Starting phenix.real_space_refine on Mon Feb 19 15:32:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dow_27624/02_2024/8dow_27624.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dow_27624/02_2024/8dow_27624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dow_27624/02_2024/8dow_27624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dow_27624/02_2024/8dow_27624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dow_27624/02_2024/8dow_27624.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dow_27624/02_2024/8dow_27624.pdb" } resolution = 3.69 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= 0.003 sd= 0.136 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 15658 2.51 5 N 4220 2.21 5 O 5037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25053 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3613 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "C" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1725 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 212} Chain: "D" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1676 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 202} Chain: "E" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3613 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "F" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "G" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1725 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 212} Chain: "H" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1676 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 202} Chain: "I" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3613 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "J" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "K" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1725 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 212} Chain: "L" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1676 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 202} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" 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: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 13.24, per 1000 atoms: 0.53 Number of scatterers: 25053 At special positions: 0 Unit cell: (184.68, 195.48, 158.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 5037 8.00 N 4220 7.00 C 15658 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.02 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 155 " 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=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 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 C 152 " - pdb=" SG CYS C 208 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 93 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 199 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.04 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 208 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 199 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 155 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.05 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.02 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.04 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 208 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 6 " " MAN N 4 " - " MAN N 5 " " BMA S 3 " - " MAN S 6 " " MAN S 4 " - " MAN S 5 " " BMA W 3 " - " MAN W 6 " " MAN W 4 " - " MAN W 5 " ALPHA1-6 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA a 3 " - " MAN a 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " NAG-ASN " NAG A 601 " - " ASN A 154 " " NAG A 602 " - " ASN A 386 " " NAG A 603 " - " ASN A 197 " " NAG A 604 " - " ASN A 355 " " NAG A 605 " - " ASN A 448 " " NAG A 606 " - " ASN A 234 " " NAG E 601 " - " ASN E 386 " " NAG E 602 " - " ASN E 197 " " NAG E 603 " - " ASN E 355 " " NAG E 604 " - " ASN E 448 " " NAG E 605 " - " ASN E 154 " " NAG E 606 " - " ASN E 234 " " NAG I 601 " - " ASN I 355 " " NAG I 602 " - " ASN I 154 " " NAG I 603 " - " ASN I 448 " " NAG I 604 " - " ASN I 386 " " NAG I 605 " - " ASN I 197 " " NAG I 606 " - " ASN I 234 " " NAG M 1 " - " ASN A 442 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 362 " " NAG Q 1 " - " ASN A 301 " " NAG R 1 " - " ASN E 442 " " NAG S 1 " - " ASN E 332 " " NAG T 1 " - " ASN E 362 " " NAG U 1 " - " ASN E 301 " " NAG V 1 " - " ASN E 262 " " NAG W 1 " - " ASN I 332 " " NAG X 1 " - " ASN I 442 " " NAG Y 1 " - " ASN I 392 " " NAG Z 1 " - " ASN I 362 " " NAG a 1 " - " ASN I 262 " " NAG b 1 " - " ASN I 301 " Time building additional restraints: 13.09 Conformation dependent library (CDL) restraints added in 4.7 seconds 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5760 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 57 sheets defined 20.4% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.619A pdb=" N VAL A 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS A 66 " --> pdb=" O LYS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.642A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.694A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HIS A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.944A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.173A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 597 