Starting phenix.real_space_refine on Tue Jul 23 14:07:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b38_44131/07_2024/9b38_44131.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b38_44131/07_2024/9b38_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b38_44131/07_2024/9b38_44131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b38_44131/07_2024/9b38_44131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b38_44131/07_2024/9b38_44131.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b38_44131/07_2024/9b38_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 Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 468": "NH1" <-> "NH2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 748": "NH1" <-> "NH2" Residue "B ARG 800": "NH1" <-> "NH2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 374": "NH1" <-> "NH2" Residue "C PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 431": "NH1" <-> "NH2" Residue "C ARG 468": "NH1" <-> "NH2" Residue "C ARG 712": "NH1" <-> "NH2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 468": "NH1" <-> "NH2" Residue "D PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 748": "NH1" <-> "NH2" Residue "D ARG 800": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 16.88, per 1000 atoms: 0.74 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 - 3.50 Amino acid : False - 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: 9.61 Conformation dependent library (CDL) restraints added in 5.4 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: 2.50 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: 6.84 Time building geometry restraints manager: 10.39 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: 98.71 - 106.51: 701 106.51 - 114.30: 13627 114.30 - 122.10: 12776 122.10 - 129.89: 4041 129.89 - 137.69: 169 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 2.440 nonbonded pdb=" OE1 GLU A 53 " pdb=" OG SER A 110 " model vdw 2.271 2.440 nonbonded pdb=" OH TYR D 443 " pdb=" OG1 THR D 740 " model vdw 2.278 2.440 nonbonded pdb=" OH TYR B 443 " pdb=" OG1 THR B 740 " model vdw 2.279 2.440 nonbonded pdb=" OH TYR C 251 " pdb=" OD1 ASP C 511 " model vdw 2.294 2.440 ... (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 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: 0.680 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: 0.740 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 64.260 Find NCS groups from input model: 2.780 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.690 ------------------------------------------------------------------------------- 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 23146 Z= 0.487 Angle : 1.296 15.888 31314 Z= 0.722 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 *********************** 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 fitting. rotamer outliers: 10 poor density : 506 time to evaluate : 2.795 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: 0.3878 time to fit residues: 293.5901 Evaluate side-chains 275 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 274 time to evaluate : 2.432 ------------------------------------------------------------------------------- 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: 0.0010 chunk 203 optimal weight: 3.9990 chunk 112 optimal weight: 30.0000 chunk 69 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 243 optimal weight: 5.9990 overall best weight: 1.6790 ------------------------------------------------------------------------------- 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 241 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 241 GLN D 350 HIS D 381 ASN D 677 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 23146 Z= 0.319 Angle : 0.900 11.327 31314 Z= 0.425 Chirality : 0.055 0.603 3704 Planarity : 0.006 0.072 3858 Dihedral : 20.710 117.558 4456 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.26 % Favored : 90.59 % Rotamer: Outliers : 2.52 % Allowed : 10.49 % Favored : 87.00 % 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: -4.17 (0.14), residues: 2704 helix: -2.33 (0.12), residues: 1108 sheet: -3.71 (0.22), residues: 380 loop : -2.76 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 798 HIS 0.010 0.001 HIS A 111 PHE 0.024 0.002 PHE B 446 TYR 0.026 0.002 TYR D 774 ARG 0.010 0.001 ARG C 481 *********************** 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 350 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 298 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8719 (mm) cc_final: 0.8494 (mt) REVERT: A 130 ILE cc_start: 0.9084 (mt) cc_final: 0.8880 (mp) REVERT: A 141 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8462 (m110) REVERT: A 185 LEU cc_start: 0.8811 (mt) cc_final: 0.8420 (mt) REVERT: A 342 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8394 (m) REVERT: A 465 ASP cc_start: 0.8401 (t70) cc_final: 0.8061 (t0) REVERT: A 651 TYR