Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 8 17:49:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sar_40277/05_2023/8sar_40277_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sar_40277/05_2023/8sar_40277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sar_40277/05_2023/8sar_40277.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sar_40277/05_2023/8sar_40277.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sar_40277/05_2023/8sar_40277_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sar_40277/05_2023/8sar_40277_neut.pdb" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.014 sd= 0.283 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 141 5.16 5 C 12452 2.51 5 N 3335 2.21 5 O 4035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 47": "OE1" <-> "OE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "B ASP 624": "OD1" <-> "OD2" Residue "B TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 664": "OD1" <-> "OD2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 231": "OE1" <-> "OE2" Residue "F GLU 275": "OE1" <-> "OE2" Residue "F ASP 340": "OD1" <-> "OD2" Residue "F TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 482": "OE1" <-> "OE2" Residue "F GLU 492": "OE1" <-> "OE2" Residue "G GLU 584": "OE1" <-> "OE2" Residue "G GLU 647": "OE1" <-> "OE2" Residue "G ASP 664": "OD1" <-> "OD2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 115": "OD1" <-> "OD2" Residue "I TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 52": "OE1" <-> "OE2" Residue "K PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 231": "OE1" <-> "OE2" Residue "K GLU 275": "OE1" <-> "OE2" Residue "K TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 482": "OE1" <-> "OE2" Residue "K GLU 492": "OE1" <-> "OE2" Residue "L GLU 654": "OE1" <-> "OE2" Residue "L GLU 657": "OE1" <-> "OE2" Residue "M ASP 31": "OD1" <-> "OD2" Residue "M PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 115": "OD1" <-> "OD2" Residue "N TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 52": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 19963 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3607 Classifications: {'peptide': 461} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 437} Chain breaks: 1 Chain: "B" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "C" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "G" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "L" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "M" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 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 chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 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 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 chiralities: 2 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "Z" 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 chiralities: 2 Chain: "a" 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 chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.29, per 1000 atoms: 0.52 Number of scatterers: 19963 At special positions: 0 Unit cell: (157.768, 157.768, 137.514, 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 141 16.00 O 4035 8.00 N 3335 7.00 C 12452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.05 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.02 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.04 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.05 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 91 " - pdb=" SG CYS I 101 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.04 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.05 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.03 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 101 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN O 8 " - " MAN O 9 " " MAN O 10 " - " MAN O 11 " " MAN S 4 " - " MAN S 5 " " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN T 8 " - " MAN T 9 " " MAN X 4 " - " MAN X 5 " " MAN Y 4 " - " MAN Y 5 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN Y 10 " - " MAN Y 11 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA O 3 " - " MAN O 4 " " MAN O 7 " - " MAN O 8 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 10 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 7 " - " MAN Y 8 " ALPHA1-6 " BMA O 3 " - " MAN O 7 " " MAN O 7 " - " MAN O 10 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 8 " " BMA Y 3 " - " MAN Y 7 " " MAN Y 7 " - " MAN Y 10 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 601 " - " ASN A 138 " " NAG F 601 " - " ASN F 138 " " NAG J 1 " - " ASN A 301 " " NAG K 601 " - " ASN K 138 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 442 " " NAG S 1 " - " ASN F 301 " " NAG T 1 " - " ASN F 332 " " NAG U 1 " - " ASN F 156 " " NAG V 1 " - " ASN F 442 " " NAG X 1 " - " ASN K 301 " " NAG Y 1 " - " ASN K 332 " " NAG Z 1 " - " ASN K 156 " " NAG a 1 " - " ASN K 442 " Time building additional restraints: 8.71 Conformation dependent library (CDL) restraints added in 2.9 seconds 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4540 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 53 sheets defined 