Starting phenix.real_space_refine on Wed Mar 20 10:31:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9r_14576/03_2024/7z9r_14576.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9r_14576/03_2024/7z9r_14576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9r_14576/03_2024/7z9r_14576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9r_14576/03_2024/7z9r_14576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9r_14576/03_2024/7z9r_14576.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9r_14576/03_2024/7z9r_14576.pdb" } resolution = 4.2 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17221 2.51 5 N 4415 2.21 5 O 5322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "Y GLU 100": "OE1" <-> "OE2" Residue "X GLU 100": "OE1" <-> "OE2" Residue "Z GLU 100": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27078 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7719 Classifications: {'peptide': 988} Link IDs: {'PTRANS': 49, 'TRANS': 938} Chain breaks: 9 Chain: "B" Number of atoms: 7745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7745 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Chain: "C" Number of atoms: 7738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7738 Classifications: {'peptide': 991} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Chain: "Y" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "X" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "Z" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: "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: 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: "L" 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: "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: 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: "O" 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: "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: 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: "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: 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: "U" 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: "V" 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: "W" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.30, per 1000 atoms: 0.53 Number of scatterers: 27078 At special positions: 0 Unit cell: (130.784, 139.36, 216.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5322 8.00 N 4415 7.00 C 17221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=1.91 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.06 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.07 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.01 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.01 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.01 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " 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 L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 165 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 122 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C 709 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " Time building additional restraints: 11.23 Conformation dependent library (CDL) restraints added in 4.5 seconds 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6246 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 55 sheets defined 24.5% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.981A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.335A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.540A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.681A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.237A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.989A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.941A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.599A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.025A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.339A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.040A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.874A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.583A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.296A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.762A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.518A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.594A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.809A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.966A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.355A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.574A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.642A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.371A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.680A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.527A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.944A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.111A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'Y' and resid 62 through 65 Processing helix chain 'Y' and resid 87 through 91 Processing helix chain 'Y' and resid 105 through 111 Processing helix chain 'X' and resid 62 through 65 Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'X' and resid 105 through 111 Processing helix chain 'Z' and resid 62 through 65 Processing helix chain 'Z' and resid 87 through 91 Processing helix chain 'Z' and resid 105 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.955A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.698A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.671A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.573A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.546A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.456A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.064A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.001A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.776A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.987A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.191A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.797A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.328A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.308A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.731A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.709A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.448A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.627A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.966A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.006A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 719 through 728 removed outlier: 