Starting phenix.real_space_refine on Fri Apr 12 14:56:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crw_7574/04_2024/6crw_7574.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crw_7574/04_2024/6crw_7574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crw_7574/04_2024/6crw_7574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crw_7574/04_2024/6crw_7574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crw_7574/04_2024/6crw_7574.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crw_7574/04_2024/6crw_7574.pdb" } resolution = 3.9 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= -0.000 sd= 0.006 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 138 5.16 5 C 16537 2.51 5 N 4192 2.21 5 O 5127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 25994 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8339 Classifications: {'peptide': 1068} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1014} Chain breaks: 6 Chain: "B" Number of atoms: 8342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8342 Classifications: {'peptide': 1068} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1014} Chain breaks: 6 Chain: "C" Number of atoms: 8334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8334 Classifications: {'peptide': 1068} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1014} Chain breaks: 6 Chain: "D" 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: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: "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: 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: "M" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "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: 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: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "S" 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: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 13.09, per 1000 atoms: 0.50 Number of scatterers: 25994 At special positions: 0 Unit cell: (150.38, 142.14, 175.1, 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 138 16.00 O 5127 8.00 N 4192 7.00 C 16537 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.06 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.55 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.02 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.02 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.02 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.02 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.02 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.02 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " 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 F 3 " - " MAN F 4 " " BMA O 3 " - " MAN O 4 " " BMA R 3 " - " MAN R 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA U 3 " - " MAN U 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " 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 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 R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1305 " - " ASN A 589 " " NAG A1310 " - " ASN A 691 " " NAG A1317 " - " ASN A1056 " " NAG B1309 " - " ASN B 589 " " NAG B1312 " - " ASN B 691 " " NAG B1322 " - " ASN B1080 " " NAG C1301 " - " ASN C 65 " " NAG C1306 " - " ASN C 227 " " NAG C1309 " - " ASN C 318 " " NAG C1310 " - " ASN C 589 " " NAG C1315 " - " ASN C 691 " " NAG C1324 " - " ASN C1056 " " NAG D 1 " - " ASN A 269 " " NAG E 1 " - " ASN A 602 " " NAG F 1 " - " ASN A 699 " " NAG G 1 " - " ASN A 783 " " NAG H 1 " - " ASN A1080 " " NAG I 1 " - " ASN A1116 " " NAG J 1 " - " ASN B 65 " " NAG K 1 " - " ASN B 269 " " NAG L 1 " - " ASN B 318 " " NAG M 1 " - " ASN B 602 " " NAG N 1 " - " ASN B 699 " " NAG O 1 " - " ASN B 783 " " NAG P 1 " - " ASN B1056 " " NAG Q 1 " - " ASN B1116 " " NAG R 1 " - " ASN C 119 " " NAG S 1 " - " ASN C 269 " " NAG T 1 " - " ASN C 602 " " NAG U 1 " - " ASN C 699 " " NAG V 1 " - " ASN C 783 " " NAG W 1 " - " ASN C1080 " " NAG X 1 " - " ASN C1116 " Time building additional restraints: 11.53 Conformation dependent library (CDL) restraints added in 4.9 seconds 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6002 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 52 sheets defined 23.3% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.650A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.778A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 removed outlier: 4.309A pdb=" N ARG A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 395' Processing helix chain 'A' and resid 403 through 409 removed outlier: 3.754A pdb=" N TYR A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.688A pdb=" N HIS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.611A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 764 removed outlier: 4.010A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN A 756 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 809 removed outlier: 3.604A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 866 removed outlier: 3.516A pdb=" N THR A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 873 removed outlier: 4.265A pdb=" N GLY A 871 " --> pdb=" O GLY A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.189A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.682A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 removed outlier: 4.152A pdb=" N SER A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1013 removed outlier: 3.775A pdb=" N VAL A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.923A pdb=" N ASP B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 395 removed outlier: 3.947A pdb=" N ARG B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 391 through 395' Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.538A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.799A pdb=" N THR B 608 " --> pdb=" O THR B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 728 through 736 Processing helix chain 'B' and resid 740 through 765 removed outlier: 4.392A pdb=" N GLN B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 809 removed outlier: 3.557A pdb=" N LYS B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 867 removed outlier: 3.737A pdb=" N THR B 865 " --> pdb=" O SER B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 873 Processing helix chain 'B' and resid 879 through 891 removed outlier: 3.919A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 900 removed outlier: 4.128A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.567A pdb=" N ILE B 913 " --> pdb=" O PHE B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.539A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 937 " --> pdb=" O VAL B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 965 Processing helix chain 'B' and resid 967 through 1013 removed outlier: 3.863A pdb=" N VAL B 973 " --> pdb=" O PRO B 969 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 980 " --> pdb=" O ASP B 976 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 984 " --> pdb=" O THR B 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 372 through 377 removed outlier: 3.742A pdb=" N LEU C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 removed outlier: 3.788A pdb=" N ARG C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.704A pdb=" N TYR C 491 " --> pdb=" O GLY C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 612 removed outlier: 3.504A pdb=" N VAL C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 736 removed outlier: 3.572A pdb=" N ALA C 732 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.784A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 745 " --> pdb=" O PHE C 741 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN C 756 " --> pdb=" O ILE C 752 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 805 removed outlier: 3.518A pdb=" N ASP C 802 " --> pdb=" O SER C 798 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 803 " --> pdb=" O PHE C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 864 Processing helix chain 'C' and resid 867 through 873 removed outlier: 3.820A pdb=" N GLY C 871 " --> pdb=" O GLY C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 890 Processing helix chain 'C' and resid 895 through 901 Processing helix chain 'C' and resid 901 through 923 Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.630A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN C 937 " --> pdb=" O VAL C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 966 removed outlier: 3.583A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 3.521A pdb=" N THR C 980 " --> pdb=" O ASP C 976 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 981 " --> pdb=" O ARG C 977 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 removed outlier: 8.284A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 90 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A 180 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 201 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N PHE A 213 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG A 38 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N LEU A 216 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 removed outlier: 3.556A pdb=" N GLY C 534 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.620A pdb=" N ASP A 57 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 260 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N THR A 261 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ASP A 277 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET A 263 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA A 275 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS A 265 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.518A pdb=" N TRP A 101 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL A 123 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE A 164 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE A 125 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU A 162 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA A 127 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASN A 129 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASN A 158 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLU A 131 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA A 156 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 149 removed outlier: 3.705A pdb=" N THR A 146 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 239 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 615 through 616 removed outlier: 5.136A pdb=" N ILE A 299 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR A 585 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLN A 301 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 583 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER A 303 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 581 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 315 removed outlier: 6.193A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE A 551 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 344 through 345 removed outlier: 3.974A pdb=" N CYS A 419 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS A 365 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AB1, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB2, first strand: chain 'A' and resid 640 through 646 removed outlier: 6.347A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N VAL A 642 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.136A pdb=" N ALA A 683 " --> pdb=" O MET B 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 694 through 710 removed outlier: 7.104A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 709 " --> pdb=" O VAL A1042 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 694 through 710 removed outlier: 7.104A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 709 " --> pdb=" O VAL A1042 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A1087 " --> pdb=" O VAL A1076 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN A1088 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N SER A1093 " --> pdb=" O GLN A1088 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 717 removed outlier: 4.358A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 769 through 771 removed outlier: 5.997A pdb=" N MET A 770 " --> pdb=" O SER C 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB9, first strand: chain 'A' and resid 822 