cc_start: 0.7489 (t80) cc_final: 0.6898 (t80) REVERT: A 655 LEU cc_start: 0.9199 (tp) cc_final: 0.8846 (mm) REVERT: A 672 ASP cc_start: 0.7996 (t0) cc_final: 0.7045 (p0) REVERT: A 677 GLN cc_start: 0.8442 (pp30) cc_final: 0.8075 (pp30) REVERT: B 316 MET cc_start: 0.9021 (ttt) cc_final: 0.8554 (ttm) REVERT: B 319 ASP cc_start: 0.7724 (t0) cc_final: 0.7404 (t0) REVERT: B 484 GLU cc_start: 0.5979 (mp0) cc_final: 0.5554 (pm20) REVERT: B 703 ASP cc_start: 0.7501 (t70) cc_final: 0.7181 (m-30) REVERT: B 770 MET cc_start: 0.7628 (tmt) cc_final: 0.7299 (tmm) REVERT: C 78 TYR cc_start: 0.8059 (p90) cc_final: 0.7753 (p90) REVERT: C 130 ILE cc_start: 0.8996 (mt) cc_final: 0.8767 (mp) REVERT: C 170 LYS cc_start: 0.8820 (mttm) cc_final: 0.8528 (mtmm) REVERT: C 316 MET cc_start: 0.8176 (ttm) cc_final: 0.7929 (ttm) REVERT: C 402 ILE cc_start: 0.8209 (tt) cc_final: 0.7814 (tp) REVERT: C 481 ARG cc_start: 0.8034 (mtt-85) cc_final: 0.7745 (mmt90) REVERT: C 517 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8058 (tt) REVERT: C 645 LEU cc_start: 0.8051 (tp) cc_final: 0.7763 (mt) REVERT: C 651 TYR cc_start: 0.7028 (t80) cc_final: 0.6341 (t80) REVERT: C 655 LEU cc_start: 0.8828 (tt) cc_final: 0.8185 (mm) REVERT: C 682 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.7279 (m-10) REVERT: C 723 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7519 (tt0) REVERT: C 737 MET cc_start: 0.8630 (mtp) cc_final: 0.8088 (mtp) REVERT: D 447 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7164 (ttmm) REVERT: D 501 MET cc_start: 0.7562 (mtt) cc_final: 0.6971 (mmt) REVERT: D 665 GLU cc_start: 0.7924 (tt0) cc_final: 0.7643 (tm-30) REVERT: D 666 SER cc_start: 0.8764 (m) cc_final: 0.8384 (t) REVERT: D 691 MET cc_start: 0.8125 (ppp) cc_final: 0.7920 (tmm) REVERT: D 696 LYS cc_start: 0.9111 (mtpt) cc_final: 0.8539 (pttm) REVERT: D 774 TYR cc_start: 0.5780 (t80) cc_final: 0.5554 (t80) REVERT: D 790 LYS cc_start: 0.8375 (mmtt) cc_final: 0.8121 (mmtt) outliers start: 52 outliers final: 22 residues processed: 333 average time/residue: 0.3102 time to fit residues: 165.2349 Evaluate side-chains 280 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 253 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 367 HIS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 682 TYR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 447 LYS 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 202 optimal weight: 9.9990 chunk 165 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 243 optimal weight: 20.0000 chunk 263 optimal weight: 7.9990 chunk 217 optimal weight: 0.5980 chunk 241 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 195 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 141 ASN A 350 HIS A 495 ASN B 196 ASN C 129 HIS C 141 ASN C 495 ASN D 111 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23146 Z= 0.225 Angle : 0.818 14.502 31314 Z= 0.376 Chirality : 0.051 0.468 3704 Planarity : 0.005 0.070 3858 Dihedral : 17.543 114.802 4456 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.93 % Favored : 90.93 % Rotamer: Outliers : 2.22 % Allowed : 12.25 % Favored : 85.53 % 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: -3.28 (0.15), residues: 2704 helix: -1.27 (0.14), residues: 1100 sheet: -3.52 (0.22), residues: 404 loop : -2.46 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 799 HIS 0.015 0.001 HIS A 367 PHE 0.032 0.002 PHE D 359 TYR 0.019 0.002 TYR B 443 ARG 0.005 0.000 ARG B 468 *********************** 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 331 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 286 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.9054 (mt) cc_final: 0.8830 (mp) REVERT: A 185 LEU cc_start: 0.8888 (mt) cc_final: 0.8541 (mt) REVERT: A 315 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6378 (t80) REVERT: A 342 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8320 (m) REVERT: A 426 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7962 (t70) REVERT: A 465 ASP cc_start: 0.8336 (t70) cc_final: 0.7846 (t0) REVERT: A 651 TYR cc_start: 0.7441 (t80) cc_final: 0.6834 (t80) REVERT: A 655 LEU cc_start: 0.9139 (tp) cc_final: 0.8776 (mm) REVERT: A 672 ASP cc_start: 0.8080 (t0) cc_final: 0.7344 (p0) REVERT: A 677 GLN cc_start: 0.8492 (pp30) cc_final: 0.8130 (pp30) REVERT: B 251 TYR cc_start: 0.8325 (m-80) cc_final: 0.8087 (m-80) REVERT: B 316 MET cc_start: 0.9013 (ttt) cc_final: 0.8600 (ttm) REVERT: B 319 ASP cc_start: 0.7802 (t0) cc_final: 0.6987 (t0) REVERT: B 484 GLU cc_start: 0.5934 (mp0) cc_final: 0.5616 (pm20) REVERT: B 501 MET cc_start: 0.6877 (mmt) cc_final: 0.6653 (mmt) REVERT: B 541 LEU cc_start: 0.8399 (tt) cc_final: 0.8168 (tp) REVERT: B 794 MET cc_start: 0.5567 (ptm) cc_final: 0.5157 (ptm) REVERT: C 78 TYR cc_start: 0.8013 (p90) cc_final: 0.7671 (p90) REVERT: C 130 ILE cc_start: 0.8991 (mt) cc_final: 0.8760 (mp) REVERT: C 140 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8179 (p0) REVERT: C 141 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8461 (m110) REVERT: C 170 LYS cc_start: 0.8762 (mttm) cc_final: 0.8481 (mtmm) REVERT: C 287 THR cc_start: 0.8492 (m) cc_final: 0.8081 (t) REVERT: C 316 MET cc_start: 0.7855 (ttm) cc_final: 0.7610 (ttm) REVERT: C 481 ARG cc_start: 0.8083 (mtt-85) cc_final: 0.7868 (mtt-85) REVERT: C 645 LEU cc_start: 0.8067 (tp) cc_final: 0.7747 (mt) REVERT: C 651 TYR cc_start: 0.6782 (t80) cc_final: 0.6103 (t80) REVERT: C 655 LEU cc_start: 0.8794 (tt) cc_final: 0.8163 (mm) REVERT: C 723 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7525 (tt0) REVERT: C 737 MET cc_start: 0.8637 (mtp) cc_final: 0.8377 (mtp) REVERT: D 447 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7065 (ttmm) REVERT: D 501 MET cc_start: 0.7720 (mtt) cc_final: 0.7086 (mmt) REVERT: D 665 GLU cc_start: 0.8038 (tt0) cc_final: 0.7589 (tm-30) REVERT: D 666 SER cc_start: 0.8679 (m) cc_final: 0.8302 (t) REVERT: D 691 MET cc_start: 0.8041 (ppp) cc_final: 0.7792 (tmm) REVERT: D 696 LYS cc_start: 0.9073 (mtpt) cc_final: 0.8557 (pttt) REVERT: D 790 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7022 (mmtt) outliers start: 45 outliers final: 21 residues processed: 314 average time/residue: 0.3052 time to fit residues: 154.0749 Evaluate side-chains 276 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 249 time to evaluate : 2.551 ------------------------------------------------------------------------------- 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 298 MET Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 794 MET 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 732 ASP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 140 ASP 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 D residue 92 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 447 LYS Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 758 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 20.0000 chunk 183 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 259 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 chunk 231 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 B 196 ASN B 350 HIS C 141 ASN D 350 HIS D 714 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 23146 Z= 0.325 Angle : 0.826 13.945 31314 Z= 0.382 Chirality : 0.052 0.448 3704 Planarity : 0.005 0.066 3858 Dihedral : 15.843 112.147 4456 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.63 % Favored : 90.22 % Rotamer: Outliers : 2.35 % Allowed : 13.42 % Favored : 84.23 % 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: -2.83 (0.16), residues: 2704 helix: -0.75 (0.15), residues: 1094 sheet: -3.39 (0.23), residues: 408 loop : -2.32 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 353 HIS 0.022 0.001 HIS A 350 PHE 0.029 0.002 PHE B 446 TYR 0.018 0.002 TYR D 252 ARG 0.010 0.001 ARG D 354 *********************** 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 304 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 256 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.9077 (mt) cc_final: 0.8851 (mp) REVERT: A 185 LEU cc_start: 0.8885 (mt) cc_final: 0.8486 (mt) REVERT: A 210 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7478 (t0) REVERT: A 342 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8378 (m) REVERT: A 426 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.8008 (t70) REVERT: A 651 TYR cc_start: 0.7446 (t80) cc_final: 0.6835 (t80) REVERT: A 655 LEU cc_start: 0.9158 (tp) cc_final: 0.8783 (mm) REVERT: B 251 TYR cc_start: 0.8351 (m-80) cc_final: 0.8080 (m-80) REVERT: B 484 GLU cc_start: 0.6035 (mp0) cc_final: 0.5636 (pm20) REVERT: B 501 MET cc_start: 0.6685 (mmt) cc_final: 0.6469 (mmt) REVERT: B 541 LEU cc_start: 0.8411 (tt) cc_final: 0.8206 (tp) REVERT: B 641 TRP cc_start: 0.6139 (t-100) cc_final: 0.5916 (t-100) REVERT: B 790 LYS cc_start: 0.8332 (mtpp) cc_final: 0.8034 (mmtt) REVERT: C 79 ASP cc_start: 0.7827 (t0) cc_final: 0.6543 (t70) REVERT: C 82 LYS cc_start: 0.7660 (tttp) cc_final: 0.7421 (tptm) REVERT: C 130 ILE cc_start: 0.8983 (mt) cc_final: 0.8762 (mp) REVERT: C 140 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8044 (p0) REVERT: C 170 LYS cc_start: 0.8749 (mttm) cc_final: 0.8412 (mtmm) REVERT: C 287 THR cc_start: 0.8429 (m) cc_final: 0.8158 (t) REVERT: C 481 ARG cc_start: 0.8124 (mtt-85) cc_final: 0.7864 (mtt-85) REVERT: C 651 TYR cc_start: 0.6855 (t80) cc_final: 0.6348 (t80) REVERT: C 655 LEU cc_start: 0.8819 (tt) cc_final: 0.8228 (mm) REVERT: C 664 MET cc_start: 0.8423 (mmm) cc_final: 0.8146 (mmt) REVERT: C 682 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.7280 (m-10) REVERT: C 723 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7474 (tt0) REVERT: C 737 MET cc_start: 0.8657 (mtp) cc_final: 0.8427 (mtp) REVERT: D 447 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7183 (ttmm) REVERT: D 501 MET cc_start: 0.7765 (mtt) cc_final: 