19.0% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.573A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.281A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 4.017A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.669A pdb=" N THR A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.689A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.571A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.588A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.831A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 663 removed outlier: 4.450A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.646A pdb=" N GLN C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.505A pdb=" N ASP D 84 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 81 through 85' Processing helix chain 'F' and resid 58 through 63 Processing helix chain 'F' and resid 68 through 73 removed outlier: 3.534A pdb=" N HIS F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 115 removed outlier: 4.222A pdb=" N ASP F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 127 removed outlier: 3.904A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL F 127 " --> pdb=" O PRO F 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 123 through 127' Processing helix chain 'F' and resid 335 through 351 Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.877A pdb=" N THR F 373 " --> pdb=" O MET F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 475 through 480 Processing helix chain 'F' and resid 481 through 484 removed outlier: 5.132A pdb=" N TYR F 484 " --> pdb=" O SER F 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 481 through 484' Processing helix chain 'G' and resid 537 through 542 Processing helix chain 'G' and resid 572 through 596 removed outlier: 3.648A pdb=" N LEU G 576 " --> pdb=" O GLY G 572 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TRP G 596 " --> pdb=" O LEU G 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 616 removed outlier: 4.319A pdb=" N SER G 615 " --> pdb=" O ASN G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 624 Processing helix chain 'G' and resid 627 through 636 removed outlier: 3.762A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 649 removed outlier: 4.024A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU G 647 " --> pdb=" O TYR G 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 653 through 663 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 58 through 63 Processing helix chain 'K' and resid 68 through 74 Processing helix chain 'K' and resid 98 through 115 removed outlier: 4.233A pdb=" N ASP K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU K 106 " --> pdb=" O ASP K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 127 removed outlier: 4.033A pdb=" N VAL K 127 " --> pdb=" O PRO K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 350 Processing helix chain 'K' and resid 368 through 373 removed outlier: 3.826A pdb=" N THR K 373 " --> pdb=" O MET K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 391 Processing helix chain 'K' and resid 475 through 480 removed outlier: 3.614A pdb=" N TRP K 479 " --> pdb=" O MET K 475 " (cutoff:3.500A) Processing helix chain 'L' and resid 537 through 542 Processing helix chain 'L' and resid 572 through 596 removed outlier: 3.576A pdb=" N LEU L 576 " --> pdb=" O GLY L 572 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TRP L 596 " --> pdb=" O LEU L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 619 through 624 Processing helix chain 'L' and resid 627 through 636 removed outlier: 3.845A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 652 removed outlier: 4.110A pdb=" N GLY L 644 " --> pdb=" O GLN L 640 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU L 647 " --> pdb=" O TYR L 643 " (cutoff:3.500A) Processing helix chain 'L' and resid 654 through 663 removed outlier: 4.300A pdb=" N LEU L 660 " --> pdb=" O ASN L 656 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.531A pdb=" N ASP N 84 " --> pdb=" O ARG N 81 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU N 85 " --> pdb=" O ALA N 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.142A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.517A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.628A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.533A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.742A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.140A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.989A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.228A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN A 332 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR A 297 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.228A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.989A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.140A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 360 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.144A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 18 through 20 Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.608A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AB7, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB9, first strand: chain 'F' and resid 494 