through 823 Processing sheet with id=AC1, first strand: chain 'A' and resid 1102 through 1107 removed outlier: 3.712A pdb=" N SER A1105 " --> pdb=" O ALA A1069 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA A1062 " --> pdb=" O ILE A1115 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 31 through 35 removed outlier: 4.184A pdb=" N LYS B 180 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 31 through 35 Processing sheet with id=AC4, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.577A pdb=" N THR B 51 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 81 through 82 removed outlier: 5.942A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA B 139 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 146 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.605A pdb=" N ARG B 126 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 615 through 616 removed outlier: 5.397A pdb=" N ILE B 299 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR B 585 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER B 303 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 581 " --> pdb=" O SER B 303 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 312 through 315 removed outlier: 6.362A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.501A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS B 419 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.066A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AD3, first strand: chain 'B' and resid 640 through 646 removed outlier: 4.757A pdb=" N THR B 678 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR B 644 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.161A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 693 through 696 removed outlier: 3.566A pdb=" N ARG B1055 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 699 through 709 removed outlier: 3.708A pdb=" N SER B 703 " --> pdb=" O THR B1048 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLY B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA B1037 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B1043 " --> pdb=" O PRO B1035 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B1045 " --> pdb=" O SER B1033 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER B1033 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B1047 " --> pdb=" O LEU B1031 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD8, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD9, first strand: chain 'B' and resid 821 through 822 removed outlier: 3.526A pdb=" N ALA B 834 " --> pdb=" O GLU B 821 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 5.346A pdb=" N VAL B1104 " --> pdb=" O PHE B1071 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE B1071 " --> pdb=" O VAL B1104 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLY B1106 " --> pdb=" O ALA B1069 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 33 through 35 removed outlier: 7.877A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR C 67 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL C 254 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 205 " --> pdb=" O PHE C 179 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N HIS C 181 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE C 203 " --> pdb=" O HIS C 181 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ARG C 183 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLN C 201 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N PHE C 185 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLY C 199 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N PHE C 187 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N TYR C 197 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN C 189 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N TYR C 195 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.729A pdb=" N THR C 260 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 81 through 82 removed outlier: 6.423A pdb=" N VAL C 123 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE C 164 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE C 125 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU C 162 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA C 127 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN C 129 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASN C 158 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLU C 131 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA C 156 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N CYS C 133 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP C 154 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASN C 135 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE C 152 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR C 150 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 298 through 301 Processing sheet with id=AE6, first strand: chain 'C' and resid 578 through 579 removed outlier: 3.655A pdb=" N GLY C 579 " --> pdb=" O PHE C 305 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.676A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE9, first strand: chain 'C' and resid 640 through 646 removed outlier: 6.101A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N VAL C 642 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 696 through 697 Processing sheet with id=AF2, first strand: chain 'C' and resid 700 through 710 removed outlier: 3.634A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AF4, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF5, first strand: chain 'C' and resid 821 through 823 Processing sheet with id=AF6, first strand: chain 'C' and resid 1058 through 1060 removed outlier: 3.551A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 3.687A pdb=" N SER C1105 " --> pdb=" O ALA C1069 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA C1062 " --> pdb=" O ILE C1115 " (cutoff:3.500A) 964 hydrogen bonds defined for protein. 2643 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: 12.91 Time building geometry restraints manager: 12.