0.7077 (mmt) REVERT: D 665 GLU cc_start: 0.8056 (tt0) cc_final: 0.7602 (tm-30) REVERT: D 666 SER cc_start: 0.8684 (m) cc_final: 0.8331 (t) REVERT: D 691 MET cc_start: 0.8089 (ppp) cc_final: 0.7777 (tmm) REVERT: D 696 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8545 (pttt) REVERT: D 735 PHE cc_start: 0.8502 (t80) cc_final: 0.8216 (t80) outliers start: 48 outliers final: 28 residues processed: 286 average time/residue: 0.3202 time to fit residues: 146.0855 Evaluate side-chains 275 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 241 time to evaluate : 2.414 ------------------------------------------------------------------------------- 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 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 426 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 682 TYR Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain D residue 92 SER 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 679 LYS Chi-restraints excluded: chain D residue 758 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 0.7980 chunk 147 optimal weight: 0.0970 chunk 3 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 106 optimal weight: 0.1980 chunk 221 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 232 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 B 111 HIS B 336 GLN B 350 HIS C 141 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23146 Z= 0.193 Angle : 0.754 12.633 31314 Z= 0.346 Chirality : 0.048 0.411 3704 Planarity : 0.004 0.064 3858 Dihedral : 14.684 110.474 4456 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.33 % Favored : 91.52 % Rotamer: Outliers : 2.27 % Allowed : 13.97 % Favored : 83.77 % 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: -2.39 (0.16), residues: 2704 helix: -0.30 (0.16), residues: 1090 sheet: -3.23 (0.23), residues: 424 loop : -2.11 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 640 HIS 0.007 0.001 HIS C 328 PHE 0.018 0.001 PHE D 359 TYR 0.027 0.001 TYR B 86 ARG 0.007 0.000 ARG D 354 *********************** 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 315 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 269 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7471 (tttp) cc_final: 0.6703 (tptm) REVERT: A 130 ILE cc_start: 0.9028 (mt) cc_final: 0.8799 (mp) REVERT: A 185 LEU cc_start: 0.8841 (mt) cc_final: 0.8521 (mt) REVERT: A 342 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8302 (m) REVERT: A 426 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8185 (t70) REVERT: A 465 ASP cc_start: 0.8254 (t70) cc_final: 0.7744 (t0) REVERT: A 651 TYR cc_start: 0.7510 (t80) cc_final: 0.6913 (t80) REVERT: A 655 LEU cc_start: 0.9142 (tp) cc_final: 0.8764 (mm) REVERT: A 672 ASP cc_start: 0.8326 (t0) cc_final: 0.7419 (p0) REVERT: B 251 TYR cc_start: 0.8254 (m-80) cc_final: 0.7966 (m-80) REVERT: B 484 GLU cc_start: 0.5972 (mp0) cc_final: 0.5609 (pm20) REVERT: B 501 MET cc_start: 0.6761 (mmt) cc_final: 0.6526 (mmt) REVERT: B 534 MET cc_start: 0.7172 (ttm) cc_final: 0.6948 (ttp) REVERT: B 665 GLU cc_start: 0.6891 (tm-30) cc_final: 0.6645 (tm-30) REVERT: B 702 TYR cc_start: 0.7936 (m-10) cc_final: 0.7524 (m-10) REVERT: B 735 PHE cc_start: 0.8252 (t80) cc_final: 0.7965 (t80) REVERT: B 737 MET cc_start: 0.8362 (ptp) cc_final: 0.7816 (pmm) REVERT: B 794 MET cc_start: 0.6049 (ptm) cc_final: 0.5370 (ptm) REVERT: C 43 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7089 (tm-30) REVERT: C 79 ASP cc_start: 0.7611 (t0) cc_final: 0.6850 (t70) REVERT: C 140 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7969 (p0) REVERT: C 141 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8338 (m110) REVERT: C 170 LYS cc_start: 0.8704 (mttm) cc_final: 0.8397 (mtmm) REVERT: C 210 ASP cc_start: 0.7708 (t0) cc_final: 0.7439 (m-30) REVERT: C 287 THR cc_start: 0.8409 (m) cc_final: 0.8130 (t) REVERT: C 315 PHE cc_start: 0.7394 (t80) cc_final: 0.7139 (t80) REVERT: C 645 LEU cc_start: 0.8056 (tp) cc_final: 0.7769 (mt) REVERT: C 651 TYR cc_start: 0.6873 (t80) cc_final: 0.6359 (t80) REVERT: C 655 LEU cc_start: 0.8917 (tt) cc_final: 0.8379 (mm) REVERT: C 664 MET cc_start: 0.8232 (mmm) cc_final: 0.7910 (mtt) REVERT: C 737 MET cc_start: 0.8606 (mtp) cc_final: 0.8357 (mtp) REVERT: D 319 ASP cc_start: 0.7711 (t0) cc_final: 0.6752 (t0) REVERT: D 447 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7097 (ttmm) REVERT: D 501 MET cc_start: 0.7805 (mtt) cc_final: 0.7115 (mmt) REVERT: D 665 GLU cc_start: 0.8070 (tt0) cc_final: 0.7398 (tm-30) REVERT: D 666 SER cc_start: 0.8658 (m) cc_final: 0.8316 (t) REVERT: D 691 MET cc_start: 0.8050 (ppp) cc_final: 0.7722 (tmm) REVERT: D 696 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8519 (pttt) REVERT: D 735 PHE cc_start: 0.8330 (t80) cc_final: 0.8076 (t80) outliers start: 46 outliers final: 17 residues processed: 298 average time/residue: 0.3246 time to fit residues: 155.1435 Evaluate side-chains 