 534 MET cc_start: 0.7652 (ttp) cc_final: 0.7182 (ttm) REVERT: B 687 ASP cc_start: 0.7627 (m-30) cc_final: 0.7127 (m-30) REVERT: B 735 PHE cc_start: 0.8525 (t80) cc_final: 0.8270 (t80) REVERT: B 737 MET cc_start: 0.8446 (ptp) cc_final: 0.8090 (pmm) REVERT: B 744 PHE cc_start: 0.8395 (t80) cc_final: 0.8173 (t80) REVERT: B 793 MET cc_start: 0.8695 (tpp) cc_final: 0.8413 (tmm) REVERT: C 141 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8360 (m110) REVERT: C 517 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8637 (tt) REVERT: C 655 LEU cc_start: 0.9052 (tt) cc_final: 0.8570 (mm) REVERT: C 669 ASP cc_start: 0.8311 (t70) cc_final: 0.8066 (t0) REVERT: C 674 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8451 (tp) REVERT: C 682 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7913 (m-10) REVERT: D 298 MET cc_start: 0.8488 (mmp) cc_final: 0.8240 (mmp) REVERT: D 319 ASP cc_start: 0.8289 (t0) cc_final: 0.8070 (t0) REVERT: D 501 MET cc_start: 0.7868 (mtt) cc_final: 0.7057 (mmt) REVERT: D 534 MET cc_start: 0.7446 (ttp) cc_final: 0.6846 (ptp) REVERT: D 665 GLU cc_start: 0.7980 (tt0) cc_final: 0.7388 (tm-30) REVERT: D 666 SER cc_start: 0.8654 (m) cc_final: 0.8356 (t) REVERT: D 681 GLU cc_start: 0.7021 (pp20) cc_final: 0.6607 (pp20) REVERT: D 691 MET cc_start: 0.8385 (ppp) cc_final: 0.7986 (tmm) REVERT: D 696 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8590 (pttt) REVERT: D 735 PHE cc_start: 0.8578 (t80) cc_final: 0.8360 (t80) outliers start: 47 outliers final: 25 residues processed: 283 average time/residue: 0.3379 time to fit residues: 151.5601 Evaluate side-chains 269 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 2.460 ------------------------------------------------------------------------------- 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 292 ILE 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 414 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 210 ASP 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 93 optimal weight: 0.9980 chunk 187 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 267 optimal weight: 6.9990 chunk 170 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 258 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 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 129 HIS A 350 HIS B 196 ASN B 350 HIS ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 350 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.136571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.095781 restraints weight = 79367.837| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 4.21 r_work: 0.3040 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23222 Z= 0.157 Angle : 0.811 10.742 31536 Z= 0.365 Chirality : 0.049 0.397 3704 Planarity : 0.004 0.060 3858 Dihedral : 13.443 106.307 4454 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.00 % Favored : 90.85 % Rotamer: Outliers : 2.18 % Allowed : 14.93 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.16), residues: 2704 helix: -0.08 (0.16), residues: 1096 sheet: -3.16 (0.23), residues: 408 loop : -2.12 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 640 HIS 0.005 0.001 HIS A 350 PHE 0.021 0.002 PHE C 228 TYR 0.015 0.001 TYR D 764 ARG 0.006 0.000 ARG B 800 Details of bonding type rmsd link_NAG-ASN : bond 0.00671 ( 32) link_NAG-ASN : angle 3.37137 ( 96) link_ALPHA1-6 : bond 0.02162 ( 6) link_ALPHA1-6 : angle 2.98119 ( 18) link_BETA1-4 : bond 0.00834 ( 26) link_BETA1-4 : angle 3.27400 ( 78) link_ALPHA1-3 : bond 0.01963 ( 6) link_ALPHA1-3 : angle 2.66613 ( 18) hydrogen bonds : bond 0.03349 ( 712) hydrogen bonds : angle 4.41862 ( 2044) SS BOND : bond 0.00817 ( 6) SS BOND : angle 2.35797 ( 12) covalent geometry : bond 0.00357 (23146) covalent geometry : angle 0.76754 (31314) *********************** 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 293 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 249 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7640 (p90) REVERT: A 185 LEU cc_start: 0.8883 (mt) cc_final: 0.8682 (mp) REVERT: A 342 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8269 (m) REVERT: A 508 