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.22: 4 1.22 - 1.38: 9799 1.38 - 1.54: 16450 1.54 - 1.70: 151 1.70 - 1.86: 186 Bond restraints: 26590 Sorted by residual: bond pdb=" C GLN A 737 " pdb=" N TYR A 738 " ideal model delta sigma weight residual 1.333 1.060 0.273 1.37e-02 5.33e+03 3.96e+02 bond pdb=" C LEU A 735 " pdb=" N LEU A 736 " ideal model delta sigma weight residual 1.335 1.553 -0.219 1.25e-02 6.40e+03 3.06e+02 bond pdb=" C LEU A 736 " pdb=" N GLN A 737 " ideal model delta sigma weight residual 1.331 1.566 -0.235 2.56e-02 1.53e+03 8.44e+01 bond pdb=" C1 MAN T 4 " pdb=" O5 MAN T 4 " ideal model delta sigma weight residual 1.399 1.455 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" C1 MAN E 4 " pdb=" C2 MAN E 4 " ideal model delta sigma weight residual 1.526 1.581 -0.055 2.00e-02 2.50e+03 7.59e+00 ... (remaining 26585 not shown) Histogram of bond angle deviations from ideal: 97.39 - 107.35: 1109 107.35 - 117.31: 18586 117.31 - 127.27: 16263 127.27 - 137.23: 219 137.23 - 147.19: 1 Bond angle restraints: 36178 Sorted by residual: angle pdb=" C GLN A 737 " pdb=" N TYR A 738 " pdb=" CA TYR A 738 " ideal model delta sigma weight residual 121.80 147.19 -25.39 2.16e+00 2.14e-01 1.38e+02 angle pdb=" CA LEU A 736 " pdb=" C LEU A 736 " pdb=" N GLN A 737 " ideal model delta sigma weight residual 116.97 107.28 9.69 1.20e+00 6.94e-01 6.53e+01 angle pdb=" N HIS B 74 " pdb=" CA HIS B 74 " pdb=" C HIS B 74 " ideal model delta sigma weight residual 114.75 106.39 8.36 1.26e+00 6.30e-01 4.41e+01 angle pdb=" CA TYR A 738 " pdb=" C TYR A 738 " pdb=" O TYR A 738 " ideal model delta sigma weight residual 120.31 112.71 7.60 1.25e+00 6.40e-01 3.70e+01 angle pdb=" C GLY B 77 " pdb=" N ASN B 78 " pdb=" CA ASN B 78 " ideal model delta sigma weight residual 122.89 116.18 6.71 1.12e+00 7.97e-01 3.59e+01 ... (remaining 36173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.14: 16192 22.14 - 44.28: 371 44.28 - 66.43: 71 66.43 - 88.57: 71 88.57 - 110.71: 49 Dihedral angle restraints: 16754 sinusoidal: 7423 harmonic: 9331 Sorted by residual: dihedral pdb=" CB CYS A1014 " pdb=" SG CYS A1014 " pdb=" SG CYS A1025 " pdb=" CB CYS A1025 " ideal model delta sinusoidal sigma weight residual 93.00 -178.01 -88.99 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CA ARG C 207 " pdb=" C ARG C 207 " pdb=" N ASP C 208 " pdb=" CA ASP C 208 " ideal model delta harmonic sigma weight residual -180.00 -136.77 -43.23 0 5.00e+00 4.00e-02 7.48e+01 dihedral pdb=" CA ARG B 207 " pdb=" C ARG B 207 " pdb=" N ASP B 208 " pdb=" CA ASP B 208 " ideal model delta harmonic sigma weight residual 180.00 -137.22 -42.78 0 5.00e+00 4.00e-02 7.32e+01 ... (remaining 16751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3784 0.088 - 0.175: 481 0.175 - 0.263: 19 0.263 - 0.351: 18 0.351 - 0.439: 1 Chirality restraints: 4303 Sorted by residual: chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.25e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 7.92e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C 119 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.81e+00 ... (remaining 4300 not shown) Planarity restraints: 4603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 736 " -0.038 2.00e-02 2.50e+03 7.96e-02 6.33e+01 pdb=" C LEU A 736 " 0.137 2.00e-02 2.50e+03 pdb=" O LEU A 736 " -0.058 2.00e-02 2.50e+03 pdb=" N GLN A 737 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 797 " 0.482 9.50e-02 1.11e+02 2.16e-01 2.88e+01 pdb=" NE ARG A 797 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 797 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 797 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 797 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 735 " -0.021 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C LEU A 735 " 0.069 2.00e-02 2.50e+03 pdb=" O LEU A 735 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU A 736 " -0.021 2.00e-02 2.50e+03 ... (remaining 4600 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 44 2.40 - 3.02: 14274 3.02 - 3.65: 37926 3.65 - 4.27: 60361 4.27 - 4.90: 97613 Nonbonded interactions: 210218 Sorted by model distance: nonbonded pdb=" O TYR A 738 " pdb=" OG SER C 950 " model vdw 1.773 2.440 nonbonded pdb=" NH1 ARG C 544 " pdb=" NE2 GLN C 546 " model vdw 1.951 3.200 nonbonded pdb=" O GLY C 77 " pdb=" OH TYR C 252 " model vdw 2.279 2.440 nonbonded pdb=" OD2 ASP C 385 " pdb=" OH TYR C 410 " model vdw 2.289 2.440 nonbonded pdb=" OG SER B 690 " pdb=" OD1 ASN B 692 " model vdw 2.290 2.440 ... (remaining 210213 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 18 through 366 or resid 371 through 823 or resid 831 throu \ gh 1120 or resid 1301 through 1310)) selection = (chain 'B' and (resid 18 through 366 or resid 371 through 662 or resid 672 throu \ gh 1120 or resid 1309 through 1322)) selection = (chain 'C' and (resid 18 through 662 or resid 672 through 823 or resid 831 throu \ gh 1120 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'W' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'O' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 8.660 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 73.500 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.273 26590 Z= 0.479 Angle : 1.004 25.387 36178 Z= 0.541 Chirality : 0.059 0.439 4303 Planarity : 0.007 0.216 4569 Dihedral : 13.466 110.709 10617 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.69 % Favored : 94.28 % Rotamer: Outliers : 0.07 % Allowed : 0.90 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.45 (0.12), residues: 3162 helix: -3.32 (0.12), residues: 643 sheet: -1.38 (0.19), residues: 647 loop : -2.30 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP B 423 HIS 0.016 0.002 HIS C 33 PHE 0.056 0.005 PHE A 501 TYR 0.030 0.003 TYR B 352 ARG 0.016 0.001 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 446 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8702 (m-30) cc_final: 0.8397 (p0) REVERT: A 383 TYR cc_start: 0.5013 (m-80) cc_final: 0.4053 (m-80) REVERT: A 417 MET cc_start: 0.2072 (tpt) cc_final: 0.0139 (pmm) REVERT: A 558 PHE cc_start: 0.6648 (t80) cc_final: 0.5378 (t80) REVERT: A 575 PRO cc_start: 0.7952 (Cg_exo) cc_final: 0.7378 (Cg_endo) REVERT: A 978 LEU cc_start: 0.9044 (tp) cc_final: 0.8837 (pp) REVERT: B 92 THR cc_start: 0.7371 (p) cc_final: 0.7156 (p) REVERT: B 107 MET cc_start: 