262 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 240 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 277 THR 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 426 ASP Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 140 ASP 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 493 ASP Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 447 LYS Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 758 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 0.5980 chunk 233 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 259 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 328 HIS B 350 HIS D 196 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 23146 Z= 0.379 Angle : 0.818 11.161 31314 Z= 0.379 Chirality : 0.051 0.401 3704 Planarity : 0.005 0.061 3858 Dihedral : 13.884 107.300 4454 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.15 % Favored : 89.70 % Rotamer: Outliers : 2.60 % Allowed : 14.30 % Favored : 83.10 % 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: -2.30 (0.16), residues: 2704 helix: -0.14 (0.16), residues: 1074 sheet: -3.14 (0.23), residues: 424 loop : -2.15 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 296 HIS 0.006 0.001 HIS D 253 PHE 0.021 0.002 PHE B 359 TYR 0.024 0.002 TYR D 252 ARG 0.007 0.001 ARG D 354 *********************** 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 306 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 252 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7946 (t70) REVERT: A 651 TYR cc_start: 0.7448 (t80) cc_final: 0.6815 (t80) REVERT: A 655 LEU cc_start: 0.9163 (tp) cc_final: 0.8822 (mm) REVERT: B 484 GLU cc_start: 0.6153 (mp0) cc_final: 0.5650 (pm20) REVERT: B 665 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6679 (tm-30) REVERT: B 702 TYR cc_start: 0.8097 (m-10) cc_final: 0.7711 (m-10) REVERT: B 735 PHE cc_start: 0.8301 (t80) cc_final: 0.7963 (t80) REVERT: B 737 MET cc_start: 0.8343 (ptp) cc_final: 0.7821 (pmm) REVERT: B 790 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8008 (ptmt) REVERT: C 79 ASP cc_start: 0.7803 (t0) cc_final: 0.6680 (t70) REVERT: C 140 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8112 (p0) REVERT: C 170 LYS cc_start: 0.8738 (mttm) cc_final: 0.8384 (mtmm) REVERT: C 287 THR cc_start: 0.8535 (m) cc_final: 0.8259 (t) REVERT: C 315 PHE cc_start: 0.7697 (t80) cc_final: 0.7258 (t80) REVERT: C 655 LEU cc_start: 0.8995 (tt) cc_final: 0.8536 (mm) REVERT: C 669 ASP cc_start: 0.7977 (t70) cc_final: 0.7762 (t0) REVERT: C 737 MET cc_start: 0.8694 (mtp) cc_final: 0.8471 (mtp) REVERT: D 209 LYS cc_start: 0.8627 (ptmt) cc_final: 0.8118 (pttm) REVERT: D 447 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6980 (ttmm) REVERT: D 501 MET cc_start: 0.7840 (mtt) cc_final: 0.7113 (mmt) REVERT: D 665 GLU cc_start: 0.8126 (tt0) cc_final: 0.7462 (tm-30) REVERT: D 666 SER cc_start: 0.8634 (m) cc_final: 0.8315 (t) REVERT: D 691 MET cc_start: 0.8169 (ppp) cc_final: 0.7836 (tmm) REVERT: D 696 LYS cc_start: 0.9039 (mtpt) cc_final: 0.8540 (pttt) REVERT: D 735 PHE cc_start: 0.8369 (t80) cc_final: 0.8068 (t80) REVERT: D 787 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6047 (pp20) outliers start: 54 outliers final: 29 residues processed: 288 average time/residue: 0.3075 time to fit residues: 144.0001 Evaluate side-chains 268 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 277 THR 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 332 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 277 THR 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 501 MET Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 745 VAL 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 664 MET Chi-restraints excluded: chain D residue 679 LYS 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 249 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 218 optimal weight: 0.8980 chunk 144 optimal weight: 0.2980 chunk 258 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 B 65 ASN B 350 HIS ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23146 Z= 0.200 Angle : 0.744 10.180 31314 Z= 0.341 Chirality : 0.048 0.430 3704 Planarity : 0.004 0.060 3858 Dihedral : 13.246 106.776 4454 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.22 % Favored : 91.63 % Rotamer: Outliers : 2.22 % Allowed : 15.65 % Favored : 82.13 % 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: -2.09 (0.16), residues: 2704 helix: 0.05 (0.16), residues: 1094 sheet: -3.08 (0.24), residues: 424 loop : -2.06 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 296 HIS 0.005 0.001 HIS C 508 PHE 0.019 0.001 PHE D 446 TYR 0.019 0.001 TYR D 764 ARG 0.006 0.000 ARG D 354 *********************** 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 298 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 253 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7242 (tttp) cc_final: 0.6373 (tptm) REVERT: A 185 LEU