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.696A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.643A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.934A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 139 through 145 removed outlier: 4.005A pdb=" N GLU C 145 " --> pdb=" O SER C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 126 through 132 Processing helix chain 'D' and resid 188 through 193 Processing helix chain 'E' and resid 62 through 67 removed outlier: 3.676A pdb=" N VAL E 65 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS E 66 " --> pdb=" O LYS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.344A pdb=" N ASP E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 138 through 151 Processing helix chain 'E' and resid 335 through 353 removed outlier: 4.008A pdb=" N HIS E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 372 Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 474 through 484 removed outlier: 4.047A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.684A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.017A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 597 removed outlier: 3.533A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.520A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.773A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 664 removed outlier: 3.756A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 139 through 145 removed outlier: 4.043A pdb=" N GLU G 145 " --> pdb=" O SER G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 170 No H-bonds generated for 'chain 'G' and resid 168 through 170' Processing helix chain 'H' and resid 84 through 88 Processing helix chain 'H' and resid 126 through 132 Processing helix chain 'H' and resid 188 through 193 Processing helix chain 'I' and resid 63 through 68 removed outlier: 3.752A pdb=" N ASN I 67 " --> pdb=" O LYS I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.407A pdb=" N ASP I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 138 through 151 Processing helix chain 'I' and resid 335 through 351 removed outlier: 3.511A pdb=" N LYS I 351 " --> pdb=" O ILE I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 377 through 381 Processing helix chain 'I' and resid 425 through 429 Processing helix chain 'I' and resid 474 through 484 removed outlier: 4.360A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 537 through 542 Processing helix chain 'J' and resid 570 through 597 Processing helix chain 'J' and resid 611 through 615 Processing helix chain 'J' and resid 618 through 625 removed outlier: 3.546A pdb=" N ILE J 622 " --> pdb=" O ASN J 618 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 636 removed outlier: 4.066A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 662 removed outlier: 3.924A pdb=" N ILE J 642 " --> pdb=" O TYR J 638 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 74 through 76 No H-bonds generated for 'chain 'K' and resid 74 through 76' Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'K' and resid 139 through 145 removed outlier: 3.605A pdb=" N GLU K 145 " --> pdb=" O SER K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 170 No H-bonds generated for 'chain 'K' and resid 168 through 170' Processing helix chain 'K' and resid 197 through 201 Processing helix chain 'L' and resid 84 through 88 Processing helix chain 'L' and resid 126 through 131 Processing helix chain 'L' and resid 188 through 193 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 removed outlier: 5.264A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.059A pdb=" N LEU A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.576A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.618A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AA8, first strand: chain 'A' and resid 316 through 323 removed outlier: 6.819A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN A 417 " --> pdb=" O ASN A 386 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 316 through 323 removed outlier: 6.819A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.996A pdb=" N TYR C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET C 34 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.119A pdb=" N TYR C 188 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.119A pdb=" N TYR C 188 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 163 through 166 Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.907A pdb=" N LEU D 38 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TYR D 54 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP D 40 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AB9, first strand: chain 'D' and resid 119 through 123 removed outlier: 3.890A pdb=" N VAL D 138 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TYR D 178 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 158 through 159 Processing sheet with id=AC2, first strand: chain 'E' and resid 495 through 498 removed outlier: 5.380A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.115A pdb=" N LEU E 84 " --> pdb=" O THR E 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC5, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.782A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 167 through 175 Processing sheet with id=AC7, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.576A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.667A pdb=" N GLU E 466 " --> pdb=" O THR E 357 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 316 