0.1778 (mmt) cc_final: 0.1446 (mmt) REVERT: B 214 ASN cc_start: 0.7239 (t0) cc_final: 0.7026 (m-40) REVERT: B 417 MET cc_start: 0.2779 (ttt) cc_final: 0.2238 (mmm) REVERT: B 515 LEU cc_start: 0.6904 (tp) cc_final: 0.6026 (pp) REVERT: C 151 MET cc_start: 0.5131 (mmt) cc_final: 0.4889 (mtt) REVERT: C 266 TYR cc_start: 0.7557 (m-10) cc_final: 0.7332 (m-10) REVERT: C 312 ASP cc_start: 0.6683 (t0) cc_final: 0.6315 (m-30) REVERT: C 329 PHE cc_start: 0.3892 (m-80) cc_final: 0.2744 (m-10) REVERT: C 347 ASN cc_start: 0.8313 (m-40) cc_final: 0.7774 (p0) REVERT: C 1059 THR cc_start: 0.7953 (p) cc_final: 0.7717 (p) outliers start: 2 outliers final: 0 residues processed: 447 average time/residue: 0.4394 time to fit residues: 297.2048 Evaluate side-chains 212 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 6.9990 chunk 241 optimal weight: 0.0570 chunk 133 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 249 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 185 optimal weight: 20.0000 chunk 288 optimal weight: 5.9990 overall best weight: 2.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS A 692 ASN A 721 ASN A 733 ASN A 877 GLN A 937 ASN A 984 GLN A 993 GLN A1088 GLN B 32 GLN B 112 GLN B 118 ASN B 149 HIS B 201 GLN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN B 733 ASN B 786 GLN B 835 GLN B 877 GLN B 907 ASN B 984 GLN B1065 HIS C 108 ASN C 147 GLN C 149 HIS C 201 GLN C 437 ASN C 599 GLN C 733 ASN C 908 GLN ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 26590 Z= 0.255 Angle : 0.716 14.340 36178 Z= 0.368 Chirality : 0.047 0.231 4303 Planarity : 0.005 0.058 4569 Dihedral : 11.507 78.807 4953 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.48 % Allowed : 6.62 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.14 (0.14), residues: 3162 helix: -0.57 (0.19), residues: 652 sheet: -0.91 (0.19), residues: 682 loop : -2.01 (0.13), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 340 HIS 0.004 0.001 HIS C 70 PHE 0.027 0.002 PHE A 83 TYR 0.022 0.002 TYR B1029 ARG 0.008 0.001 ARG A 965 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 239 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8689 (m-30) cc_final: 0.8376 (p0) REVERT: A 383 TYR cc_start: 0.5001 (m-80) cc_final: 0.4042 (m-80) REVERT: A 417 MET cc_start: 0.2155 (tpt) cc_final: 0.0247 (ptp) REVERT: A 494 TYR cc_start: 0.6670 (m-80) cc_final: 0.6387 (m-80) REVERT: A 952 PHE cc_start: 0.7260 (m-80) cc_final: 0.6868 (m-80) REVERT: A 985 SER cc_start: 0.9237 (m) cc_final: 0.8967 (t) REVERT: B 37 MET cc_start: 0.7928 (mmp) cc_final: 0.7488 (mmp) REVERT: B 107 MET cc_start: 0.2594 (mmt) cc_final: 0.2322 (mmt) REVERT: B 417 MET cc_start: 0.2673 (ttt) cc_final: 0.2354 (mmm) REVERT: B 515 LEU cc_start: 0.6979 (tp) cc_final: 0.6713 (pp) REVERT: B 708 VAL cc_start: 0.9165 (t) cc_final: 0.8908 (m) REVERT: C 151 MET cc_start: 0.5015 (mmt) cc_final: 0.4730 (mtt) REVERT: C 224 LEU cc_start: 0.8014 (mt) cc_final: 0.7660 (mt) REVERT: C 296 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7551 (m-30) REVERT: C 312 ASP cc_start: 0.6877 (t0) cc_final: 0.6282 (m-30) REVERT: C 329 PHE cc_start: 0.4399 (m-80) cc_final: 0.3500 (m-10) REVERT: C 347 ASN cc_start: 0.8424 (m-40) cc_final: 0.7779 (p0) REVERT: C 417 MET cc_start: 0.5145 (tpp) cc_final: 0.4801 (tpp) REVERT: C 936 GLN cc_start: 0.8220 (mm110) cc_final: 0.7728 (mm-40) outliers start: 41 outliers final: 21 residues processed: 268 average time/residue: 0.3684 time to fit residues: 162.3737 Evaluate side-chains 209 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 187 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 851 MET Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 1009 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 240 optimal weight: 6.9990 chunk 196 optimal weight: 8.9990 chunk 79 optimal weight: 0.0040 chunk 289 optimal weight: 0.7980 chunk 312 optimal weight: 5.9990 chunk 257 optimal weight: 20.0000 chunk 286 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 232 optimal weight: 30.0000 overall best weight: 3.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS A 661 HIS A 993 GLN B 201 GLN B 214 ASN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 HIS B 877 GLN ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 26590 Z= 0.267 Angle : 0.689 14.842 36178 Z= 0.351 Chirality : 0.046 0.237 4303 Planarity : 0.004 0.043 4569 Dihedral : 9.240 60.468 4953 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.76 % Allowed : 8.28 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.82 (0.14), residues: 3162 helix: 0.12 (0.20), residues: 655 sheet: -0.90 (0.19), residues: 671 loop : -1.89 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 245 HIS 0.005 0.001 HIS C 33 PHE 0.028 0.002 PHE C 334 TYR 0.019 0.002 TYR B 197 ARG 0.007 0.001 ARG C 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 197 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.2750 (mmt) cc_final: 0.2370 (mmt) REVERT: A 166 ASP cc_start: 0.8661 (m-30) cc_final: 0.8322 (p0) REVERT: A 383 TYR cc_start: 0.5305 (m-80) cc_final: 0.4358 (m-80) REVERT: A 417 MET cc_start: 0.2216 (tpt) cc_final: 0.0655 (ptp) REVERT: A 494 TYR cc_start: 0.6878 (m-80) cc_final: 0.6397 (m-80) REVERT: A 952 PHE cc_start: 0.7363 (m-80) cc_final: 0.7035 (m-80) REVERT: B 515 LEU cc_start: 0.6875 (tp) cc_final: 0.6590 (pp) REVERT: C 224 LEU cc_start: 0.8308 (mt) cc_final: 0.7997 (mt) REVERT: C 296 ASP cc_start: 0.7826 (m-30) cc_final: 0.7501 (m-30) REVERT: C 329 PHE cc_start: 0.4339 (m-80) cc_final: 0.3458 (m-10) REVERT: C 347 ASN cc_start: 0.8539 (m-40) cc_final: 0.7796 (p0) REVERT: C 576 CYS cc_start: 0.6246 (OUTLIER) cc_final: 0.5860 (t) REVERT: C 936 GLN cc_start: 0.8228 (mm110) cc_final: 0.7767 (mm-40) REVERT: C 967 ASP cc_start: 0.8920 (p0) cc_final: 0.8557 (p0) outliers start: 49 outliers final: 28 residues processed: 234 average time/residue: 0.3558 time to fit residues: 140.0717 Evaluate side-chains 205 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 176 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 1009 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.0980 chunk 217 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 290 optimal weight: 0.7980 chunk 307 optimal