cc_start: 0.8860 (mt) cc_final: 0.8541 (mt) REVERT: A 298 MET cc_start: 0.8559 (ptp) cc_final: 0.8285 (ppp) REVERT: A 315 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7193 (t80) REVERT: A 342 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8353 (m) REVERT: A 426 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7970 (t70) REVERT: A 651 TYR cc_start: 0.7520 (t80) cc_final: 0.6906 (t80) REVERT: A 655 LEU cc_start: 0.9152 (tp) cc_final: 0.8777 (mm) REVERT: B 484 GLU cc_start: 0.5682 (mp0) cc_final: 0.5365 (pm20) REVERT: B 665 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6644 (tm-30) REVERT: B 666 SER cc_start: 0.8615 (m) cc_final: 0.8344 (p) REVERT: B 702 TYR cc_start: 0.8100 (m-10) cc_final: 0.7660 (m-10) REVERT: B 735 PHE cc_start: 0.8042 (t80) cc_final: 0.7742 (t80) REVERT: B 737 MET cc_start: 0.8332 (ptp) cc_final: 0.7882 (pmm) REVERT: C 79 ASP cc_start: 0.7751 (t0) cc_final: 0.7026 (t70) REVERT: C 140 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.7889 (p0) REVERT: C 170 LYS cc_start: 0.8653 (mttm) cc_final: 0.8316 (mtmm) REVERT: C 185 LEU cc_start: 0.8729 (mt) cc_final: 0.8512 (mp) REVERT: C 287 THR cc_start: 0.8508 (m) cc_final: 0.8221 (t) REVERT: C 315 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7342 (t80) REVERT: C 655 LEU cc_start: 0.8989 (tt) cc_final: 0.8538 (mm) REVERT: C 669 ASP cc_start: 0.7896 (t70) cc_final: 0.7693 (t0) REVERT: C 737 MET cc_start: 0.8566 (mtp) cc_final: 0.8348 (mtp) REVERT: D 447 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6872 (ttmm) REVERT: D 501 MET cc_start: 0.7835 (mtt) cc_final: 0.7103 (mmt) REVERT: D 665 GLU cc_start: 0.8058 (tt0) cc_final: 0.7385 (tm-30) REVERT: D 666 SER cc_start: 0.8603 (m) cc_final: 0.8296 (t) REVERT: D 691 MET cc_start: 0.8140 (ppp) cc_final: 0.7820 (tmm) REVERT: D 696 LYS cc_start: 0.8999 (mtpt) cc_final: 0.8503 (pttt) REVERT: D 735 PHE cc_start: 0.8272 (t80) cc_final: 0.7982 (t80) outliers start: 45 outliers final: 25 residues processed: 281 average time/residue: 0.3099 time to fit residues: 139.7260 Evaluate side-chains 272 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 241 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 426 ASP 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 721 ASN Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 277 THR 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 315 PHE Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 661 VAL 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 664 MET Chi-restraints excluded: chain D residue 732 ASP 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 159 optimal weight: 0.2980 chunk 103 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 175 optimal weight: 0.4980 chunk 127 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 B 196 ASN B 350 HIS D 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23146 Z= 0.218 Angle : 0.741 12.415 31314 Z= 0.340 Chirality : 0.048 0.385 3704 Planarity : 0.004 0.058 3858 Dihedral : 12.473 105.584 4454 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.15 % Favored : 90.78 % Rotamer: Outliers : 1.85 % Allowed : 15.86 % Favored : 82.30 % 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: -1.91 (0.17), residues: 2704 helix: 0.23 (0.16), residues: 1094 sheet: -3.02 (0.24), residues: 426 loop : -1.97 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 640 HIS 0.005 0.001 HIS D 253 PHE 0.025 0.001 PHE D 337 TYR 0.019 0.001 TYR D 764 ARG 0.006 0.000 ARG D 354 *********************** 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 287 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 251 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.8807 (mt) cc_final: 0.8482 (mt) REVERT: A 298 MET cc_start: 0.8475 (ptp) cc_final: 0.8230 (ppp) REVERT: A 315 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.7237 (t80) REVERT: A 426 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7953 (t70) REVERT: A 651 TYR cc_start: 0.7523 (t80) cc_final: 0.6898 (t80) REVERT: A 655 LEU cc_start: 0.9138 (tp) cc_final: 0.8746 (mm) REVERT: A 664 MET cc_start: 0.8072 (mmt) cc_final: 0.7832 (mmt) REVERT: B 484 GLU cc_start: 0.5684 (mp0) cc_final: 0.5396 (pm20) REVERT: B 665 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6476 (tm-30) REVERT: B 666 SER cc_start: 0.8622 (m) cc_final: 0.8306 (t) REVERT: B 691 MET cc_start: 0.7868 (ppp) cc_final: 0.7642 (tmm) REVERT: B 702 TYR cc_start: 0.8121 (m-10) cc_final: 0.7698 (m-10) REVERT: B 735 PHE cc_start: 0.7946 (t80) cc_final: 0.7690 (t80) REVERT: B 737 MET cc_start: 0.8451 (ptp) cc_final: 0.7968 (pmm) REVERT: C 79 ASP cc_start: 0.7777 (t0) cc_final: 0.7059 (t70) REVERT: C 82 LYS cc_start: 0.7131 (tptm) cc_final: 0.6832 (tptp) REVERT: C 140 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7885 (p0) REVERT: C 170 LYS cc_start: 0.8669 (mttm) cc_final: 0.8326 (mtmm) REVERT: C 287 THR cc_start: 0.8541 (m) cc_final: 0.8257 (t) REVERT: C 