through 499 removed outlier: 4.990A pdb=" N VAL F 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS G 604 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.756A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 75 through 76 removed outlier: 7.007A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'F' and resid 170 through 177 Processing sheet with id=AC5, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.678A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 259 through 260 removed outlier: 3.759A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 12.079A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.964A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.188A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL F 295 " --> pdb=" O ASN F 332 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN F 332 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR F 297 " --> pdb=" O HIS F 330 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS F 421 " --> pdb=" O PHE F 382 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.188A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.964A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 12.079A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 304 through 308 Processing sheet with id=AC9, first strand: chain 'F' and resid 359 through 360 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.140A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.118A pdb=" N HIS H 116 " --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AD5, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.604A pdb=" N GLY I 12 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET I 49 " --> pdb=" O TRP I 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.604A pdb=" N GLY I 12 " --> pdb=" O THR I 108 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AD8, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AD9, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.166A pdb=" N VAL K 36 " --> pdb=" O THR L 606 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS L 604 " --> pdb=" O VAL K 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 45 through 46 removed outlier: 3.525A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AE3, first strand: chain 'K' and resid 91 through 94 removed outlier: 3.517A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 170 through 177 Processing sheet with id=AE5, first strand: chain 'K' and resid 259 through 260 removed outlier: 3.744A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 12.030A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL K 295 " --> pdb=" O ASN K 332 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN K 332 " --> pdb=" O VAL K 295 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR K 297 " --> pdb=" O HIS K 330 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N HIS K 330 " --> pdb=" O THR K 297 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS K 421 " --> pdb=" O PHE K 382 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 271 through 273 removed outlier: 11.192A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 12.030A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 302 through 308 removed outlier: 5.938A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 359 through 360 Processing sheet with id=AE9, first strand: chain 'K' and resid 423 through 424 Processing sheet with id=AF1, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'M' and resid 10 through 12 removed outlier: 5.140A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 10 through 12 removed outlier: 4.106A pdb=" N HIS M 116 " --> pdb=" O THR M 98 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 18 through 20 Processing sheet with id=AF5, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.697A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET N 49 " --> pdb=" O TRP N 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 9 through 12 Processing sheet with id=AF7, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AF8, first strand: chain 'N' and resid 18 through 23 693 hydrogen bonds defined for protein. 1788 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: 7.08 Time building geometry restraints manager: 9.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6333 1.35 - 1.47: 5310 1.47 - 1.60: 8544 1.60 - 1.73: 4 1.73 - 1.86: 191 Bond restraints: 20382 Sorted by residual: bond pdb=" C1 MAN T 10 " pdb=" C2 MAN T 10 " ideal model delta sigma weight residual 1.526 1.611 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1 MAN Y 8 " pdb=" C2 MAN Y 8 " ideal model delta sigma weight residual 1.526 1.611 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1 MAN O 8 " pdb=" C2 MAN O 8 " ideal model delta sigma weight residual 1.526 1.607 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C2 MAN Y 8 " pdb=" O2 MAN Y 8 " ideal model delta sigma weight residual 1.407 1.480 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C2 MAN T 10 " pdb=" O2 MAN T 10 " ideal model delta sigma weight residual 1.407 1.480 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 20377 not shown) Histogram of bond angle deviations from ideal: 96.46 - 105.38: 413 105.38 - 114.29: 12206 114.29 - 123.21: 13659 