weight: 7.9990 chunk 151 optimal weight: 0.7980 chunk 275 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN A 630 GLN A 661 HIS A 692 ASN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26590 Z= 0.208 Angle : 0.627 15.890 36178 Z= 0.317 Chirality : 0.045 0.221 4303 Planarity : 0.004 0.047 4569 Dihedral : 7.910 59.206 4953 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.84 % Allowed : 9.00 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.62 (0.14), residues: 3162 helix: 0.59 (0.20), residues: 661 sheet: -0.81 (0.19), residues: 672 loop : -1.89 (0.13), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 423 HIS 0.004 0.001 HIS B 149 PHE 0.034 0.002 PHE C 334 TYR 0.039 0.002 TYR B 197 ARG 0.009 0.000 ARG B 965 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 193 time to evaluate : 2.955 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 166 ASP cc_start: 0.8653 (m-30) cc_final: 0.8324 (p0) REVERT: A 383 TYR cc_start: 0.5268 (m-80) cc_final: 0.4337 (m-80) REVERT: A 417 MET cc_start: 0.2004 (tpt) cc_final: 0.0761 (pmm) REVERT: A 494 TYR cc_start: 0.7085 (m-80) cc_final: 0.6582 (m-80) REVERT: A 952 PHE cc_start: 0.7478 (m-80) cc_final: 0.7108 (m-80) REVERT: B 515 LEU cc_start: 0.6953 (tp) cc_final: 0.6701 (pp) REVERT: C 224 LEU cc_start: 0.8243 (mt) cc_final: 0.8005 (mt) REVERT: C 296 ASP cc_start: 0.7761 (m-30) cc_final: 0.7465 (m-30) REVERT: C 329 PHE cc_start: 0.4223 (m-80) cc_final: 0.3404 (m-10) REVERT: C 347 ASN cc_start: 0.8498 (m-40) cc_final: 0.7789 (p0) REVERT: C 576 CYS cc_start: 0.6122 (OUTLIER) cc_final: 0.5783 (t) REVERT: C 936 GLN cc_start: 0.8158 (mm110) cc_final: 0.7765 (mm-40) outliers start: 51 outliers final: 32 residues processed: 228 average time/residue: 0.3504 time to fit residues: 135.4869 Evaluate side-chains 211 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 178 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1085 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 741 PHE Chi-restraints excluded: chain C residue 868 TRP Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1009 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 30.0000 chunk 174 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 228 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 212 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 156 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 181 HIS A 189 ASN A 280 GLN A 661 HIS A1095 GLN B 29 ASN B 70 HIS B 122 ASN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 835 GLN B 896 ASN ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 HIS C 746 ASN ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.122 26590 Z= 0.591 Angle : 0.966 16.125 36178 Z= 0.493 Chirality : 0.053 0.317 4303 Planarity : 0.006 0.061 4569 Dihedral : 8.740 59.977 4953 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 2.77 % Allowed : 11.01 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.14), residues: 3162 helix: -0.63 (0.18), residues: 679 sheet: -1.29 (0.19), residues: 665 loop : -2.26 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 619 HIS 0.010 0.002 HIS B 149 PHE 0.044 0.003 PHE A 83 TYR 0.039 0.003 TYR B 197 ARG 0.008 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 167 time to evaluate : 3.101 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 166 ASP cc_start: 0.8668 (m-30) cc_final: 0.8122 (p0) REVERT: A 197 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7239 (m-80) REVERT: A 417 MET cc_start: 0.2483 (tpt) cc_final: 0.1289 (pmm) REVERT: A 679 MET cc_start: 0.7958 (mpp) cc_final: 0.7585 (mtm) REVERT: A 738 TYR cc_start: 0.5969 (OUTLIER) cc_final: 0.5381 (m-80) REVERT: A 770 MET cc_start: 0.8188 (mmp) cc_final: 0.7859 (mmm) REVERT: B 253 PHE cc_start: 0.7673 (m-10) cc_final: 0.7317 (m-80) REVERT: B 515 LEU cc_start: 0.7184 (tp) cc_final: 0.6911 (pp) REVERT: B 916 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9085 (tt) REVERT: B 967 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6056 (m-30) REVERT: C 217 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8056 (mtmm) REVERT: C 296 ASP cc_start: 0.7990 (m-30) cc_final: 0.7746 (m-30) REVERT: C 329 PHE cc_start: 0.4791 (m-80) cc_final: 0.4273 (m-10) REVERT: C 543 LYS cc_start: 0.8393 (mttt) cc_final: 0.8026 (mmtm) REVERT: C 722 MET cc_start: 0.8375 (tpt) cc_final: 0.8078 (tpp) REVERT: C 967 ASP cc_start: 0.8736 (p0) cc_final: 0.8476 (p0) REVERT: C 1066 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6598 (tt0) outliers start: 77 outliers final: 46 residues processed: 223 average time/residue: 0.3322 time to fit residues: 126.1174 Evaluate side-chains 203 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 152 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1085 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 741 PHE Chi-restraints excluded: chain C residue 868 TRP Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1019 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 3.9990 chunk 276 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 307 optimal weight: 0.9980 chunk 255 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS A 692 ASN A 947 GLN B 29 ASN B 835 GLN B 984 GLN C 630 GLN C 806 ASN ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26590 Z= 0.192 Angle : 0.660 16.654 36178 Z= 0.332 Chirality : 0.046 0.252 4303 Planarity : 0.004 0.047 4569 Dihedral : 7.527 59.588 4953 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.80 % Allowed : 12.85 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.89 (0.14), residues: 3162 helix: 0.42 (0.20), residues: 679 sheet: -1.02 (0.19), residues: 681 loop : -2.10 (0.13), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 868 HIS 0.004 0.001 HIS A 611 PHE 0.033 0.002 PHE A 83 TYR 0.037 0.002 TYR B 197 ARG 0.008 0.000 ARG B 965 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 196 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8609 (m-30) cc_final: 0.8157 (p0) REVERT: A 417 MET cc_start: 0.1671 (tpt) cc_final: 0.1133 (mpp) REVERT: A 679 MET cc_start: 0.7879 (mpp) cc_final: 0.7567 (mtm) REVERT: A 770 MET cc_start: 0.8131 (mmp) cc_final: 0.7809 (mmm) REVERT: A 952 PHE cc_start: 0.7615 (m-80) cc_final: 0.7086 (m-80) REVERT: A 1085 