through 323 removed outlier: 5.318A pdb=" N TYR E 318 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASN E 300 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE E 443 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 373 through 375 removed outlier: 4.769A pdb=" N GLN E 417 " --> pdb=" O ASN E 386 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.967A pdb=" N TYR G 33 " --> pdb=" O ASP G 99 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 132 through 136 removed outlier: 6.129A pdb=" N TYR G 188 " --> pdb=" O ASP G 156 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 132 through 136 removed outlier: 6.129A pdb=" N TYR G 188 " --> pdb=" O ASP G 156 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 162 through 166 removed outlier: 4.412A pdb=" N TYR G 206 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.835A pdb=" N LEU H 38 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR H 54 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP H 40 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AD9, first strand: chain 'H' and resid 19 through 24 Processing sheet with id=AE1, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.779A pdb=" N VAL H 138 " --> pdb=" O PHE H 123 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N TYR H 178 " --> pdb=" O ASN H 143 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN H 165 " --> pdb=" O THR H 183 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 158 through 159 Processing sheet with id=AE3, first strand: chain 'I' and resid 495 through 498 removed outlier: 5.292A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 45 through 47 removed outlier: 4.072A pdb=" N LEU I 84 " --> pdb=" O THR I 244 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AE6, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.565A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE I 93 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY I 237 " --> pdb=" O PHE I 93 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 167 through 175 Processing sheet with id=AE8, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.583A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 271 through 273 removed outlier: 7.060A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 316 through 323 removed outlier: 6.827A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 11.311A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 10.678A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.959A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.001A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 11.809A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU I 466 " --> pdb=" O THR I 357 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'K' and resid 11 through 12 removed outlier: 5.056A pdb=" N TYR K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 132 through 136 removed outlier: 6.147A pdb=" N TYR K 188 " --> pdb=" O ASP K 156 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 132 through 136 removed outlier: 6.147A pdb=" N TYR K 188 " --> pdb=" O ASP K 156 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 162 through 166 Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.046A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU L 38 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR L 54 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.046A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AG1, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AG2, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.968A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 158 through 159 1002 hydrogen bonds defined for protein. 2574 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.89 Time building geometry restraints manager: 12.90 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: 5937 1.33 - 1.45: 5234 1.45 - 1.57: 14236 1.57 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 25587 Sorted by residual: bond pdb=" C5 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C3 BMA W 3 " pdb=" O3 BMA W 3 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C5 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C3 BMA N 3 " pdb=" O3 BMA N 3 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C5 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 25582 not shown) Histogram of bond angle deviations from ideal: 97.54 - 105.04: 543 105.04 - 112.53: 11938 112.53 - 120.03: 11168 120.03 - 127.52: 10813 127.52 - 135.02: 349 Bond angle restraints: 34811 Sorted by residual: angle pdb=" N THR E 450 " pdb=" CA THR E 450 " pdb=" C THR E 450 " ideal model delta sigma weight residual 110.80 127.49 -16.69 2.13e+00 2.20e-01 6.14e+01 angle pdb=" N ARG A 446 " pdb=" CA ARG A 446 " pdb=" C ARG A 446 " ideal model delta sigma weight residual 109.72 122.22 -12.50 1.60e+00 3.91e-01 6.10e+01 angle pdb=" CA PHE F 519 " pdb=" CB PHE F 519 " pdb=" CG PHE F 519 " ideal model delta sigma weight residual 113.80 121.48 -7.68 1.00e+00 1.00e+00 5.90e+01 angle pdb=" N THR I 450 " pdb=" CA THR I 450 " pdb=" C THR I 450 " ideal model delta sigma weight residual 110.80 127.04 -16.24 2.13e+00 2.20e-01 5.81e+01 angle pdb=" CA PHE B 519 " pdb=" CB PHE B 519 " pdb=" CG PHE B 519 " ideal model delta sigma weight residual 113.80 121.32 -7.52 1.00e+00 1.00e+00 5.66e+01 ... (remaining 34806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.31: 