123.21 - 132.13: 1370 132.13 - 141.05: 70 Bond angle restraints: 27718 Sorted by residual: angle pdb=" C LEU F 122 " pdb=" N THR F 123 " pdb=" CA THR F 123 " ideal model delta sigma weight residual 121.80 141.05 -19.25 2.44e+00 1.68e-01 6.22e+01 angle pdb=" N ASN G 651 " pdb=" CA ASN G 651 " pdb=" C ASN G 651 " ideal model delta sigma weight residual 112.57 103.79 8.78 1.13e+00 7.83e-01 6.03e+01 angle pdb=" C LEU K 122 " pdb=" N THR K 123 " pdb=" CA THR K 123 " ideal model delta sigma weight residual 121.80 137.14 -15.34 2.44e+00 1.68e-01 3.95e+01 angle pdb=" C LEU A 122 " pdb=" N THR A 123 " pdb=" CA THR A 123 " ideal model delta sigma weight residual 121.80 137.03 -15.23 2.44e+00 1.68e-01 3.90e+01 angle pdb=" C MET B 535 " pdb=" N THR B 536 " pdb=" CA THR B 536 " ideal model delta sigma weight residual 122.08 130.65 -8.57 1.47e+00 4.63e-01 3.40e+01 ... (remaining 27713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 10574 17.66 - 35.32: 971 35.32 - 52.99: 152 52.99 - 70.65: 30 70.65 - 88.31: 30 Dihedral angle restraints: 11757 sinusoidal: 4660 harmonic: 7097 Sorted by residual: dihedral pdb=" CB CYS F 201 " pdb=" SG CYS F 201 " pdb=" SG CYS F 433 " pdb=" CB CYS F 433 " ideal model delta sinusoidal sigma weight residual -86.00 1.14 -87.14 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CA GLY A 431 " pdb=" C GLY A 431 " pdb=" N ARG A 432 " pdb=" CA ARG A 432 " ideal model delta harmonic sigma weight residual -180.00 -144.10 -35.90 0 5.00e+00 4.00e-02 5.16e+01 dihedral pdb=" CA CYS A 433 " pdb=" C CYS A 433 " pdb=" N MET A 434 " pdb=" CA MET A 434 " ideal model delta harmonic sigma weight residual 180.00 147.13 32.87 0 5.00e+00 4.00e-02 4.32e+01 ... (remaining 11754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 3258 0.189 - 0.379: 37 0.379 - 0.568: 0 0.568 - 0.757: 0 0.757 - 0.946: 1 Chirality restraints: 3296 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 138 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.24e+01 chirality pdb=" C4 NAG K 601 " pdb=" C3 NAG K 601 " pdb=" C5 NAG K 601 " pdb=" O4 NAG K 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.21 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA THR F 123 " pdb=" N THR F 123 " pdb=" C THR F 123 " pdb=" CB THR F 123 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 3293 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K 178 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO K 179 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO K 179 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO K 179 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 424 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C ILE K 424 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE K 424 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN K 425 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 178 " -0.048 5.00e-02 4.00e+02 7.15e-02 8.18e+00 pdb=" N PRO F 179 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO F 179 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 179 " -0.040 5.00e-02 4.00e+02 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3842 2.78 - 3.31: 17582 3.31 - 3.84: 32335 3.84 - 4.37: 36117 4.37 - 4.90: 64001 Nonbonded interactions: 153877 Sorted by model distance: nonbonded pdb=" OH TYR I 48 " pdb=" O3 MAN T 5 " model vdw 2.247 2.440 nonbonded pdb=" OG1 THR H 87 " pdb=" OD1 ASP H 89 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR N 48 " pdb=" O3 MAN Y 5 " model vdw 2.265 2.440 nonbonded pdb=" OH TYR D 48 " pdb=" O3 MAN O 5 " model vdw 2.268 2.440 nonbonded pdb=" OG1 THR M 87 " pdb=" OD1 ASP M 89 " model vdw 2.269 2.440 ... (remaining 153872 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' selection = (chain 'F' and (resid 32 through 321 or resid 322 through 505 or resid 601)) selection = (chain 'K' and (resid 32 through 321 or resid 322 through 505 or resid 601)) } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'S' selection = chain 'X' } ncs_group { reference = (chain 'O' and (resid 2 or resid 5 through 11)) selection = (chain 'T' and (resid 1 or resid 4 through 10)) selection = (chain 'Y' and (resid 2 or resid 5 through 11)) } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'a' } 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: 2.830 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: 7.730 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 50.590 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.200 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 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 : 0.006 0.085 20382 Z= 0.391 Angle : 1.113 19.245 27718 Z= 0.595 Chirality : 0.064 0.946 3296 Planarity : 0.007 0.082 3453 Dihedral : 14.504 88.309 7082 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.42 % Favored : 92.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.15), residues: 2439 helix: -2.62 (0.20), residues: 400 sheet: -0.19 (0.20), residues: 665 loop : -1.89 (0.14), residues: 1374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3035 time to fit residues: 62.8268 Evaluate side-chains 104 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 2.498 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 5.9990 chunk 184 optimal weight: 0.0770 chunk 102 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 190 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 220 optimal weight: 20.