315 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7364 (t80) REVERT: C 655 LEU cc_start: 0.8997 (tt) cc_final: 0.8547 (mm) REVERT: C 669 ASP cc_start: 0.7900 (t70) cc_final: 0.7694 (t0) REVERT: C 737 MET cc_start: 0.8571 (mtp) cc_final: 0.8361 (mtp) REVERT: D 340 MET cc_start: 0.8621 (tpp) cc_final: 0.8137 (mmm) REVERT: D 447 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6751 (ttmm) REVERT: D 501 MET cc_start: 0.7818 (mtt) cc_final: 0.7021 (mmp) REVERT: D 665 GLU cc_start: 0.7843 (tt0) cc_final: 0.7319 (tm-30) REVERT: D 666 SER cc_start: 0.8568 (m) cc_final: 0.8309 (t) REVERT: D 691 MET cc_start: 0.8113 (ppp) cc_final: 0.7773 (tmm) REVERT: D 696 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8514 (pttt) REVERT: D 735 PHE cc_start: 0.8160 (t80) cc_final: 0.7882 (t80) REVERT: D 787 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6170 (pp20) REVERT: D 792 HIS cc_start: 0.6605 (p90) cc_final: 0.5846 (p-80) outliers start: 36 outliers final: 22 residues processed: 275 average time/residue: 0.3168 time to fit residues: 139.8422 Evaluate side-chains 267 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 240 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 426 ASP 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 721 ASN Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 277 THR 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 315 PHE Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 661 VAL 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 732 ASP Chi-restraints excluded: chain D residue 758 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 6.9990 chunk 225 optimal weight: 0.8980 chunk 240 optimal weight: 8.9990 chunk 144 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 chunk 227 optimal weight: 0.8980 chunk 239 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 B 350 HIS ** C 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN D 350 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23146 Z= 0.198 Angle : 0.724 11.411 31314 Z= 0.333 Chirality : 0.047 0.380 3704 Planarity : 0.004 0.058 3858 Dihedral : 11.967 105.753 4454 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.67 % Favored : 91.26 % Rotamer: Outliers : 1.85 % Allowed : 15.77 % Favored : 82.38 % 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: -1.69 (0.17), residues: 2704 helix: 0.49 (0.16), residues: 1082 sheet: -2.92 (0.24), residues: 426 loop : -1.91 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 640 HIS 0.005 0.001 HIS A 508 PHE 0.019 0.001 PHE D 446 TYR 0.020 0.001 TYR D 764 ARG 0.009 0.000 ARG C 748 *********************** 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 287 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 251 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.8783 (mt) cc_final: 0.8448 (mt) REVERT: A 226 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8782 (t) REVERT: A 315 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7272 (t80) REVERT: A 426 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8170 (t70) REVERT: A 651 TYR cc_start: 0.7536 (t80) cc_final: 0.6849 (t80) REVERT: A 655 LEU cc_start: 0.9124 (tp) cc_final: 0.8724 (mm) REVERT: B 484 GLU cc_start: 0.5639 (mp0) cc_final: 0.5383 (pm20) REVERT: B 665 GLU cc_start: 0.6748 (tm-30) cc_final: 0.6406 (tm-30) REVERT: B 666 SER cc_start: 0.8630 (m) cc_final: 0.8324 (t) REVERT: B 691 MET cc_start: 0.7858 (ppp) cc_final: 0.7633 (tmm) REVERT: B 702 TYR cc_start: 0.8161 (m-10) cc_final: 0.7742 (m-10) REVERT: B 735 PHE cc_start: 0.7852 (t80) cc_final: 0.7603 (t80) REVERT: B 737 MET cc_start: 0.8447 (ptp) cc_final: 0.7974 (pmm) REVERT: C 170 LYS cc_start: 0.8609 (mttm) cc_final: 0.8267 (mtmm) REVERT: C 248 MET cc_start: 0.9095 (mmt) cc_final: 0.8760 (mmt) REVERT: C 315 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7368 (t80) REVERT: C 655 LEU cc_start: 0.9001 (tt) cc_final: 0.8560 (mm) REVERT: C 664 MET cc_start: 0.8178 (mmt) cc_final: 0.7916 (tpp) REVERT: C 669 ASP cc_start: 0.7870 (t70) cc_final: 0.7649 (t0) REVERT: D 340 MET cc_start: 0.8719 (tpp) cc_final: 0.8298 (mmm) REVERT: D 447 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6834 (ttmm) REVERT: D 501 MET cc_start: 0.7797 (mtt) cc_final: 0.7145 (mmt) REVERT: D 665 GLU cc_start: 0.7919 (tt0) cc_final: 0.7267 (tm-30) REVERT: D 666 SER cc_start: 0.8558 (m) cc_final: 0.8270 (t) REVERT: D 691 MET cc_start: 0.8131 (ppp) cc_final: 0.7798 (tmm) REVERT: D 696 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8457 (pttt) REVERT: D 735 PHE cc_start: 0.7951 (t80) cc_final: 0.7670 (t80) REVERT: D 787 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6198 (pp20) outliers start: 36 outliers final: 25 residues processed: 271 average time/residue: 0.3081 time to fit residues: 134.8795 Evaluate side-chains 266 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 236 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 640 