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7234 (m90) REVERT: A 651 TYR cc_start: 0.7550 (t80) cc_final: 0.6907 (t80) REVERT: A 655 LEU cc_start: 0.9212 (tp) cc_final: 0.8837 (mm) REVERT: A 674 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8451 (tp) REVERT: B 534 MET cc_start: 0.7633 (ttp) cc_final: 0.7200 (ttm) REVERT: B 666 SER cc_start: 0.8652 (m) cc_final: 0.8360 (p) REVERT: B 687 ASP cc_start: 0.7626 (m-30) cc_final: 0.7174 (m-30) REVERT: B 702 TYR cc_start: 0.8481 (m-10) cc_final: 0.8153 (m-10) REVERT: B 735 PHE cc_start: 0.8261 (t80) cc_final: 0.7950 (t80) REVERT: B 737 MET cc_start: 0.8480 (ptp) cc_final: 0.8168 (pmm) REVERT: B 744 PHE cc_start: 0.8442 (t80) cc_final: 0.8221 (t80) REVERT: B 793 MET cc_start: 0.8507 (tpp) cc_final: 0.8121 (tmm) REVERT: C 185 LEU cc_start: 0.8877 (mt) cc_final: 0.8470 (mp) REVERT: C 508 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.7185 (m90) REVERT: C 517 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8511 (tp) REVERT: C 655 LEU cc_start: 0.9020 (tt) cc_final: 0.8561 (mm) REVERT: C 669 ASP cc_start: 0.8162 (t70) cc_final: 0.7936 (t0) REVERT: C 674 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8178 (tp) REVERT: C 682 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7654 (m-10) REVERT: D 298 MET cc_start: 0.8513 (mmp) cc_final: 0.8256 (mmp) REVERT: D 319 ASP cc_start: 0.8165 (t0) cc_final: 0.7946 (t0) REVERT: D 340 MET cc_start: 0.8121 (tpp) cc_final: 0.7568 (mmt) REVERT: D 501 MET cc_start: 0.7767 (mtt) cc_final: 0.6850 (mmm) REVERT: D 534 MET cc_start: 0.7349 (ttp) cc_final: 0.6744 (ptp) REVERT: D 665 GLU cc_start: 0.8024 (tt0) cc_final: 0.7384 (tm-30) REVERT: D 666 SER cc_start: 0.8669 (m) cc_final: 0.8359 (t) REVERT: D 691 MET cc_start: 0.8257 (ppp) cc_final: 0.7871 (tmm) REVERT: D 696 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8532 (pttt) REVERT: D 735 PHE cc_start: 0.8373 (t80) cc_final: 0.8124 (t80) REVERT: D 787 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6194 (pp20) outliers start: 44 outliers final: 25 residues processed: 276 average time/residue: 0.3304 time to fit residues: 146.5971 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 : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 ILE 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 375 ILE Chi-restraints excluded: chain A residue 438 ILE 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 199 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 210 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 66 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 211 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 216 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 223 optimal weight: 2.9990 chunk 246 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS C 141 ASN D 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.138055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.096269 restraints weight = 91131.490| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 5.03 r_work: 0.3004 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23222 Z= 0.152 Angle : 0.796 11.154 31536 Z= 0.359 Chirality : 0.049 0.389 3704 Planarity : 0.004 0.059 3858 Dihedral : 12.723 105.727 4454 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.04 % Favored : 90.89 % Rotamer: Outliers : 2.06 % Allowed : 15.14 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.16), residues: 2704 helix: 0.09 (0.16), residues: 1096 sheet: -3.13 (0.23), residues: 422 loop : -2.05 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 640 HIS 0.018 0.001 HIS A 350 PHE 0.020 0.001 PHE C 228 TYR 0.030 0.001 TYR B 86 ARG 0.015 0.000 ARG A 349 Details of bonding type rmsd link_NAG-ASN : bond 0.00671 ( 32) link_NAG-ASN : angle 3.25194 ( 96) link_ALPHA1-6 : bond 0.02322 ( 6) link_ALPHA1-6 : angle 2.98581 ( 18) link_BETA1-4 : bond 0.00855 ( 26) link_BETA1-4 : angle 3.24823 ( 78) link_ALPHA1-3 : bond 0.02023 ( 6) link_ALPHA1-3 : angle 2.74980 ( 18) hydrogen bonds : bond 0.03260 ( 712) hydrogen bonds : angle 4.35057 ( 2044) SS BOND : bond 0.00149 ( 6) SS BOND : angle 0.96968 ( 12) covalent geometry : bond 0.00342 (23146) covalent geometry : angle 0.75467 (31314) *********************** 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 283 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8182 (OUTLIER) cc_final: 0.7773 (p90) REVERT: A 342 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8252 (m) REVERT: A 350 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7371 (t-90) REVERT: A 508 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.7035 (m90) REVERT: A 651 TYR cc_start: 0.7477 (t80) cc_final: 0.6768 (t80) REVERT: A 655 LEU cc_start: 0.9206 (tp) cc_final: 0.8829 (mm) REVERT: B 534 MET cc_start: 0.7669 (ttp) cc_final: 0.6993 (tpp) REVERT: B 666 SER cc_start: 0.8601 (m) cc_final: 0.8309 (p) REVERT: B 687 ASP cc_start: 0.7673 (m-30) cc_final: 0.7235 (m-30) REVERT: B 702 TYR cc_start: 0.8501 (m-10) cc_final: 0.8205 (m-10) REVERT: B 735 PHE cc_start: 0.8177 (t80) cc_final: 0.7904 (t80) REVERT: B 737 MET cc_start: 0.8475 (ptp) cc_final: 0.8108 (pmm) REVERT: B 793 MET cc_start: 0.8592 (tpp) cc_final: 0.8232 (tmm) REVERT: C 185 LEU cc_start: 0.8870 (mt) cc_final: 0.8358 (mp) REVERT: C 508 HIS cc_start: 0.7782 (OUTLIER) cc_final: 0.7022 (m90) REVERT: C 655 LEU cc_start: 0.9063 (tt) cc_final: 0.8589 (mm) REVERT: C 674 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8034 (tp) REVERT: C 682 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7636 (m-10) REVERT: D 298 MET cc_start: 0.8486 (mmp) cc_final: 0.8211 (mmp) REVERT: D 340 MET cc_start: 0.8070 (tpp) cc_final: 0.7515 (mmt) REVERT: D 501 MET cc_start: 0.7805 (mtt) cc_final: 0.7019 (mmp) REVERT: D 534 MET cc_start: 0.7355 (ttp) cc_final: 0.6502 (tpp) REVERT: D 665 GLU cc_start: 0.8085 (tt0) cc_final: 0.7380 (tm-30) REVERT: D 666 SER cc_start: 0.8602 (m) cc_final: 0.8237 (t) REVERT: D 691 MET cc_start: 0.8255 (ppp) cc_final: 0.7893 (tmm) REVERT: D 696 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8533 (pttt) REVERT: D 735 PHE cc_start: 0.8220 (t80) cc_final: 0.7962 (t80) REVERT: D 787 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6419 (pp20) outliers start: 41 outliers final: 23 residues processed: 269 average time/residue: 0.3272 time to fit residues: 142.3455 Evaluate side-chains 266 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 ILE 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 375 ILE 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 199 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 210 ASP 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 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 794 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 111 optimal weight: 40.0000 chunk 171 optimal weight: 0.9990 chunk 164 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 228 optimal weight: 0.0370 chunk 235 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- 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 C 141 ASN D 196 ASN D 350 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.137870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.095540 restraints weight = 62614.284| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.95 r_work: 0.3071 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4603 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= 0.158 Angle : 0.791 11.204 31536 Z= 0.357 Chirality : 0.048 0.384 3704 Planarity : 0.004 0.058 3858 Dihedral : 12.099 105.384 4454 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.07 % Favored : 90.85 % Rotamer: Outliers : 1.80 % Allowed : 15.60 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.16), residues: 2704 helix: 0.23 (0.16), residues: 1096 sheet: -3.04 (0.23), residues: 436 loop : -2.00 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 640 HIS 0.005 0.001 HIS D 253 PHE 0.020 0.002 PHE C 228 TYR 0.015 0.001 TYR D 764 ARG 0.005 0.000 ARG B 800 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 32) link_NAG-ASN : angle 3.17637 ( 96) link_ALPHA1-6 : bond 0.02395 ( 6) link_ALPHA1-6 : angle 3.04716 ( 18) link_BETA1-4 : bond 0.00850 ( 26) link_BETA1-4 : angle 3.20291 ( 78) link_ALPHA1-3 : bond 0.02057 ( 6) link_ALPHA1-3 : angle 2.78104 ( 18) hydrogen bonds : bond 0.03233 ( 712) hydrogen bonds : angle 4.29680 ( 2044) SS BOND : bond 0.00167 ( 6) SS BOND : angle 0.77444 ( 12) covalent geometry : bond 0.00361 (23146) covalent geometry : angle 0.75029 (31314) *********************** 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 270 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7654 (p90) REVERT: A 342 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8143 (m) REVERT: A 360 MET cc_start: 0.8774 (tpt) cc_final: 0.8443 (tpp) REVERT: A 508 HIS cc_start: 0.7778 (OUTLIER) cc_final: 0.7050 (m90) REVERT: A 651 TYR cc_start: 0.7410 (t80) cc_final: 0.6660 (t80) REVERT: A 655 LEU cc_start: 0.9178 (tp) cc_final: 0.8795 (mm) REVERT: B 534 MET cc_start: 0.7605 (ttp) cc_final: 0.7038 (tpp) REVERT: B 666 SER cc_start: 0.8645 (m) cc_final: 0.8338 (t) REVERT: B 687 ASP cc_start: 0.7671 (m-30) cc_final: 0.7234 (m-30) REVERT: B 735 PHE cc_start: 0.8154 (t80) cc_final: 0.7884 (t80) REVERT: B 737 MET cc_start: 0.8462 (ptp) cc_final: 0.8121 (pmm) REVERT: B 793 MET cc_start: 0.8554 (tpp) cc_final: 0.8247 (tmm) REVERT: C 508 HIS cc_start: 0.7659 (OUTLIER) cc_final: 0.6958 (m90) REVERT: C 655 LEU cc_start: 0.9033 (tt) cc_final: 0.8585 (mm) REVERT: C 674 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8475 (tp) REVERT: C 682 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.7590 (m-10) REVERT: D 298 MET cc_start: 0.8349 (mmp) cc_final: 0.8123 (mmp) REVERT: D 340 MET cc_start: 0.7836 (tpp) cc_final: 0.7293 (mmt) REVERT: D 501 MET cc_start: 0.7789 (mtt) cc_final: 0.7022 (mmp) REVERT: D 534 MET cc_start: 0.7464 (ttp) cc_final: 0.6565 (tpp) REVERT: D 665 GLU cc_start: 0.7988 (tt0) cc_final: 0.7384 (tm-30) REVERT: D 666 SER cc_start: 0.8580 (m) cc_final: 0.8229 (t) REVERT: D 691 MET cc_start: 0.8254 (ppp) cc_final: 0.7874 (tmm) REVERT: D 696 LYS cc_start: 0.9011 (mtpt) cc_final: 0.8528 (pttt) REVERT: D 787 GLU cc_start: 0.7441 (mm-30) cc_final: 0.6570 (pp20) outliers start: 35 outliers final: 26 residues processed: 257 average time/residue: 0.3221 time to fit residues: 133.9493 Evaluate side-chains 260 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 292 ILE 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 350 HIS Chi-restraints excluded: chain A residue 375 ILE 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 199 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 640 TRP 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 661 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 682 TYR 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 199 optimal weight: 0.0040 chunk 234 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 219 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 198 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.139527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.100651 restraints weight = 88772.616| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 4.83 r_work: 0.3042 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23222 Z= 0.135 Angle : 0.780 13.725 31536 Z= 0.351 Chirality : 0.047 0.378 3704 Planarity : 0.004 0.056 3858 Dihedral : 11.685 105.404 4454 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.44 % Favored : 91.48 % Rotamer: Outliers : 1.68 % Allowed : 15.69 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.17), residues: 2704 helix: 0.45 (0.16), residues: 1078 sheet: -2.95 (0.24), residues: 438 loop : -1.96 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 640 HIS 0.023 0.001 HIS A 350 PHE 0.021 0.001 PHE C 228 TYR 0.027 0.001 TYR D 478 ARG 0.015 0.000 ARG D 468 Details of bonding type rmsd link_NAG-ASN : bond 0.00719 ( 32) link_NAG-ASN : angle 3.11527 ( 96) link_ALPHA1-6 : bond 0.02437 ( 6) link_ALPHA1-6 : angle 3.08788 ( 18) link_BETA1-4 : bond 0.00853 ( 26) link_BETA1-4 : angle 3.12026 ( 78) link_ALPHA1-3 : bond 0.02126 ( 6) link_ALPHA1-3 : angle 2.84817 ( 18) hydrogen bonds : bond 0.03105 ( 712) hydrogen bonds : angle 4.20033 ( 2044) SS BOND : bond 0.00263 ( 6) SS BOND : angle 1.02419 ( 12) covalent geometry : bond 0.00294 (23146) covalent geometry : angle 0.74006 (31314) ********************** 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 276 