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 287 HIS B 540 GLN B 652 GLN F 249 HIS G 540 GLN H 39 GLN I 40 GLN K 249 HIS L 540 GLN M 39 GLN N 40 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 20382 Z= 0.282 Angle : 0.709 11.519 27718 Z= 0.362 Chirality : 0.048 0.664 3296 Planarity : 0.005 0.063 3453 Dihedral : 6.508 64.898 2656 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.79 % Favored : 91.80 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.16), residues: 2439 helix: -1.50 (0.24), residues: 393 sheet: -0.24 (0.20), residues: 670 loop : -1.73 (0.15), residues: 1376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 123 average time/residue: 0.2958 time to fit residues: 60.2945 Evaluate side-chains 102 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 2.322 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1827 time to fit residues: 5.7542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 238 optimal weight: 30.0000 chunk 196 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 177 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS B 652 GLN C 113 ASN D 32 HIS F 249 HIS F 422 GLN H 116 HIS I 32 HIS K 249 HIS K 422 GLN M 116 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 20382 Z= 0.310 Angle : 0.721 11.899 27718 Z= 0.366 Chirality : 0.049 0.605 3296 Planarity : 0.005 0.066 3453 Dihedral : 6.535 70.490 2656 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.80 % Favored : 89.83 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.86 (0.16), residues: 2439 helix: -1.01 (0.26), residues: 393 sheet: -0.37 (0.20), residues: 688 loop : -1.80 (0.15), residues: 1358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 107 time to evaluate : 3.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 19 residues processed: 139 average time/residue: 0.2835 time to fit residues: 66.6552 Evaluate side-chains 114 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 2.454 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1896 time to fit residues: 9.8520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 221 optimal weight: 8.9990 chunk 234 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 210 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN ** L 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 20382 Z= 0.337 Angle : 0.743 11.299 27718 Z= 0.374 Chirality : 0.049 0.623 3296 Planarity : 0.005 0.064 3453 Dihedral : 6.690 74.598 2656 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.41 % Favored : 89.26 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.98 (0.16), residues: 2439 helix: -0.97 (0.26), residues: 393 sheet: -0.56 (0.20), residues: 669 loop : -1.85 (0.15), residues: 1377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 94 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 37 residues processed: 159 average time/residue: 0.2715 time to fit residues: 73.4354 Evaluate side-chains 127 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 90 time to evaluate : 2.458 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1847 time to fit residues: 16.3776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 200 optimal weight: 0.2980 chunk 162 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 0.6980 chunk 210 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 HIS H 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 20382 Z= 0.191 Angle : 0.634 11.421 27718 Z= 0.316 Chirality : 0.046 0.531 3296 Planarity : 0.004 0.056 3453 Dihedral : 6.174 72.129 2656 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.45 % Favored : 91.23 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.16), residues: 2439 helix: -0.67 (0.26), residues: 393 sheet: -0.39 (0.20), residues: 681 loop : -1.72 (0.16), residues: 1365 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 113 average time/residue: 0.2865 time to fit residues: 54.1228 Evaluate side-chains 99 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 2.399 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2249 time to fit residues: 7.0371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 195 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 77 optimal weight: 40.0000 chunk 123 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 637 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 HIS G 637 ASN K 105 HIS L 637 ASN ** L 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 20382 Z= 0.421 Angle : 0.806 11.370 27718 Z= 0.403 Chirality : 0.052 0.672 3296 Planarity : 0.005 0.069 3453 Dihedral : 6.875 75.767 2656 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.10 % Favored : 87.58 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.16), residues: 2439 helix: -1.04 (0.25), residues: 392 sheet: -0.74 (0.20), residues: 657 loop : -2.01 (0.15), residues: 1390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 90 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 19 residues processed: 126 average time/residue: 0.2970 time to fit residues: 62.6153 Evaluate side-chains 107 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 2.416 