15281 22.31 - 44.63: 769 44.63 - 66.94: 114 66.94 - 89.25: 75 89.25 - 111.57: 25 Dihedral angle restraints: 16264 sinusoidal: 7285 harmonic: 8979 Sorted by residual: dihedral pdb=" C ARG A 446 " pdb=" N ARG A 446 " pdb=" CA ARG A 446 " pdb=" CB ARG A 446 " ideal model delta harmonic sigma weight residual -122.60 -149.65 27.05 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" N ARG A 446 " pdb=" C ARG A 446 " pdb=" CA ARG A 446 " pdb=" CB ARG A 446 " ideal model delta harmonic sigma weight residual 122.80 148.98 -26.18 0 2.50e+00 1.60e-01 1.10e+02 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 170.00 -77.00 1 1.00e+01 1.00e-02 7.44e+01 ... (remaining 16261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.277: 4047 0.277 - 0.554: 52 0.554 - 0.831: 4 0.831 - 1.109: 6 1.109 - 1.386: 10 Chirality restraints: 4119 Sorted by residual: chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.01 -1.39 2.00e-02 2.50e+03 4.80e+03 chirality pdb=" C1 BMA V 3 " pdb=" O4 NAG V 2 " pdb=" C2 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.03 -1.37 2.00e-02 2.50e+03 4.72e+03 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.03 -1.37 2.00e-02 2.50e+03 4.72e+03 ... (remaining 4116 not shown) Planarity restraints: 4410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 623 " -0.268 2.00e-02 2.50e+03 1.36e-01 4.61e+02 pdb=" CG TRP F 623 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP F 623 " 0.087 2.00e-02 2.50e+03 pdb=" CD2 TRP F 623 " 0.127 2.00e-02 2.50e+03 pdb=" NE1 TRP F 623 " 0.076 2.00e-02 2.50e+03 pdb=" CE2 TRP F 623 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 623 " 0.177 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 623 " -0.169 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 623 " 0.060 2.00e-02 2.50e+03 pdb=" CH2 TRP F 623 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 623 " -0.234 2.00e-02 2.50e+03 1.19e-01 3.56e+02 pdb=" CG TRP J 623 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP J 623 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP J 623 " 0.118 2.00e-02 2.50e+03 pdb=" NE1 TRP J 623 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 TRP J 623 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP J 623 " 0.160 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 623 " -0.137 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 623 " 0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP J 623 " -0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 623 " 0.231 2.00e-02 2.50e+03 1.18e-01 3.47e+02 pdb=" CG TRP B 623 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 623 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 TRP B 623 " -0.111 2.00e-02 2.50e+03 pdb=" NE1 TRP B 623 " -0.067 2.00e-02 2.50e+03 pdb=" CE2 TRP B 623 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 623 " -0.163 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 623 " 0.135 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 623 " -0.047 2.00e-02 2.50e+03 pdb=" CH2 TRP B 623 " 0.126 2.00e-02 2.50e+03 ... (remaining 4407 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 12276 2.98 - 3.46: 24784 3.46 - 3.94: 41683 3.94 - 4.42: 45741 4.42 - 4.90: 76933 Nonbonded interactions: 201417 Sorted by model distance: nonbonded pdb=" O2 MAN N 4 " pdb=" O3 MAN N 4 " model vdw 2.498 2.432 nonbonded pdb=" OD1 ASP D 175 " pdb=" OG1 THR D 177 " model vdw 2.526 2.440 nonbonded pdb=" OD1 ASP H 175 " pdb=" OG1 THR H 177 " model vdw 2.547 2.440 nonbonded pdb=" OG SER H 10 " pdb=" OE2 GLU H 110 " model vdw 2.548 2.440 nonbonded pdb=" OD2 ASP K 113 " pdb=" O4 MAN W 5 " model vdw 2.550 2.440 ... (remaining 201412 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 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'O' selection = chain 'V' 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: 4.370 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: 0.030 Extract box with map and model: 8.840 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 80.660 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 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 : 0.014 0.078 25587 Z= 0.893 Angle : 1.915 16.694 34811 Z= 1.237 Chirality : 0.131 1.386 4119 Planarity : 0.016 0.151 4376 Dihedral : 15.275 111.568 10360 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 1.33 % Allowed : 7.63 % Favored : 91.03 % Rotamer: Outliers : 1.03 % Allowed : 3.94 % Favored : 95.03 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.25 (0.15), residues: 3078 helix: -1.83 (0.19), residues: 435 sheet: -0.39 (0.18), residues: 813 loop : -0.73 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.268 0.029 TRP F 623 HIS 0.036 0.006 HIS C 111 PHE 0.114 0.018 PHE K 27 TYR 0.152 0.022 TYR E 400 ARG 0.011 0.002 ARG G 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8470 (mtp) cc_final: 0.8110 (mtp) REVERT: C 213 LYS cc_start: 0.9524 (mmtt) cc_final: 0.9232 (mmtm) REVERT: C 218 LYS cc_start: 0.9113 (pttt) cc_final: 0.8667 (tttp) REVERT: E 66 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.6638 (p-80) REVERT: E 151 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: F 530 MET cc_start: 0.8571 (mtp) cc_final: 0.8240 (mtp) REVERT: G 213 LYS cc_start: 0.9364 (mmtt) cc_final: 0.8977 (mmtm) REVERT: J 530 MET cc_start: 0.8294 (mtp) cc_final: 0.8036 (mtp) REVERT: K 218 LYS cc_start: 0.9104 (pttt) cc_final: 0.8766 (tttp) outliers start: 28 outliers