5.988A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.777A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.344A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.699A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.556A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.669A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.917A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.550A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.882A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.977A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.001A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.712A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.166A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.574A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 3 through 8 Processing sheet with id=AF3, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.288A pdb=" N GLY Y 10 " --> pdb=" O THR Y 124 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER Y 126 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET Y 12 " --> pdb=" O SER Y 126 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG Y 38 " --> pdb=" O PHE Y 47 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.288A pdb=" N GLY Y 10 " --> pdb=" O THR Y 124 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER Y 126 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET Y 12 " --> pdb=" O SER Y 126 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 3 through 8 Processing sheet with id=AF6, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.293A pdb=" N GLY X 10 " --> pdb=" O THR X 124 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER X 126 " --> pdb=" O GLY X 10 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET X 12 " --> pdb=" O SER X 126 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ARG X 38 " --> pdb=" O PHE X 47 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N PHE X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.293A pdb=" N GLY X 10 " --> pdb=" O THR X 124 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER X 126 " --> pdb=" O GLY X 10 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET X 12 " --> pdb=" O SER X 126 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 3 through 8 Processing sheet with id=AF9, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.287A pdb=" N GLY Z 10 " --> pdb=" O THR Z 124 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N SER Z 126 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET Z 12 " --> pdb=" O SER Z 126 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG Z 38 " --> pdb=" O PHE Z 47 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N PHE Z 47 " --> pdb=" O ARG Z 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.287A pdb=" N GLY Z 10 " --> pdb=" O THR Z 124 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N SER Z 126 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET Z 12 " --> pdb=" O SER Z 126 " (cutoff:3.500A) 1140 hydrogen bonds defined for protein. 3021 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: 13.49 Time building geometry restraints manager: 12.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5965 1.33 - 1.46: 9667 1.46 - 1.59: 11885 1.59 - 1.72: 0 1.72 - 1.85: 153 Bond restraints: 27670 Sorted by residual: bond pdb=" C ASP C 138 " pdb=" N PRO C 139 " ideal model delta sigma weight residual 1.333 1.384 -0.051 1.17e-02 7.31e+03 1.89e+01 bond pdb=" C ASP A 138 " pdb=" N PRO A 139 " ideal model delta sigma weight residual 1.333 1.383 -0.050 1.17e-02 7.31e+03 1.84e+01 bond pdb=" CE1 HIS C1064 " pdb=" NE2 HIS C1064 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.57e+01 bond pdb=" N ASN A 81 " pdb=" CA ASN A 81 " ideal model delta sigma weight residual 1.458 1.533 -0.075 1.90e-02 2.77e+03 1.56e+01 bond pdb=" C ASN A 81 " pdb=" N PRO A 82 " ideal model delta sigma weight residual 1.331 1.381 -0.051 1.31e-02 5.83e+03 1.49e+01 ... (remaining 27665 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.64: 641 105.64 - 113.03: 13896 113.03 - 120.41: 11955 120.41 - 127.79: 11023 127.79 - 135.18: 110 Bond angle restraints: 37625 Sorted by residual: angle pdb=" C CYS A 166 " pdb=" CA CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sigma weight residual 112.05 99.52 12.53 1.52e+00 4.33e-01 6.79e+01 angle pdb=" C PHE C 329 " pdb=" CA PHE C 329 " pdb=" CB PHE C 329 " ideal model delta sigma weight residual 109.22 120.23 -11.01 1.52e+00 4.33e-01 5.24e+01 angle pdb=" N SER B1147 " pdb=" CA SER B1147 " pdb=" CB SER B1147 " ideal model delta sigma weight residual 110.50 120.69 -10.19 1.70e+00 3.46e-01 3.60e+01 angle pdb=" N ASN B1108 " pdb=" CA ASN B1108 " pdb=" C ASN B1108 " ideal model delta sigma weight residual 111.82 118.77 -6.95 1.16e+00 7.43e-01 3.59e+01 angle pdb=" CA ASP B 745 " pdb=" CB ASP B 745 " pdb=" CG ASP B 745 " ideal model delta sigma weight residual 112.60 118.58 -5.98 1.00e+00 1.00e+00 3.58e+01 ... (remaining 37620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.83: 16166 20.83 - 41.65: 848 41.65 - 62.48: 183 62.48 - 83.30: 53 83.30 - 104.13: 29 Dihedral angle restraints: 17279 sinusoidal: 7552 harmonic: 9727 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -174.98 88.98 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 171.46 -78.46 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 168.78 -75.78 1 1.00e+01 1.00e-02 7.24e+01 ... (remaining 17276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 3793 0.144 - 0.288: 582 0.288 - 0.431: 51 0.431 - 0.575: 9 0.575 - 0.719: 2 Chirality restraints: 4437 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.07e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 2.02e+02 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.92e+02 ... (remaining 4434 not shown) Planarity restraints: 4808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 1 " 0.363 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C7 NAG P 1 " -0.094 2.00e-02 2.50e+03 pdb=" C8 NAG P 1 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG P 1 " -0.548 2.00e-02 2.50e+03 pdb=" O7 NAG P 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.354 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG M 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.150 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1305 " -0.345 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG C1305 " 0.089 2.00e-02 2.50e+03 pdb=" C8 NAG C1305 " -0.167 2.00e-02 2.50e+03 pdb=" N2 NAG C1305 " 0.521 2.00e-02 2.50e+03 pdb=" O7 NAG C1305 " -0.099 2.00e-02 2.50e+03 ... (remaining 4805 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.93: 1 1.93 - 2.67: 476 2.67 - 3.41: 35695 3.41 - 4.16: 67112 4.16 - 4.90: 116021 Nonbonded interactions: 219305 Sorted by model distance: nonbonded pdb=" OE1 GLU A 