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1820 time to fit residues: 9.7700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 133 optimal weight: 0.3980 chunk 171 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 234 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 20382 Z= 0.221 Angle : 0.663 11.321 27718 Z= 0.330 Chirality : 0.047 0.545 3296 Planarity : 0.004 0.058 3453 Dihedral : 6.358 73.108 2656 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.43 % Favored : 90.28 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.16), residues: 2439 helix: -0.81 (0.26), residues: 405 sheet: -0.54 (0.20), residues: 680 loop : -1.87 (0.16), residues: 1354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 113 average time/residue: 0.2872 time to fit residues: 54.5673 Evaluate side-chains 100 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1929 time to fit residues: 6.3965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 70 optimal weight: 0.3980 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 184 optimal weight: 0.3980 chunk 213 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 20382 Z= 0.170 Angle : 0.616 11.456 27718 Z= 0.306 Chirality : 0.046 0.520 3296 Planarity : 0.004 0.053 3453 Dihedral : 5.891 69.975 2656 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.31 % Favored : 90.45 % Rotamer Outliers : 0.61 % 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: -1.72 (0.17), residues: 2439 helix: -0.54 (0.26), residues: 405 sheet: -0.38 (0.20), residues: 677 loop : -1.76 (0.16), residues: 1357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 110 average time/residue: 0.3129 time to fit residues: 56.7383 Evaluate side-chains 99 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 2.341 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1781 time to fit residues: 5.1822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 0.0070 chunk 204 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 171 optimal weight: 0.2980 chunk 66 optimal weight: 9.9990 chunk 197 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 overall best weight: 3.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 20382 Z= 0.221 Angle : 0.640 11.506 27718 Z= 0.318 Chirality : 0.046 0.556 3296 Planarity : 0.004 0.056 3453 Dihedral : 5.970 71.311 2656 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.23 % Favored : 90.53 % Rotamer Outliers : 0.33 % 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: -1.70 (0.17), residues: 2439 helix: -0.50 (0.26), residues: 405 sheet: -0.42 (0.20), residues: 690 loop : -1.74 (0.16), residues: 1344 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 104 average time/residue: 0.2933 time to fit residues: 51.0886 Evaluate side-chains 96 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 2.309 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1722 time to fit residues: 3.7562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 10.0000 chunk 140 optimal weight: 0.0050 chunk 109 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 242 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 118 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 overall best weight: 5.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 20382 Z= 0.291 Angle : 0.705 11.668 27718 Z= 0.348 Chirality : 0.048 0.595 3296 Planarity : 0.004 0.059 3453 Dihedral : 6.315 74.683 2656 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.15 % Favored : 88.60 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.97 (0.16), residues: 2439 helix: -0.76 (0.26), residues: 417 sheet: -0.58 (0.21), residues: 667 loop : -1.91 (0.15), residues: 1355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 2.560 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 98 average time/residue: 0.3097 time to fit residues: 50.9524 Evaluate side-chains 93 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 2.163 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1853 time to fit residues: 3.5144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 193 optimal weight: 0.0980 chunk 80 optimal weight: 20.0000 chunk 198 optimal weight: 0.8980 chunk 24 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 169 optimal weight: 3.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.073522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.063402 restraints weight = 93006.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.064738 restraints weight = 57009.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.065623 restraints weight = 41399.560| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 20382 Z= 0.206 Angle : 0.638 11.336 27718 Z= 0.315 Chirality : 0.046 0.536 3296 Planarity : 0.004 0.055 3453 Dihedral : 6.021 72.960 2656 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.27 % Favored : 90.49 % Rotamer Outliers : 0.14 % 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: -1.80 (0.16), residues: 2439 helix: -0.61 (0.26), residues: 417 sheet: -0.37 (0.21), residues: 672 loop : -1.87 (0.16), residues: 1350 =============================================================================== Job complete usr+sys time: 2598.68 seconds wall clock time: 50 minutes 17.10 seconds (3017.10 seconds total)