PHE cc_start: 0.5233 (OUTLIER) cc_final: 0.4538 (p90) REVERT: B 916 ILE cc_start: 0.9361 (tp) cc_final: 0.9047 (tt) REVERT: C 134 ASP cc_start: 0.2087 (OUTLIER) cc_final: 0.1621 (p0) REVERT: C 224 LEU cc_start: 0.8046 (mt) cc_final: 0.7740 (tp) REVERT: C 296 ASP cc_start: 0.7749 (m-30) cc_final: 0.7427 (m-30) REVERT: C 329 PHE cc_start: 0.4712 (m-80) cc_final: 0.4160 (m-10) REVERT: C 543 LYS cc_start: 0.8488 (mttt) cc_final: 0.8040 (mmtm) REVERT: C 576 CYS cc_start: 0.6198 (OUTLIER) cc_final: 0.5848 (t) REVERT: C 600 ASP cc_start: 0.8113 (m-30) cc_final: 0.7363 (m-30) outliers start: 50 outliers final: 37 residues processed: 236 average time/residue: 0.3563 time to fit residues: 139.5337 Evaluate side-chains 206 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 166 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1085 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 868 TRP Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 964 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 224 optimal weight: 20.0000 chunk 174 optimal weight: 0.7980 chunk 259 optimal weight: 30.0000 chunk 171 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 186 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26590 Z= 0.282 Angle : 0.696 15.293 36178 Z= 0.350 Chirality : 0.046 0.264 4303 Planarity : 0.004 0.042 4569 Dihedral : 7.353 59.977 4953 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.27 % Allowed : 13.60 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.93 (0.14), residues: 3162 helix: 0.43 (0.20), residues: 681 sheet: -1.08 (0.20), residues: 667 loop : -2.13 (0.13), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 423 HIS 0.009 0.001 HIS A1065 PHE 0.032 0.002 PHE A 83 TYR 0.036 0.002 TYR B 197 ARG 0.009 0.001 ARG B 761 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 164 time to evaluate : 2.812 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 166 ASP cc_start: 0.8590 (m-30) cc_final: 0.8116 (p0) REVERT: A 197 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7363 (m-80) REVERT: A 417 MET cc_start: 0.1965 (tpt) cc_final: 0.1538 (pmm) REVERT: A 545 PHE cc_start: 0.4364 (OUTLIER) cc_final: 0.3854 (m-10) REVERT: A 679 MET cc_start: 0.7972 (mpp) cc_final: 0.7663 (mtm) REVERT: A 952 PHE cc_start: 0.7733 (m-80) cc_final: 0.7239 (m-80) REVERT: A 1085 PHE cc_start: 0.5520 (OUTLIER) cc_final: 0.4812 (p90) REVERT: B 56 GLN cc_start: 0.8333 (mp10) cc_final: 0.7884 (mm-40) REVERT: B 916 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9028 (tt) REVERT: B 1018 GLN cc_start: 0.4497 (tp40) cc_final: 0.3726 (tp-100) REVERT: C 224 LEU cc_start: 0.8068 (mt) cc_final: 0.7712 (tp) REVERT: C 296 ASP cc_start: 0.7790 (m-30) cc_final: 0.7444 (m-30) REVERT: C 329 PHE cc_start: 0.4625 (m-80) cc_final: 0.4055 (m-10) REVERT: C 347 ASN cc_start: 0.8495 (m-40) cc_final: 0.7781 (p0) REVERT: C 543 LYS cc_start: 0.8460 (mttt) cc_final: 0.8066 (mmtm) REVERT: C 576 CYS cc_start: 0.6353 (OUTLIER) cc_final: 0.6018 (t) outliers start: 63 outliers final: 44 residues processed: 213 average time/residue: 0.3403 time to fit residues: 122.1671 Evaluate side-chains 211 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 162 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1085 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 868 TRP Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 964 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 60 optimal weight: 0.0040 chunk 59 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 208 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN A 692 ASN B 112 GLN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26590 Z= 0.210 Angle : 0.647 15.885 36178 Z= 0.325 Chirality : 0.045 0.294 4303 Planarity : 0.004 0.041 4569 Dihedral : 6.948 58.074 4953 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.27 % Allowed : 13.93 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.82 (0.14), residues: 3162 helix: 0.60 (0.20), residues: 678 sheet: -1.02 (0.20), residues: 661 loop : -2.08 (0.13), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 868 HIS 0.006 0.001 HIS A1065 PHE 0.030 0.002 PHE A 83 TYR 0.039 0.001 TYR B 197 ARG 0.006 0.000 ARG B 761 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 171 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8560 (m-30) cc_final: 0.8123 (p0) REVERT: A 417 MET cc_start: 0.1931 (tpt) cc_final: 0.1594 (pmm) REVERT: A 679 MET cc_start: 0.7915 (mpp) cc_final: 0.7584 (mtm) REVERT: A 770 MET cc_start: 0.7966 (mmp) cc_final: 0.7544 (mmm) REVERT: A 931 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7484 (mm110) REVERT: A 952 PHE cc_start: 0.7755 (m-80) cc_final: 0.7293 (m-80) REVERT: A 1085 PHE cc_start: 0.5336 (OUTLIER) cc_final: 0.4634 (p90) REVERT: B 56 GLN cc_start: 0.8302 (mp10) cc_final: 0.8097 (mp10) REVERT: B 916 ILE cc_start: 0.9412 (tp) cc_final: 0.9049 (tt) REVERT: B 1018 GLN cc_start: 0.4676 (tp40) cc_final: 0.3810 (tp-100) REVERT: C 107 MET cc_start: 0.6325 (mmt) cc_final: 0.6117 (mmp) REVERT: C 134 ASP cc_start: 0.2548 (OUTLIER) cc_final: 0.2333 (p0) REVERT: C 224 LEU cc_start: 0.8274 (mt) cc_final: 0.7945 (tp) REVERT: C 329 PHE cc_start: 0.4376 (m-80) cc_final: 0.3626 (m-10) REVERT: C 347 ASN cc_start: 0.8377 (m-40) cc_final: 0.7651 (p0) REVERT: C 543 LYS cc_start: 0.8450 (mttt) cc_final: 0.8074 (mmtm) REVERT: C 576 CYS cc_start: 0.6093 (OUTLIER) cc_final: 0.5687 (t) REVERT: C 600 ASP cc_start: 0.8090 (m-30) cc_final: 0.7464 (m-30) REVERT: C 936 GLN cc_start: 0.8287 (mm110) cc_final: 0.7896 (mm-40) outliers start: 63 outliers final: 48 residues processed: 221 average time/residue: 0.3405 time to fit residues: 128.2755 Evaluate side-chains 211 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 159 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1085 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 741 PHE Chi-restraints excluded: chain C residue 868 TRP Chi-restraints excluded: chain C residue 894 THR Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 1098 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 267 optimal weight: 6.9990 chunk 285 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 124 optimal weight: 0.0970 chunk 224 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 