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 244 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7690 (p90) REVERT: A 86 TYR cc_start: 0.6674 (m-80) cc_final: 0.6384 (m-80) REVERT: A 342 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.8078 (m) REVERT: A 360 MET cc_start: 0.8812 (tpt) cc_final: 0.8423 (tpp) REVERT: A 508 HIS cc_start: 0.7560 (OUTLIER) cc_final: 0.6716 (m90) REVERT: A 651 TYR cc_start: 0.7464 (t80) cc_final: 0.6704 (t80) REVERT: A 655 LEU cc_start: 0.9197 (tp) cc_final: 0.8814 (mm) REVERT: B 534 MET cc_start: 0.7585 (ttp) cc_final: 0.6948 (tpp) REVERT: B 666 SER cc_start: 0.8639 (m) cc_final: 0.8326 (t) REVERT: B 687 ASP cc_start: 0.7545 (m-30) cc_final: 0.7190 (m-30) REVERT: B 691 MET cc_start: 0.8022 (ppp) cc_final: 0.7670 (tmm) REVERT: B 702 TYR cc_start: 0.8603 (m-10) cc_final: 0.8307 (m-10) REVERT: B 737 MET cc_start: 0.8476 (ptp) cc_final: 0.8155 (pmm) REVERT: B 793 MET cc_start: 0.8585 (tpp) cc_final: 0.8307 (tmm) REVERT: C 508 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.6690 (m90) REVERT: C 655 LEU cc_start: 0.9074 (tt) cc_final: 0.8608 (mm) REVERT: C 674 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8393 (tp) REVERT: C 682 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.7598 (m-10) REVERT: C 794 MET cc_start: 0.7239 (mtm) cc_final: 0.7016 (mtm) REVERT: D 340 MET cc_start: 0.7875 (tpp) cc_final: 0.7350 (mmt) REVERT: D 501 MET cc_start: 0.7846 (mtt) cc_final: 0.7041 (mmp) REVERT: D 534 MET cc_start: 0.7547 (ttp) cc_final: 0.6897 (tpp) REVERT: D 665 GLU cc_start: 0.8025 (tt0) cc_final: 0.7409 (tm-30) REVERT: D 666 SER cc_start: 0.8565 (m) cc_final: 0.8207 (t) REVERT: D 691 MET cc_start: 0.8231 (ppp) cc_final: 0.7872 (tmm) REVERT: D 696 LYS cc_start: 0.8997 (mtpt) cc_final: 0.8491 (pttt) REVERT: D 787 GLU cc_start: 0.7441 (mm-30) cc_final: 0.6445 (pp20) outliers start: 32 outliers final: 22 residues processed: 261 average time/residue: 0.3235 time to fit residues: 136.8894 Evaluate side-chains 259 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 292 ILE 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 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 199 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 640 TRP 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 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 794 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 225 optimal weight: 2.9990 chunk 259 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 174 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 232 optimal weight: 7.9990 chunk 242 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 D 136 HIS D 196 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.139406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.101320 restraints weight = 98930.986| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 5.16 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23222 Z= 0.143 Angle : 0.781 13.863 31536 Z= 0.352 Chirality : 0.047 0.373 3704 Planarity : 0.004 0.058 3858 Dihedral : 11.313 104.744 4454 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.70 % Favored : 91.22 % Rotamer: Outliers : 1.64 % Allowed : 15.73 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.17), residues: 2704 helix: 0.56 (0.16), residues: 1072 sheet: -2.94 (0.23), residues: 438 loop : -1.90 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 640 HIS 0.005 0.001 HIS B 253 PHE 0.021 0.001 PHE C 228 TYR 0.015 0.001 TYR D 764 ARG 0.011 0.000 ARG D 468 Details of bonding type rmsd link_NAG-ASN : bond 0.00678 ( 32) link_NAG-ASN : angle 3.09754 ( 96) link_ALPHA1-6 : bond 0.02469 ( 6) link_ALPHA1-6 : angle 3.21110 ( 18) link_BETA1-4 : bond 0.00837 ( 26) link_BETA1-4 : angle 3.02888 ( 78) link_ALPHA1-3 : bond 0.02146 ( 6) link_ALPHA1-3 : angle 2.87022 ( 18) hydrogen bonds : bond 0.03145 ( 712) hydrogen bonds : angle 4.18923 ( 2044) SS BOND : bond 0.00232 ( 6) SS BOND : angle 0.97619 ( 12) covalent geometry : bond 0.00321 (23146) covalent geometry : angle 0.74237 (31314) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12841.20 seconds wall clock time: 221 minutes 9.51 seconds (13269.51 seconds total)