TRP Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 277 THR 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 315 PHE Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 661 VAL 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 732 ASP 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 254 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 266 optimal weight: 5.9990 chunk 245 optimal weight: 20.0000 chunk 212 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS B 111 HIS ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 350 HIS ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS C 754 GLN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 328 HIS D 350 HIS D 792 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.140 23146 Z= 0.564 Angle : 0.901 12.735 31314 Z= 0.425 Chirality : 0.054 0.392 3704 Planarity : 0.005 0.056 3858 Dihedral : 11.953 106.621 4454 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.67 % Favored : 89.22 % Rotamer: Outliers : 1.72 % Allowed : 16.19 % Favored : 82.09 % 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: -2.17 (0.16), residues: 2704 helix: -0.04 (0.15), residues: 1104 sheet: -3.13 (0.24), residues: 410 loop : -2.11 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 296 HIS 0.011 0.002 HIS D 253 PHE 0.032 0.003 PHE D 337 TYR 0.034 0.003 TYR D 252 ARG 0.005 0.001 ARG A 349 ********************** 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 262 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 229 time to evaluate : 2.903 Fit side-chains revert: symmetry clash REVERT: A 441 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7606 (mt-10) REVERT: A 651 TYR cc_start: 0.7537 (t80) cc_final: 0.6925 (t80) REVERT: A 655 LEU cc_start: 0.9220 (tp) cc_final: 0.8893 (mm) REVERT: A 723 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7569 (tt0) REVERT: B 484 GLU cc_start: 0.6005 (mp0) cc_final: 0.5160 (pm20) REVERT: B 665 GLU cc_start: 0.6931 (tm-30) cc_final: 0.6577 (tm-30) REVERT: B 666 SER cc_start: 0.8672 (m) cc_final: 0.8346 (t) REVERT: B 735 PHE cc_start: 0.8318 (t80) cc_final: 0.8046 (t80) REVERT: B 737 MET cc_start: 0.8367 (ptp) cc_final: 0.7926 (pmm) REVERT: C 82 LYS cc_start: 0.7523 (tptp) cc_final: 0.7304 (tptp) REVERT: C 140 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7865 (p0) REVERT: C 170 LYS cc_start: 0.8777 (mttm) cc_final: 0.8406 (mtmm) REVERT: C 315 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7361 (t80) REVERT: C 655 LEU cc_start: 0.9080 (tt) cc_final: 0.8619 (mm) REVERT: C 664 MET cc_start: 0.8309 (mmt) cc_final: 0.7880 (tpp) REVERT: D 209 LYS cc_start: 0.8589 (ptmt) cc_final: 0.8185 (pttm) REVERT: D 447 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6729 (ttmm) REVERT: D 501 MET cc_start: 0.7845 (mtt) cc_final: 0.6940 (mmm) REVERT: D 665 GLU cc_start: 0.8002 (tt0) cc_final: 0.7330 (tm-30) REVERT: D 666 SER cc_start: 0.8692 (m) cc_final: 0.8396 (t) REVERT: D 691 MET cc_start: 0.8271 (ppp) cc_final: 0.7879 (tmm) REVERT: D 696 LYS cc_start: 0.9030 (mtpt) cc_final: 0.8551 (pttt) REVERT: D 735 PHE cc_start: 0.8074 (t80) cc_final: 0.7782 (t80) REVERT: D 787 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6171 (pp20) outliers start: 33 outliers final: 23 residues processed: 250 average time/residue: 0.3114 time to fit residues: 125.9877 Evaluate side-chains 244 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 414 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 732 ASP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 277 THR 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 315 PHE Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 745 VAL 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 732 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 212 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN B 350 HIS D 136 HIS D 350 HIS D 792 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.137866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.099132 restraints weight = 88216.728| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 4.66 r_work: 0.3020 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23146 Z= 0.221 Angle : 0.746 12.843 31314 Z= 0.344 Chirality : 0.047 0.377 3704 Planarity : 0.004 0.058 3858 Dihedral : 11.622 105.326 4454 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.22 % Favored : 91.70 % Rotamer: Outliers : 1.68 % Allowed : 16.82 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.08 % 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: -1.72 (0.17), residues: 2704 helix: 0.50 (0.16), residues: 1078 sheet: -2.90 (0.23), residues: 438 loop : -1.96 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 296 HIS 0.006 0.001 HIS A 508 PHE 0.020 0.001 PHE D 446 TYR 0.020 0.001 TYR D 764 ARG 0.005 0.000 ARG D 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4670.95 seconds wall clock time: 84 minutes 57.94 seconds (5097.94 seconds total)