281 " pdb=" OD1 ASN A 282 " model vdw 1.182 3.040 nonbonded pdb=" SG CYS A 131 " pdb=" CA CYS A 166 " model vdw 1.927 3.064 nonbonded pdb=" O GLN B 613 " pdb=" OD1 ASP B 614 " model vdw 1.941 3.040 nonbonded pdb=" O THR A 333 " pdb=" OD1 ASN A 334 " model vdw 1.984 3.040 nonbonded pdb=" OD1 ASN C 137 " pdb=" N ASP C 138 " model vdw 2.047 2.520 ... (remaining 219300 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 27 through 66 or resid 82 through 113 or resid 116 through \ 140 or resid 166 through 263 or resid 265 through 676 or resid 690 through 827 \ or resid 856 through 1147 or resid 1301 through 1307)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 140 or resid 166 through \ 196 or resid 200 through 211 or resid 215 through 263 or resid 265 through 827 \ or resid 856 through 1147 or resid 1301 through 1307)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 113 or resid 116 through \ 140 or resid 166 through 196 or resid 200 through 211 or resid 215 through 1147 \ or resid 1301 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 1.260 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: 7.110 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 73.200 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.340 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 27670 Z= 0.533 Angle : 1.395 13.596 37625 Z= 0.896 Chirality : 0.105 0.719 4437 Planarity : 0.023 0.310 4766 Dihedral : 14.179 104.130 10907 Min Nonbonded Distance : 1.182 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 1.21 % Allowed : 4.62 % Favored : 94.17 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % 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: -1.16 (0.13), residues: 3289 helix: -0.33 (0.19), residues: 678 sheet: -0.16 (0.17), residues: 798 loop : -1.21 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.006 TRP B 353 HIS 0.033 0.007 HIS C 655 PHE 0.052 0.008 PHE B 565 TYR 0.058 0.007 TYR B 365 ARG 0.027 0.002 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 602 time to evaluate : 3.063 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 33 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7485 (p) REVERT: A 55 PHE cc_start: 0.8308 (m-80) cc_final: 0.7904 (m-80) REVERT: A 108 THR cc_start: 0.7057 (OUTLIER) cc_final: 0.6678 (t) REVERT: A 277 LEU cc_start: 0.8823 (mt) cc_final: 0.8622 (mm) REVERT: A 319 ARG cc_start: 0.7571 (ttm170) cc_final: 0.7302 (mtp-110) REVERT: A 347 PHE cc_start: 0.7690 (m-80) cc_final: 0.6559 (m-80) REVERT: A 355 ARG cc_start: 0.6656 (ttm170) cc_final: 0.6229 (mtp85) REVERT: A 511 VAL cc_start: 0.6728 (t) cc_final: 0.6296 (m) REVERT: A 565 PHE cc_start: 0.8493 (p90) cc_final: 0.8240 (p90) REVERT: A 666 ILE cc_start: 0.9133 (mt) cc_final: 0.8885 (mp) REVERT: A 758 SER cc_start: 0.8440 (m) cc_final: 0.8161 (p) REVERT: A 825 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7890 (mtmt) REVERT: A 1041 ASP cc_start: 0.9072 (m-30) cc_final: 0.8569 (t0) REVERT: A 1050 MET cc_start: 0.7821 (ptt) cc_final: 0.7433 (ptp) REVERT: A 1139 ASP cc_start: 0.8379 (t0) cc_final: 0.8012 (t0) REVERT: B 41 LYS cc_start: 0.6821 (mttm) cc_final: 0.6343 (mmtp) REVERT: B 53 ASP cc_start: 0.7882 (t0) cc_final: 0.7587 (t0) REVERT: B 194 PHE cc_start: 0.8760 (m-80) cc_final: 0.8542 (m-10) REVERT: B 202 LYS cc_start: 0.5901 (mttp) cc_final: 0.5655 (mmmt) REVERT: B 223 LEU cc_start: 0.8527 (mp) cc_final: 0.8282 (mp) REVERT: B 266 TYR cc_start: 0.9034 (m-80) cc_final: 0.8565 (m-80) REVERT: B 321 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7344 (pm20) REVERT: B 347 PHE cc_start: 0.8055 (m-80) cc_final: 0.7494 (m-10) REVERT: B 389 ASP cc_start: 0.7927 (m-30) cc_final: 0.7406 (t0) REVERT: B 420 ASP cc_start: 0.8342 (m-30) cc_final: 0.8012 (m-30) REVERT: B 442 ASP cc_start: 0.7035 (m-30) cc_final: 0.6558 (m-30) REVERT: B 493 GLN cc_start: 0.7815 (tt0) cc_final: 0.7371 (tm-30) REVERT: B 532 ASN cc_start: 0.8336 (m-40) cc_final: 0.8117 (t0) REVERT: B 558 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7596 (mttt) REVERT: B 663 ASP cc_start: 0.9063 (t0) cc_final: 0.8775 (m-30) REVERT: B 698 SER cc_start: 0.8528 (t) cc_final: 0.7913 (p) REVERT: B 702 GLU cc_start: 0.8671 (tt0) cc_final: 0.8399 (tt0) REVERT: B 748 GLU cc_start: 0.7862 (mp0) cc_final: 0.7631 (mt-10) REVERT: B 825 LYS cc_start: 0.8048 (mmtt) cc_final: 0.7682 (tptt) REVERT: B 868 GLU cc_start: 0.8385 (pt0) cc_final: 0.7714 (tm-30) REVERT: B 895 GLN cc_start: 0.9219 (pm20) cc_final: 0.8805 (pm20) REVERT: B 968 SER cc_start: 0.9343 (m) cc_final: 0.8583 (p) REVERT: B 997 ILE cc_start: 0.8870 (mt) cc_final: 0.8647 (mt) REVERT: B 1050 MET cc_start: 0.8613 (ptt) cc_final: 0.8395 (ptp) REVERT: B 1066 THR cc_start: 0.9589 (p) cc_final: 0.9328 (t) REVERT: B 1097 SER cc_start: 0.8757 (t) cc_final: 0.8399 (p) REVERT: C 44 ARG cc_start: 0.6981 (mtt90) cc_final: 0.6760 (mtt90) REVERT: C 88 ASP cc_start: 0.8095 (m-30) cc_final: 0.7550 (t70) REVERT: C 169 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7482 (mp0) REVERT: C 201 PHE cc_start: 0.7780 (t80) cc_final: 0.7579 (t80) REVERT: C 565 PHE cc_start: 0.8120 (p90) cc_final: 0.7913 (p90) REVERT: C 697 MET cc_start: 0.8831 (ptm) cc_final: 0.8522 (ptm) REVERT: C 773 GLU cc_start: 0.8322 (tt0) cc_final: 0.8087 (tp30) REVERT: C 780 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8830 (tp30) REVERT: C 819 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8313 (mt-10) REVERT: C 1100 THR cc_start: 0.7740 (p) cc_final: 0.7457 (p) REVERT: C 1101 HIS cc_start: 0.7453 (m90) cc_final: 0.7197 (m90) REVERT: C 1135 ASN cc_start: 0.5914 (t0) cc_final: 0.5452 (t0) REVERT: Y 36 TRP cc_start: 0.5928 (m100) cc_final: 0.5251 (m100) REVERT: Y 62 ASP cc_start: 0.6673 (m-30) cc_final: 0.6182 (p0) REVERT: Y 79 VAL cc_start: 0.7463 (p) cc_final: 0.6449 (m) REVERT: Y 88 TYR cc_start: 0.7292 (t80) cc_final: 0.6980 (m-10) REVERT: Y 105 LEU cc_start: 0.8029 (tp) cc_final: 0.7713 (tp) REVERT: Z 34 MET cc_start: 0.3444 (mmm) cc_final: 0.2727 (ppp) REVERT: Z 83 MET cc_start: -0.2953 (mtp) cc_final: -0.3188 (mtp) outliers start: 35 outliers final: 4 residues processed: 625 average time/residue: 0.3957 time to fit residues: 385.6326 Evaluate side-chains 259 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 253 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 280 optimal weight: 0.7980 chunk 251 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 134 optimal weight: 0.0570 chunk 260 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 301 optimal weight: 3.