258 optimal weight: 9.9990 chunk 270 optimal weight: 5.9990 chunk 284 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26590 Z= 0.178 Angle : 0.628 15.905 36178 Z= 0.313 Chirality : 0.045 0.299 4303 Planarity : 0.004 0.040 4569 Dihedral : 6.523 55.781 4953 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.09 % Allowed : 14.21 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.14), residues: 3162 helix: 0.82 (0.21), residues: 678 sheet: -0.90 (0.20), residues: 657 loop : -2.04 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 868 HIS 0.005 0.001 HIS A1065 PHE 0.041 0.002 PHE A 316 TYR 0.037 0.001 TYR B 197 ARG 0.007 0.000 ARG B 761 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 175 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.5685 (ptm) cc_final: 0.5031 (tmm) REVERT: A 166 ASP cc_start: 0.8536 (m-30) cc_final: 0.8136 (p0) REVERT: A 170 LEU cc_start: 0.4280 (OUTLIER) cc_final: 0.2462 (tp) REVERT: A 679 MET cc_start: 0.7937 (mpp) cc_final: 0.7620 (mtm) REVERT: A 770 MET cc_start: 0.8084 (mmp) cc_final: 0.7655 (mmm) REVERT: A 931 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7618 (mm110) REVERT: A 952 PHE cc_start: 0.7772 (m-80) cc_final: 0.7298 (m-80) REVERT: B 916 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9051 (tt) REVERT: B 1011 MET cc_start: 0.8540 (tpp) cc_final: 0.8140 (tpp) REVERT: B 1013 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7098 (mm-30) REVERT: C 134 ASP cc_start: 0.2519 (OUTLIER) cc_final: 0.2306 (p0) REVERT: C 329 PHE cc_start: 0.4502 (m-80) cc_final: 0.3781 (m-10) REVERT: C 347 ASN cc_start: 0.8396 (m-40) cc_final: 0.7664 (p0) REVERT: C 497 VAL cc_start: -0.1514 (OUTLIER) cc_final: -0.2068 (p) REVERT: C 543 LYS cc_start: 0.8483 (mttt) cc_final: 0.8112 (mmtm) REVERT: C 600 ASP cc_start: 0.8053 (m-30) cc_final: 0.7458 (m-30) REVERT: C 936 GLN cc_start: 0.8233 (mm110) cc_final: 0.7854 (mm-40) outliers start: 58 outliers final: 45 residues processed: 219 average time/residue: 0.3568 time to fit residues: 130.2412 Evaluate side-chains 212 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 162 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 741 PHE Chi-restraints excluded: chain C residue 868 TRP Chi-restraints excluded: chain C residue 894 THR Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1086 ILE Chi-restraints excluded: chain C residue 1098 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 6.9990 chunk 302 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 316 optimal weight: 3.9990 chunk 291 optimal weight: 20.0000 chunk 252 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN B 56 GLN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26590 Z= 0.198 Angle : 0.632 15.902 36178 Z= 0.316 Chirality : 0.045 0.297 4303 Planarity : 0.004 0.040 4569 Dihedral : 6.433 55.601 4953 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.91 % Allowed : 14.50 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.66 (0.14), residues: 3162 helix: 0.84 (0.21), residues: 679 sheet: -0.88 (0.20), residues: 656 loop : -2.03 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 423 HIS 0.005 0.001 HIS A1065 PHE 0.057 0.002 PHE B 179 TYR 0.039 0.001 TYR B 197 ARG 0.006 0.000 ARG B 747 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 165 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.5812 (ptm) cc_final: 0.5109 (tmm) REVERT: A 166 ASP cc_start: 0.8544 (m-30) cc_final: 0.8115 (p0) REVERT: A 679 MET cc_start: 0.7961 (mpp) cc_final: 0.7672 (mtm) REVERT: A 770 MET cc_start: 0.8060 (mmp) cc_final: 0.7655 (mmm) REVERT: A 931 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7622 (mm110) REVERT: A 952 PHE cc_start: 0.7771 (m-80) cc_final: 0.7332 (m-80) REVERT: B 179 PHE cc_start: 0.6184 (t80) cc_final: 0.5588 (t80) REVERT: B 916 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9083 (tt) REVERT: B 1011 MET cc_start: 0.8580 (tpp) cc_final: 0.8182 (tpp) REVERT: B 1013 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7197 (mm-30) REVERT: C 107 MET cc_start: 0.6267 (mmp) cc_final: 0.6033 (mmp) REVERT: C 224 LEU cc_start: 0.8435 (mt) cc_final: 0.8070 (tp) REVERT: C 329 PHE cc_start: 0.4523 (m-80) cc_final: 0.3916 (m-10) REVERT: C 347 ASN cc_start: 0.8399 (m-40) cc_final: 0.7635 (p0) REVERT: C 497 VAL cc_start: -0.1515 (OUTLIER) cc_final: -0.2035 (p) REVERT: C 543 LYS cc_start: 0.8465 (mttt) cc_final: 0.8129 (mmtm) REVERT: C 600 ASP cc_start: 0.8069 (m-30) cc_final: 0.7504 (m-30) REVERT: C 936 GLN cc_start: 0.8236 (mm110) cc_final: 0.7867 (mm-40) outliers start: 53 outliers final: 47 residues processed: 204 average time/residue: 0.3330 time to fit residues: 115.8239 Evaluate side-chains 212 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 162 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 741 PHE Chi-restraints excluded: chain C residue 868 TRP Chi-restraints excluded: chain C residue 894 THR Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1098 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.9990 chunk 268 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 252 optimal weight: 0.0570 chunk 105 optimal weight: 9.9990 chunk 259 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.114238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.089258 restraints weight = 117377.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.088526 restraints weight = 83312.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.088607 restraints weight = 67127.129| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26590 Z= 0.217 Angle : 0.646 15.992 36178 Z= 0.321 Chirality : 0.045 0.252 4303 Planarity : 0.004 0.043 4569 Dihedral : 6.350 55.867 4953 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.02 % Allowed : 14.43 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.64 (0.14), residues: 3162 helix: 0.83 (0.21), residues: 679 sheet: -0.89 (0.20), residues: 635 loop : -1.99 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 423 HIS 0.005 0.001 HIS A1065 PHE 0.045 0.002 PHE B 179 TYR 0.039 0.001 TYR B 197 ARG 0.006 0.000 ARG B 761 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4491.18 seconds wall clock time: 84 minutes 11.74 seconds (5051.74 seconds total)