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 563 GLN A 564 GLN A 784 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1011 GLN A1048 HIS A1071 GLN B 207 HIS B 388 ASN B 506 GLN B 519 HIS B 613 GLN B1048 HIS B1071 GLN C 81 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 607 GLN C 655 HIS ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN C1048 HIS Y 3 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 27670 Z= 0.195 Angle : 0.652 10.468 37625 Z= 0.327 Chirality : 0.047 0.280 4437 Planarity : 0.004 0.049 4766 Dihedral : 9.946 95.906 4986 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.14 % Allowed : 2.34 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.25 (0.14), residues: 3289 helix: 0.96 (0.20), residues: 682 sheet: 0.06 (0.17), residues: 784 loop : -0.68 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 64 HIS 0.008 0.001 HIS B 519 PHE 0.038 0.002 PHE B 565 TYR 0.028 0.001 TYR B 508 ARG 0.009 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 388 time to evaluate : 3.098 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.8112 (m-80) cc_final: 0.7768 (m-80) REVERT: A 56 LEU cc_start: 0.9304 (tp) cc_final: 0.9087 (tp) REVERT: A 81 ASN cc_start: 0.6145 (p0) cc_final: 0.5718 (t0) REVERT: A 166 CYS cc_start: 0.6578 (OUTLIER) cc_final: 0.6270 (m) REVERT: A 287 ASP cc_start: 0.8703 (t0) cc_final: 0.8313 (m-30) REVERT: A 347 PHE cc_start: 0.7692 (m-80) cc_final: 0.6092 (m-10) REVERT: A 355 ARG cc_start: 0.6801 (ttm170) cc_final: 0.6336 (mtp85) REVERT: A 565 PHE cc_start: 0.8483 (p90) cc_final: 0.8137 (p90) REVERT: A 658 ASN cc_start: 0.8018 (m-40) cc_final: 0.7205 (t0) REVERT: A 745 ASP cc_start: 0.8800 (m-30) cc_final: 0.8460 (t0) REVERT: A 758 SER cc_start: 0.7983 (m) cc_final: 0.7645 (p) REVERT: A 869 MET cc_start: 0.8503 (mtm) cc_final: 0.8154 (mtm) REVERT: A 1041 ASP cc_start: 0.9026 (m-30) cc_final: 0.8407 (t0) REVERT: B 239 GLN cc_start: 0.5326 (tp40) cc_final: 0.5025 (tp40) REVERT: B 347 PHE cc_start: 0.8254 (m-80) cc_final: 0.7577 (m-10) REVERT: B 357 ARG cc_start: 0.8341 (ttp80) cc_final: 0.8093 (mtp180) REVERT: B 389 ASP cc_start: 0.8195 (m-30) cc_final: 0.7701 (t0) REVERT: B 508 TYR cc_start: 0.7705 (m-80) cc_final: 0.7373 (m-80) REVERT: B 558 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7260 (mttt) REVERT: B 584 ILE cc_start: 0.8900 (pt) cc_final: 0.8692 (tp) REVERT: B 698 SER cc_start: 0.8525 (t) cc_final: 0.8016 (p) REVERT: B 702 GLU cc_start: 0.8609 (tt0) cc_final: 0.8314 (tt0) REVERT: B 825 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7579 (tttt) REVERT: B 868 GLU cc_start: 0.8308 (pt0) cc_final: 0.7632 (tm-30) REVERT: B 895 GLN cc_start: 0.9447 (pm20) cc_final: 0.8854 (pm20) REVERT: B 968 SER cc_start: 0.9414 (m) cc_final: 0.8768 (p) REVERT: B 1097 SER cc_start: 0.8773 (t) cc_final: 0.8408 (p) REVERT: C 88 ASP cc_start: 0.8043 (m-30) cc_final: 0.7708 (t70) REVERT: C 169 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7501 (mp0) REVERT: C 204 TYR cc_start: 0.7341 (m-80) cc_final: 0.6962 (m-80) REVERT: C 565 PHE cc_start: 0.8040 (p90) cc_final: 0.7807 (p90) REVERT: C 697 MET cc_start: 0.8646 (ptm) cc_final: 0.8397 (ptm) REVERT: C 734 THR cc_start: 0.9366 (m) cc_final: 0.9141 (t) REVERT: C 819 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8462 (mt-10) REVERT: C 856 ASN cc_start: 0.5993 (m-40) cc_final: 0.5724 (m-40) REVERT: C 900 MET cc_start: 0.8294 (mtp) cc_final: 0.7968 (mtm) REVERT: C 1100 THR cc_start: 0.7918 (p) cc_final: 0.7648 (p) REVERT: C 1101 HIS cc_start: 0.7337 (m90) cc_final: 0.7119 (m90) REVERT: Y 36 TRP cc_start: 0.5770 (m100) cc_final: 0.5168 (m100) REVERT: Y 83 MET cc_start: 0.5926 (mtp) cc_final: 0.5412 (ptp) REVERT: Y 88 TYR cc_start: 0.7356 (t80) cc_final: 0.6984 (m-10) REVERT: Z 34 MET cc_start: 0.3645 (mmm) cc_final: 0.2763 (ppp) outliers start: 4 outliers final: 2 residues processed: 392 average time/residue: 0.3498 time to fit residues: 228.1315 Evaluate side-chains 216 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 213 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 167 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 250 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 302 optimal weight: 0.0970 chunk 326 optimal weight: 20.0000 chunk 268 optimal weight: 0.6980 chunk 299 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 242 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 784 GLN A 804 GLN A 926 GLN A 935 GLN A1142 GLN B 234 ASN B 762 GLN B 787 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27670 Z= 0.184 Angle : 0.589 8.937 37625 Z= 0.300 Chirality : 0.045 0.248 4437 Planarity : 0.003 0.050 4766 Dihedral : 8.387 82.590 4986 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.14 % Allowed : 2.59 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.07 (0.14), residues: 3289 helix: 1.40 (0.21), residues: 681 sheet: 0.13 (0.17), residues: 796 loop : -0.47 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 104 HIS 0.011 0.001 HIS B 519 PHE 0.027 0.001 PHE B 275 TYR 0.032 0.001 TYR A 904 ARG 0.008 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 321 time to evaluate : 2.937 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 55 PHE cc_start: 0.8075 (m-80) cc_final: 0.7725 (m-80) REVERT: A 287 ASP cc_start: 0.8707 (t0) cc_final: 0.8352 (m-30) REVERT: A 347 PHE cc_start: 0.7610 (m-80) cc_final: 0.6414 (m-10) REVERT: A 365 TYR cc_start: 0.8067 (m-10) cc_final: 0.7636 (m-10) REVERT: A 565 PHE cc_start: 0.8507 (p90) cc_final: 0.8279 (p90) REVERT: A 658 ASN cc_start: 0.7983 (m-40) cc_final: 0.7295 (t0) REVERT: A 666 ILE cc_start: 0.8960 (mt) cc_final: 0.8740 (mt) REVERT: A 758 SER cc_start: 0.7878 (m) cc_final: 0.7345 (p) REVERT: A 1041 ASP cc_start: 0.9064 (m-30) cc_final: 0.8477 (t0) REVERT: B 104 TRP cc_start: 0.7054 (m-10) cc_final: 0.6714 (m-90) REVERT: B 239 GLN cc_start: 0.4927 (tp40) cc_final: 0.4662 (tp-100) REVERT: B 347 PHE cc_start: 0.8249 (m-80) cc_final: 0.7551 (m-10) REVERT: B 389 ASP cc_start: 0.8433 (m-30) cc_final: 0.8186 (t0) REVERT: B 508 TYR cc_start: 0.7729 (m-80) cc_final: 0.7367 (m-80) REVERT: B 510 VAL cc_start: 0.9221 (t) cc_final: 0.8824 (m) REVERT: B 558 LYS cc_start: 0.7716 (mmtt) cc_final: 0.7155 (mttt) REVERT: B 698 SER cc_start: 0.8571 (t) cc_final: 0.8139 (p) REVERT: B 702 GLU cc_start: 0.8648 (tt0) cc_final: 0.8371 (tt0) REVERT: B 825 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7745 (tppt) REVERT: B 868 GLU cc_start: 0.8261 (pt0) cc_final: 0.7599 (tm-30) REVERT: B 895 GLN cc_start: 0.9431 (pm20) cc_final: 0.8902 (pm20) REVERT: B 968 SER cc_start: 0.9499 (m) cc_final: 0.8863 (p) REVERT: C 88 ASP cc_start: 0.8017 (m-30) cc_final: 0.7670 (t70) REVERT: C 106 PHE cc_start: 0.8269 (m-80) cc_final: 0.7765 (m-80) REVERT: C 169 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7632 (mp0) REVERT: C 565 PHE cc_start: 0.8026 (p90) cc_final: 0.7808 (p90) REVERT: C 663 ASP cc_start: 0.8807 (m-30) cc_final: 0.8603 (m-30) REVERT: C 734 THR cc_start: 0.9375 (m) cc_final: 0.9167 (t) REVERT: C 819 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8615 (mt-10) REVERT: C 900 MET cc_start: 0.8454 (mtp) cc_final: 0.8134 (mtm) REVERT: C 1066 THR cc_start: 0.9297 (p) cc_final: 0.9082 (t) REVERT: C 1100 THR cc_start: 0.7751 (p) cc_final: 0.7171 (p) REVERT: C 1101 HIS cc_start: 0.7138 (m90) cc_final: 0.6818 (m90) REVERT: C 1136 THR cc_start: 0.9017 (m) cc_final: 0.8764 (t) REVERT: Y 36 TRP cc_start: 0.5772 (m100) cc_final: 0.5160 (m100) REVERT: Y 70 ILE cc_start: 0.7124 (tt) cc_final: 0.6694 (tp) REVERT: Y 79 VAL cc_start: 0.7539 (p) cc_final: 0.6834 (p) REVERT: Y 83 MET cc_start: 0.5903 (mtp) cc_final: 0.5441 (ptp) REVERT: Y 88 TYR cc_start: 0.7341 (t80) cc_final: 0.6996 (m-10) REVERT: Z 34 MET cc_start: 0.3763 (mmm) cc_final: 0.2767 (ppp) outliers start: 4 outliers final: 1 residues processed: 325 average time/residue: 0.3606 time to fit residues: 193.1004 Evaluate side-chains 210 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 298 optimal weight: 20.0000 chunk 227 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 303 optimal weight: 9.9990 chunk 320 optimal weight: 30.0000 chunk 158 optimal weight: 5.9990 chunk 287 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 317 ASN A 655 HIS A 779 GLN B 30 ASN B 207 HIS B 218 GLN B 234 ASN B 388 ASN B 563 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 239 GLN C 414 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 955 ASN C 965 GLN C1005 GLN Y 77 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 27670 Z= 0.522 Angle : 0.864 13.533 37625 Z= 0.439 Chirality : 0.054 0.331 4437 Planarity : 0.006 0.099 4766 Dihedral : 8.347 65.780 4986 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.28 % Allowed : 4.03 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.61 (0.14), residues: 3289 helix: 0.42 (0.20), residues: 670 sheet: 0.18 (0.17), residues: 811 loop : -0.98 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 353 HIS 0.018 0.003 HIS B 519 PHE 0.035 0.003 PHE B 238 TYR 0.034 0.002 TYR A 904 ARG 0.028 0.001 ARG C1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 257 time to evaluate : 3.012 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: A 55 PHE cc_start: 0.7762 (m-80) cc_final: 0.7332 (m-80) REVERT: A 102 ARG cc_start: 0.7302 (ptt180) cc_final: 0.6926 (mtm180) REVERT: A 347 PHE cc_start: 0.7504 (m-80) cc_final: 0.6342 (m-10) REVERT: A 418 ILE cc_start: 0.6514 (mm) cc_final: 0.5960 (mm) REVERT: A 495 TYR cc_start: 0.5090 (m-80) cc_final: 0.4343 (m-80) REVERT: A 658 ASN cc_start: 0.8216 (m-40) cc_final: 0.7444 (t0) REVERT: A 666 ILE cc_start: 0.9097 (mt) cc_final: 0.8842 (mt) REVERT: A 698 SER cc_start: 0.9070 (t) cc_final: 0.8797 (p) REVERT: A 758 SER cc_start: 0.8319 (m) cc_final: 0.7945 (p) REVERT: A 896 ILE cc_start: 0.9356 (tt) cc_final: 0.9139 (pt) REVERT: A 1041 ASP cc_start: 0.9134 (m-30) cc_final: 0.8695 (t0) REVERT: B 347 PHE cc_start: 0.8331 (m-80) cc_final: 0.7526 (m-10) REVERT: B 468 ILE cc_start: 0.8791 (pt) cc_final: 0.8290 (mm) REVERT: B 558 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7608 (mmtt) REVERT: B 702 GLU cc_start: 0.8658 (tt0) cc_final: 0.7910 (tm-30) REVERT: B 968 SER cc_start: 0.9506 (m) cc_final: 0.9011 (p) REVERT: C 106 PHE cc_start: 0.8417 (m-80) cc_final: 0.8199 (m-80) REVERT: C 169 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7592 (mp0) REVERT: C 242 LEU cc_start: 0.8477 (pp) cc_final: 0.8136 (tt) REVERT: C 290 ASP cc_start: 0.8523 (t70) cc_final: 0.8230 (t0) REVERT: C 697 MET cc_start: 0.8407 (ptm) cc_final: 0.8151 (ptm) REVERT: C 1066 THR cc_start: 0.9433 (p) cc_final: 0.9208 (t) REVERT: C 1136 THR cc_start: 0.9169 (m) cc_final: 0.8967 (t) REVERT: Y 36 TRP cc_start: 0.5536 (m100) cc_final: 0.5212 (m100) REVERT: Y 83 MET cc_start: 0.5705 (mtp) cc_final: 0.4907 (ptp) REVERT: Y 88 TYR cc_start: 0.7403 (t80) cc_final: 0.7012 (m-80) REVERT: Y 102 VAL cc_start: 0.7754 (t) cc_final: 0.7542 (p) REVERT: Z 34 MET cc_start: 0.3656 (mmm) cc_final: 0.3335 (pmm) outliers start: 8 outliers final: 2 residues processed: 265 average time/residue: 0.3912 time to fit residues: 176.4386 Evaluate side-chains 179 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 177 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 267 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 238 optimal weight: 30.0000 chunk 132 optimal weight: 5.9990 chunk 273 optimal weight: 0.9980 chunk 221 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 288 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 207 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 450 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 955 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27670 Z= 0.193 Angle : 0.596 12.921 37625 Z= 0.304 Chirality : 0.046 0.238 4437 Planarity : 0.004 0.064 4766 Dihedral : 6.893 62.802 4986 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.07 % Allowed : 1.41 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.14), residues: 3289 helix: 1.19 (0.20), residues: 653 sheet: 0.34 (0.17), residues: 798 loop : -0.70 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 64 HIS 0.006 0.001 HIS B1048 PHE 0.033 0.002 PHE A 497 TYR 0.018 0.001 TYR C 369 ARG 0.007 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 272 time to evaluate : 3.007 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 55 PHE cc_start: 0.7576 (m-80) cc_final: 0.7275 (m-80) REVERT: A 102 ARG cc_start: 0.7393 (ptt180) cc_final: 0.7013 (mtm180) REVERT: A 347 PHE cc_start: 0.7699 (m-80) cc_final: 0.6631 (m-10) REVERT: A 393 THR cc_start: 0.6740 (m) cc_final: 0.6528 (p) REVERT: A 418 ILE cc_start: 0.6871 (mm) cc_final: 0.6501 (mm) REVERT: A 495 TYR cc_start: 0.4739 (m-80) cc_final: 0.3736 (m-80) REVERT: A 658 ASN cc_start: 0.8154 (m-40) cc_final: 0.7379 (t0) REVERT: A 666 ILE cc_start: 0.9020 (mt) cc_final: 0.8763 (mt) REVERT: A 698 SER cc_start: 0.8711 (t) cc_final: 0.8350 (p) REVERT: A 758 SER cc_start: 0.8038 (m) cc_final: 0.7572 (p) REVERT: A 1041 ASP cc_start: 0.9125 (m-30) cc_final: 0.8721 (t0) REVERT: A 1050 MET cc_start: 0.7808 (ptt) cc_final: 0.7540 (ptt) REVERT: B 53 ASP cc_start: 0.7852 (t0) cc_final: 0.7626 (t0) REVERT: B 54 LEU cc_start: 0.8346 (mm) cc_final: 0.7821 (tp) REVERT: B 347 PHE cc_start: 0.8354 (m-80) cc_final: 0.7529 (m-10) REVERT: B 389 ASP cc_start: 0.8838 (m-30) cc_final: 0.8638 (t70) REVERT: B 420 ASP cc_start: 0.8272 (m-30) cc_final: 0.8032 (m-30) REVERT: B 465 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7620 (tm-30) REVERT: B 468 ILE cc_start: 0.8798 (pt) cc_final: 0.8327 (mm) REVERT: B 510 VAL cc_start: 0.9208 (t) cc_final: 0.8821 (m) REVERT: B 558 LYS cc_start: 0.7816 (mmtt) cc_final: 0.7259 (mttt) REVERT: B 702 GLU cc_start: 0.8669 (tt0) cc_final: 0.7938 (tm-30) REVERT: B 895 GLN cc_start: 0.9333 (pm20) cc_final: 0.9078 (pm20) REVERT: B 968 SER cc_start: 0.9540 (m) cc_final: 0.9051 (p) REVERT: C 106 PHE cc_start: 0.8352 (m-80) cc_final: 0.7996 (m-80) REVERT: C 169 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7587 (mp0) REVERT: C 242 LEU cc_start: 0.8427 (pp) cc_final: 0.8097 (tt) REVERT: C 697 MET cc_start: 0.8164 (ptm) cc_final: 0.7924 (ptm) REVERT: C 882 ILE cc_start: 0.9252 (mt) cc_final: 0.9021 (mp) REVERT: C 1066 THR cc_start: 0.9366 (p) cc_final: 0.9164 (t) REVERT: C 1136 THR cc_start: 0.9158 (m) cc_final: 0.8958 (t) REVERT: Y 34 MET cc_start: 0.7231 (tpp) cc_final: 0.6649 (mtm) REVERT: Y 36 TRP cc_start: 0.5382 (m100) cc_final: 0.5147 (m100) REVERT: Y 62 ASP cc_start: 0.6997 (t0) cc_final: 0.6685 (p0) REVERT: Y 94 TYR cc_start: 0.4982 (m-80) cc_final: 0.4757 (m-80) REVERT: Z 34 MET cc_start: 0.4166 (mmm) cc_final: 0.3665 (pmm) outliers start: 2 outliers final: 1 residues processed: 274 average time/residue: 0.3638 time to fit residues: 165.0222 Evaluate side-chains 182 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 107 optimal weight: 8.9990 chunk 288 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 188 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 321 optimal weight: 8.9990 chunk 266 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 493 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 955 ASN C1005 GLN Y 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27670 Z= 0.187 Angle : 0.569 11.896 37625 Z= 0.289 Chirality : 0.045 0.248 4437 Planarity : 0.004 0.093 4766 Dihedral : 6.234 58.468 4986 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.03 % Allowed : 1.31 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.03 (0.14), residues: 3289 helix: 1.35 (0.21), residues: 664 sheet: 0.36 (0.17), residues: 820 loop : -0.63 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 104 HIS 0.004 0.001 HIS B 519 PHE 0.028 0.001 PHE B 559 TYR 0.034 0.001 TYR A 495 ARG 0.017 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 3.103 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 55 PHE cc_start: 0.7645 (m-80) cc_final: 0.7366 (m-80) REVERT: A 102 ARG cc_start: 0.7400 (ptt180) cc_final: 0.7018 (mtm180) REVERT: A 347 PHE cc_start: 0.7591 (m-80) cc_final: 0.6541 (m-10) REVERT: A 418 ILE cc_start: 0.7061 (mm) cc_final: 0.6643 (mm) REVERT: A 658 ASN cc_start: 0.8163 (m-40) cc_final: 0.7423 (t0) REVERT: A 666 ILE cc_start: 0.8946 (mt) cc_final: 0.8696 (mt) REVERT: A 698 SER cc_start: 0.8581 (t) cc_final: 0.8231 (p) REVERT: A 758 SER cc_start: 0.8148 (m) cc_final: 0.7678 (p) REVERT: A 896 ILE cc_start: 0.9185 (tt) cc_final: 0.8902 (pt) REVERT: A 1041 ASP cc_start: 0.9105 (m-30) cc_final: 0.8480 (t0) REVERT: B 53 ASP cc_start: 0.7859 (t0) cc_final: 0.7573 (t0) REVERT: B 54 LEU cc_start: 0.8221 (mm) cc_final: 0.7669 (tp) REVERT: B 104 TRP cc_start: 0.7173 (m-10) cc_final: 0.6284 (m-90) REVERT: B 202 LYS cc_start: 0.5602 (mppt) cc_final: 0.5168 (mmtm) REVERT: B 347 PHE cc_start: 0.8317 (m-80) cc_final: 0.7515 (m-10) REVERT: B 420 ASP cc_start: 0.8301 (m-30) cc_final: 0.8007 (m-30) REVERT: B 468 ILE cc_start: 0.8749 (pt) cc_final: 0.8267 (mm) REVERT: B 510 VAL cc_start: 0.9270 (t) cc_final: 0.8819 (m) REVERT: B 558 LYS cc_start: 0.7806 (mmtt) cc_final: 0.7186 (mttt) REVERT: B 702 GLU cc_start: 0.8697 (tt0) cc_final: 0.7965 (tm-30) REVERT: B 775 ASP cc_start: 0.9107 (t0) cc_final: 0.8658 (t70) REVERT: B 895 GLN cc_start: 0.9318 (pm20) cc_final: 0.9047 (pm20) REVERT: B 968 SER cc_start: 0.9520 (m) cc_final: 0.9016 (p) REVERT: C 106 PHE cc_start: 0.8359 (m-80) cc_final: 0.8039 (m-80) REVERT: C 169 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7569 (mp0) REVERT: C 324 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6602 (mp0) REVERT: C 697 MET cc_start: 0.8231 (ptm) cc_final: 0.7960 (ptm) REVERT: C 1066 THR cc_start: 0.9383 (p) cc_final: 0.9177 (t) REVERT: C 1136 THR cc_start: 0.9136 (m) cc_final: 0.8905 (t) REVERT: Y 34 MET cc_start: 0.7273 (tpp) cc_final: 0.6713 (mtm) REVERT: Y 36 TRP cc_start: 0.5638 (m100) cc_final: 0.5193 (m100) REVERT: Y 62 ASP cc_start: 0.6989 (t0) cc_final: 0.6668 (p0) REVERT: Y 81 LEU cc_start: 0.5647 (tp) cc_final: 0.5444 (tp) REVERT: Y 83 MET cc_start: 0.5124 (mtp) cc_final: 0.4893 (ptp) REVERT: Y 94 TYR cc_start: 0.5207 (m-80) cc_final: 0.4610 (m-10) REVERT: Z 34 MET cc_start: 0.4152 (mmm) cc_final: 0.3649 (pmm) outliers start: 1 outliers final: 1 residues processed: 252 average time/residue: 0.3541 time to fit residues: 150.8097 Evaluate side-chains 180 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 4.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 309 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 270 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 319 optimal weight: 0.7980 chunk 200 optimal weight: 0.4980 chunk 195 optimal weight: 0.6980 chunk 147 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 317 ASN A 493 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 81 ASN C 493 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 955 ASN Y 122 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27670 Z= 0.189 Angle : 0.552 12.292 37625 Z= 0.282 Chirality : 0.044 0.212 4437 Planarity : 0.004 0.061 4766 Dihedral : 5.707 50.838 4986 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.03 % Allowed : 1.00 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.14), residues: 3289 helix: 1.58 (0.21), residues: 655 sheet: 0.37 (0.17), residues: 830 loop : -0.60 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 104 HIS 0.005 0.001 HIS B 519 PHE 0.015 0.001 PHE A1095 TYR 0.021 0.001 TYR A 495 ARG 0.009 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 256 time to evaluate : 2.855 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 55 PHE cc_start: 0.7655 (m-80) cc_final: 0.7393 (m-80) REVERT: A 102 ARG cc_start: 0.7327 (ptt180) cc_final: 0.6965 (mtm180) REVERT: A 418 ILE cc_start: 0.6964 (mm) cc_final: 0.6717 (mm) REVERT: A 658 ASN cc_start: 0.8136 (m-40) cc_final: 0.7381 (t0) REVERT: A 666 ILE cc_start: 0.8936 (mt) cc_final: 0.8683 (mt) REVERT: A 758 SER cc_start: 0.8090 (m) cc_final: 0.7607 (p) REVERT: A 896 ILE cc_start: 0.9233 (tt) cc_final: 0.8935 (pt) REVERT: A 1107 ARG cc_start: 0.8780 (ptp90) cc_final: 0.8416 (ptp-170) REVERT: B 53 ASP cc_start: 0.7857 (t0) cc_final: 0.7569 (t0) REVERT: B 54 LEU cc_start: 0.8265 (mm) cc_final: 0.7723 (tp) REVERT: B 102 ARG cc_start: 0.8676 (mtt180) cc_final: 0.8256 (mmm-85) REVERT: B 104 TRP cc_start: 0.7200 (m-10) cc_final: 0.6329 (m-90) REVERT: B 202 LYS cc_start: 0.5596 (mppt) cc_final: 0.5270 (mmtm) REVERT: B 347 PHE cc_start: 0.8197 (m-80) cc_final: 0.7416 (m-10) REVERT: B 452 LEU cc_start: 0.8229 (mt) cc_final: 0.7936 (mt) REVERT: B 468 ILE cc_start: 0.8815 (pt) cc_final: 0.8343 (mm) REVERT: B 493 GLN cc_start: 0.7896 (tt0) cc_final: 0.7694 (tm-30) REVERT: B 510 VAL cc_start: 0.9289 (t) cc_final: 0.8838 (m) REVERT: B 558 LYS cc_start: 0.7855 (mmtt) cc_final: 0.7239 (mttt) REVERT: B 702 GLU cc_start: 0.8559 (tt0) cc_final: 0.7795 (tm-30) REVERT: B 775 ASP cc_start: 0.9104 (t0) cc_final: 0.8647 (t70) REVERT: B 895 GLN cc_start: 0.9306 (pm20) cc_final: 0.8959 (pm20) REVERT: B 968 SER cc_start: 0.9475 (m) cc_final: 0.8984 (p) REVERT: C 106 PHE cc_start: 0.8346 (m-80) cc_final: 0.7995 (m-80) REVERT: C 169 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7581 (mp0) REVERT: C 269 TYR cc_start: 0.8347 (m-10) cc_final: 0.8142 (m-80) REVERT: C 324 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6496 (mp0) REVERT: C 329 PHE cc_start: 0.6949 (m-80) cc_final: 0.6284 (m-10) REVERT: C 697 MET cc_start: 0.8101 (ptm) cc_final: 0.7832 (ptm) REVERT: C 901 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: C 1136 THR cc_start: 0.9138 (m) cc_final: 0.8903 (t) REVERT: Y 34 MET cc_start: 0.7330 (tpp) cc_final: 0.6759 (mtm) REVERT: Y 36 TRP cc_start: 0.5761 (m100) cc_final: 0.5195 (m100) REVERT: Y 62 ASP cc_start: 0.7115 (t0) cc_final: 0.6809 (p0) REVERT: Y 81 LEU cc_start: 0.5889 (tp) cc_final: 0.5570 (tt) REVERT: Y 83 MET cc_start: 0.5190 (mtp) cc_final: 0.4623 (ptp) REVERT: Y 94 TYR cc_start: 0.5388 (m-80) cc_final: 0.4933 (m-10) REVERT: Z 34 MET cc_start: 0.4141 (mmm) cc_final: 0.3649 (pmm) outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.3480 time to fit residues: 149.9578 Evaluate side-chains 185 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 191 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 203 optimal weight: 9.9990 chunk 218 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 251 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27670 Z= 0.173 Angle : 0.538 10.913 37625 Z= 0.275 Chirality : 0.044 0.204 4437 Planarity : 0.004 0.060 4766 Dihedral : 5.342 44.407 4986 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.14), residues: 3289 helix: 1.62 (0.21), residues: 655 sheet: 0.43 (0.17), residues: 824 loop : -0.54 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 104 HIS 0.004 0.001 HIS A 207 PHE 0.020 0.001 PHE C 898 TYR 0.017 0.001 TYR C 369 ARG 0.005 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7687 (m-80) cc_final: 0.7456 (m-80) REVERT: A 102 ARG cc_start: 0.7425 (ptt180) cc_final: 0.7091 (mtm180) REVERT: A 369 TYR cc_start: 0.8428 (t80) cc_final: 0.8176 (t80) REVERT: A 393 THR cc_start: 0.7622 (p) cc_final: 0.7382 (p) REVERT: A 418 ILE cc_start: 0.7037 (mm) cc_final: 0.6800 (mm) REVERT: A 658 ASN cc_start: 0.8194 (m-40) cc_final: 0.7488 (t0) REVERT: A 758 SER cc_start: 0.7972 (m) cc_final: 0.7455 (p) REVERT: A 869 MET cc_start: 0.8747 (mtt) cc_final: 0.8518 (mtm) REVERT: A 896 ILE cc_start: 0.9228 (tt) cc_final: 0.8939 (pt) REVERT: A 1041 ASP cc_start: 0.8956 (m-30) cc_final: 0.8494 (t0) REVERT: A 1107 ARG cc_start: 0.8840 (ptp90) cc_final: 0.8497 (ptp-170) REVERT: B 53 ASP cc_start: 0.7857 (t0) cc_final: 0.7559 (t0) REVERT: B 54 LEU cc_start: 0.8173 (mm) cc_final: 0.7622 (tp) REVERT: B 102 ARG cc_start: 0.8687 (mtt180) cc_final: 0.8324 (mmm-85) REVERT: B 104 TRP cc_start: 0.7363 (m-10) cc_final: 0.6472 (m-90) REVERT: B 202 LYS cc_start: 0.5703 (mppt) cc_final: 0.5249 (mmtm) REVERT: B 347 PHE cc_start: 0.8180 (m-80) cc_final: 0.7443 (m-10) REVERT: B 452 LEU cc_start: 0.8213 (mt) cc_final: 0.7981 (mt) REVERT: B 468 ILE cc_start: 0.8828 (pt) cc_final: 0.8366 (mm) REVERT: B 493 GLN cc_start: 0.7972 (tt0) cc_final: 0.7721 (tm-30) REVERT: B 510 VAL cc_start: 0.9306 (t) cc_final: 0.8890 (m) REVERT: B 558 LYS cc_start: 0.7970 (mmtt) cc_final: 0.7418 (mttt) REVERT: B 702 GLU cc_start: 0.8602 (tt0) cc_final: 0.7812 (tm-30) REVERT: B 775 ASP cc_start: 0.9098 (t0) cc_final: 0.8626 (t70) REVERT: B 895 GLN cc_start: 0.9206 (pm20) cc_final: 0.8854 (pm20) REVERT: B 968 SER cc_start: 0.9430 (m) cc_final: 0.8939 (p) REVERT: B 1072 GLU cc_start: 0.9075 (pt0) cc_final: 0.8811 (pm20) REVERT: C 106 PHE cc_start: 0.8332 (m-80) cc_final: 0.8129 (m-80) REVERT: C 169 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7563 (mp0) REVERT: C 269 TYR cc_start: 0.8341 (m-10) cc_final: 0.8140 (m-80) REVERT: C 324 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6490 (mp0) REVERT: C 329 PHE cc_start: 0.7043 (m-80) cc_final: 0.6357 (m-10) REVERT: C 1136 THR cc_start: 0.9130 (m) cc_final: 0.8891 (t) REVERT: Y 34 MET cc_start: 0.7309 (tpp) cc_final: 0.6755 (mtm) REVERT: Y 36 TRP cc_start: 0.5645 (m100) cc_final: 0.5125 (m100) REVERT: Y 62 ASP cc_start: 0.7133 (t0) cc_final: 0.6837 (p0) REVERT: Y 83 MET cc_start: 0.5179 (mtp) cc_final: 0.4497 (ptp) REVERT: Y 94 TYR cc_start: 0.5503 (m-80) cc_final: 0.5068 (m-10) REVERT: Z 34 MET cc_start: 0.4118 (mmm) cc_final: 0.3647 (pmm) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.3458 time to fit residues: 149.3017 Evaluate side-chains 179 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 291 optimal weight: 2.9990 chunk 306 optimal weight: 3.9990 chunk 279 optimal weight: 0.5980 chunk 298 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 234 optimal weight: 0.1980 chunk 91 optimal weight: 5.9990 chunk 269 optimal weight: 0.9990 chunk 282 optimal weight: 0.7980 chunk 297 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 450 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 27670 Z= 0.156 Angle : 0.522 10.726 37625 Z= 0.268 Chirality : 0.044 0.211 4437 Planarity : 0.003 0.061 4766 Dihedral : 5.083 40.293 4986 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.03 % Allowed : 0.38 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.15), residues: 3289 helix: 1.79 (0.21), residues: 649 sheet: 0.50 (0.17), residues: 824 loop : -0.47 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.006 0.001 HIS A 207 PHE 0.030 0.001 PHE B 392 TYR 0.017 0.001 TYR C 369 ARG 0.004 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 2.973 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: A 55 PHE cc_start: 0.7678 (m-80) cc_final: 0.7436 (m-80) REVERT: A 102 ARG cc_start: 0.7444 (ptt180) cc_final: 0.7086 (mtm180) REVERT: A 393 THR cc_start: 0.7597 (p) cc_final: 0.7357 (p) REVERT: A 418 ILE cc_start: 0.6980 (mm) cc_final: 0.6737 (mm) REVERT: A 658 ASN cc_start: 0.8209 (m-40) cc_final: 0.7502 (t0) REVERT: A 758 SER cc_start: 0.7917 (m) cc_final: 0.7363 (p) REVERT: A 817 PHE cc_start: 0.7984 (t80) cc_final: 0.7540 (t80) REVERT: A 869 MET cc_start: 0.8603 (mtt) cc_final: 0.8360 (mtm) REVERT: A 896 ILE cc_start: 0.9193 (tt) cc_final: 0.8884 (pt) REVERT: A 1041 ASP cc_start: 0.8909 (m-30) cc_final: 0.8466 (t0) REVERT: B 53 ASP cc_start: 0.7849 (t0) cc_final: 0.7551 (t0) REVERT: B 54 LEU cc_start: 0.8152 (mm) cc_final: 0.7606 (tp) REVERT: B 102 ARG cc_start: 0.8745 (mtt180) cc_final: 0.8409 (mmm-85) REVERT: B 104 TRP cc_start: 0.7370 (m-10) cc_final: 0.6468 (m-90) REVERT: B 202 LYS cc_start: 0.5876 (mppt) cc_final: 0.5430 (mmtm) REVERT: B 347 PHE cc_start: 0.8146 (m-80) cc_final: 0.7419 (m-10) REVERT: B 452 LEU cc_start: 0.8145 (mt) cc_final: 0.7889 (mt) REVERT: B 468 ILE cc_start: 0.8809 (pt) cc_final: 0.8343 (mm) REVERT: B 510 VAL cc_start: 0.9299 (t) cc_final: 0.8880 (m) REVERT: B 558 LYS cc_start: 0.7994 (mmtt) cc_final: 0.7433 (mttt) REVERT: B 702 GLU cc_start: 0.8563 (tt0) cc_final: 0.7789 (tm-30) REVERT: B 775 ASP cc_start: 0.9099 (t0) cc_final: 0.8602 (t70) REVERT: B 895 GLN cc_start: 0.9196 (pm20) cc_final: 0.8822 (pm20) REVERT: B 968 SER cc_start: 0.9382 (m) cc_final: 0.8873 (p) REVERT: B 1072 GLU cc_start: 0.9052 (pt0) cc_final: 0.8746 (pm20) REVERT: C 106 PHE cc_start: 0.8243 (m-80) cc_final: 0.7957 (m-80) REVERT: C 169 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7570 (mp0) REVERT: C 204 TYR cc_start: 0.7609 (m-80) cc_final: 0.6964 (m-80) REVERT: C 329 PHE cc_start: 0.7136 (m-80) cc_final: 0.6446 (m-10) REVERT: C 1136 THR cc_start: 0.9135 (m) cc_final: 0.8902 (t) REVERT: Y 34 MET cc_start: 0.7284 (tpp) cc_final: 0.6730 (mtm) REVERT: Y 36 TRP cc_start: 0.5679 (m100) cc_final: 0.5175 (m100) REVERT: Y 62 ASP cc_start: 0.7292 (t0) cc_final: 0.7025 (p0) REVERT: Y 81 LEU cc_start: 0.5823 (tp) cc_final: 0.4540 (tt) REVERT: Y 83 MET cc_start: 0.5544 (mtp) cc_final: 0.5123 (mpp) REVERT: Y 94 TYR cc_start: 0.5683 (m-80) cc_final: 0.5222 (m-10) REVERT: Y 105 LEU cc_start: 0.8468 (tp) cc_final: 0.8248 (tp) REVERT: Y 109 TYR cc_start: 0.7503 (m-80) cc_final: 0.7099 (m-80) REVERT: Z 34 MET cc_start: 0.4105 (mmm) cc_final: 0.3639 (pmm) outliers start: 1 outliers final: 1 residues processed: 270 average time/residue: 0.3470 time to fit residues: 156.9594 Evaluate side-chains 186 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 195 optimal weight: 2.9990 chunk 315 optimal weight: 8.9990 chunk 192 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 219 optimal weight: 0.9990 chunk 330 optimal weight: 10.0000 chunk 304 optimal weight: 9.9990 chunk 263 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 321 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27670 Z= 0.201 Angle : 0.540 10.685 37625 Z= 0.278 Chirality : 0.044 0.219 4437 Planarity : 0.004 0.162 4766 Dihedral : 5.137 39.874 4986 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.15), residues: 3289 helix: 1.59 (0.21), residues: 661 sheet: 0.52 (0.17), residues: 824 loop : -0.49 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 64 HIS 0.006 0.001 HIS A 207 PHE 0.031 0.001 PHE B 559 TYR 0.018 0.001 TYR C 369 ARG 0.018 0.000 ARG A 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7696 (m-80) cc_final: 0.7384 (m-80) REVERT: A 393 THR cc_start: 0.7502 (p) cc_final: 0.7245 (p) REVERT: A 418 ILE cc_start: 0.6852 (mm) cc_final: 0.6590 (mm) REVERT: A 658 ASN cc_start: 0.8239 (m-40) cc_final: 0.7551 (t0) REVERT: A 758 SER cc_start: 0.7885 (m) cc_final: 0.7350 (p) REVERT: A 817 PHE cc_start: 0.7992 (t80) cc_final: 0.7526 (t80) REVERT: A 869 MET cc_start: 0.8707 (mtt) cc_final: 0.8433 (mtm) REVERT: A 1041 ASP cc_start: 0.8873 (m-30) cc_final: 0.8459 (t0) REVERT: B 53 ASP cc_start: 0.7833 (t0) cc_final: 0.7529 (t0) REVERT: B 54 LEU cc_start: 0.8184 (mm) cc_final: 0.7626 (tp) REVERT: B 102 ARG cc_start: 0.8740 (mtt180) cc_final: 0.8433 (mmm-85) REVERT: B 104 TRP cc_start: 0.7453 (m-10) cc_final: 0.6518 (m-90) REVERT: B 347 PHE cc_start: 0.8149 (m-80) cc_final: 0.7413 (m-10) REVERT: B 468 ILE cc_start: 0.8835 (pt) cc_final: 0.8333 (mm) REVERT: B 493 GLN cc_start: 0.8021 (tt0) cc_final: 0.7767 (tm-30) REVERT: B 510 VAL cc_start: 0.9304 (t) cc_final: 0.8878 (m) REVERT: B 558 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7323 (mttt) REVERT: B 702 GLU cc_start: 0.8516 (tt0) cc_final: 0.7808 (tm-30) REVERT: B 775 ASP cc_start: 0.9106 (t0) cc_final: 0.8632 (t70) REVERT: B 895 GLN cc_start: 0.9178 (pm20) cc_final: 0.8842 (pm20) REVERT: B 968 SER cc_start: 0.9406 (m) cc_final: 0.8898 (p) REVERT: B 1072 GLU cc_start: 0.9065 (pt0) cc_final: 0.8743 (pm20) REVERT: C 106 PHE cc_start: 0.8318 (m-80) cc_final: 0.8094 (m-80) REVERT: C 169 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7600 (mp0) REVERT: C 329 PHE cc_start: 0.7151 (m-80) cc_final: 0.6372 (m-10) REVERT: C 1136 THR cc_start: 0.9129 (m) cc_final: 0.8895 (t) REVERT: Y 34 MET cc_start: 0.7329 (tpp) cc_final: 0.6766 (mtm) REVERT: Y 36 TRP cc_start: 0.5719 (m100) cc_final: 0.5191 (m100) REVERT: Y 62 ASP cc_start: 0.7435 (t0) cc_final: 0.7176 (p0) REVERT: Y 83 MET cc_start: 0.5580 (mtp) cc_final: 0.5176 (mpp) REVERT: Y 94 TYR cc_start: 0.5751 (m-80) cc_final: 0.5302 (m-10) REVERT: Z 34 MET cc_start: 0.4093 (mmm) cc_final: 0.3629 (pmm) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.3323 time to fit residues: 141.8971 Evaluate side-chains 174 residues out of total 2901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 209 optimal weight: 1.9990 chunk 280 optimal weight: 0.0870 chunk 80 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 263 optimal weight: 0.9980 chunk 110 optimal weight: 0.0050 chunk 270 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 overall best weight: 0.5972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 207 HIS A 913 GLN A 935 GLN A 955 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN C 81 ASN C 321 GLN C 544 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.132714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096043 restraints weight = 64135.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.095621 restraints weight = 58432.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.096197 restraints weight = 46160.122| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 27670 Z= 0.148 Angle : 0.516 10.435 37625 Z= 0.266 Chirality : 0.044 0.221 4437 Planarity : 0.004 0.113 4766 Dihedral : 4.905 36.217 4986 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.07 % Allowed : 0.24 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.15), residues: 3289 helix: 1.70 (0.21), residues: 655 sheet: 0.58 (0.17), residues: 827 loop : -0.39 (0.15), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 64 HIS 0.006 0.001 HIS A 207 PHE 0.027 0.001 PHE B 392 TYR 0.017 0.001 TYR B1067 ARG 0.014 0.000 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4915.55 seconds wall clock time: 90 minutes 35.08 seconds (5435.08 seconds total)