final: 4 residues processed: 116 average time/residue: 0.4993 time to fit residues: 85.6720 Evaluate side-chains 63 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 504 ARG Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain I residue 149 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 7.9990 chunk 231 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 79 optimal weight: 50.0000 chunk 156 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 145 optimal weight: 4.9990 chunk 178 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN D 176 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 25587 Z= 0.381 Angle : 0.852 11.791 34811 Z= 0.435 Chirality : 0.051 0.295 4119 Planarity : 0.005 0.053 4376 Dihedral : 11.553 77.364 4783 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.59 % Favored : 93.99 % Rotamer: Outliers : 0.81 % Allowed : 6.30 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.75 (0.15), residues: 3078 helix: -0.20 (0.23), residues: 489 sheet: -0.28 (0.17), residues: 918 loop : -0.63 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP I 112 HIS 0.009 0.002 HIS I 330 PHE 0.021 0.002 PHE E 376 TYR 0.020 0.002 TYR I 61 ARG 0.005 0.001 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 61 time to evaluate : 3.125 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: C 213 LYS cc_start: 0.9556 (mmtt) cc_final: 0.9267 (mmtm) REVERT: E 151 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7616 (mm-30) REVERT: E 417 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8170 (mp10) REVERT: F 530 MET cc_start: 0.8436 (mtp) cc_final: 0.7961 (mtp) REVERT: G 213 LYS cc_start: 0.9439 (mmtt) cc_final: 0.9082 (mmtm) REVERT: G 218 LYS cc_start: 0.9044 (pttt) cc_final: 0.8731 (tttp) outliers start: 22 outliers final: 7 residues processed: 81 average time/residue: 0.4147 time to fit residues: 54.8735 Evaluate side-chains 66 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain K residue 89 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 chunk 76 optimal weight: 40.0000 chunk 278 optimal weight: 40.0000 chunk 300 optimal weight: 30.0000 chunk 247 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 223 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN E 404 ASN I 315 GLN K 176 HIS L 96 ASN L 142 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 25587 Z= 0.402 Angle : 0.785 11.821 34811 Z= 0.397 Chirality : 0.049 0.254 4119 Planarity : 0.005 0.058 4376 Dihedral : 9.793 67.977 4775 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.95 % Favored : 92.66 % Rotamer: Outliers : 1.55 % Allowed : 7.88 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.76 (0.15), residues: 3078 helix: 0.36 (0.24), residues: 483 sheet: -0.51 (0.16), residues: 984 loop : -0.68 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP I 112 HIS 0.009 0.002 HIS I 330 PHE 0.025 0.002 PHE A 376 TYR 0.024 0.002 TYR E 61 ARG 0.006 0.001 ARG I 419 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 60 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 LYS cc_start: 0.9566 (mmtt) cc_final: 0.9231 (mppt) REVERT: E 135 THR cc_start: 0.3569 (OUTLIER) cc_final: 0.3282 (p) REVERT: E 417 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8180 (mp10) REVERT: F 530 MET cc_start: 0.8471 (mtp) cc_final: 0.7892 (mtp) REVERT: G 213 LYS cc_start: 0.9427 (mmtt) cc_final: 0.9060 (mmtm) REVERT: G 218 LYS cc_start: 0.9094 (pttt) cc_final: 0.8681 (tttp) REVERT: I 467 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.7936 (p) REVERT: K 218 LYS cc_start: 0.9092 (pttt) cc_final: 0.8666 (tptt) outliers start: 42 outliers final: 17 residues processed: 96 average time/residue: 0.3716 time to fit residues: 58.8657 Evaluate side-chains 76 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 56 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain L residue 195 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 20.0000 chunk 209 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 279 optimal weight: 30.0000 chunk 295 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 264 optimal weight: 7.9990 chunk 79 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 ASN H 195 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 142 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25587 Z= 0.330 Angle : 0.708 10.666 34811 Z= 0.357 Chirality : 0.047 0.246 4119 Planarity : 0.004 0.058 4376 Dihedral : 8.900 72.056 4775 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.01 % Favored : 93.66 % Rotamer: Outliers : 1.33 % Allowed : 9.06 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.64 (0.16), residues: 3078 helix: 0.87 (0.25), residues: 465 sheet: -0.58 (0.16), residues: 1011 loop : -0.61 (0.17), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 112 HIS 0.007 0.002 HIS I 374 PHE 0.022 0.002 PHE E 376 TYR 0.022 0.002 TYR A 61 ARG 0.003 0.000 ARG L 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 56 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 LYS cc_start: 0.9560 (mmtt) cc_final: 0.9213 (mppt) REVERT: E 135 THR cc_start: 0.3680 (OUTLIER) cc_final: 0.3436 (p) REVERT: E 417 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8204 (mp10) REVERT: F 530 MET cc_start: 0.8473 (mtp) cc_final: 0.7980 (mtp) REVERT: G 34 MET cc_start: 0.9181 (mmm) cc_final: 0.8817 (mmm) REVERT: G 213 LYS cc_start: 0.9478 (mmtt) cc_final: 0.9072 (mmtm) REVERT: G 218 LYS cc_start: 0.9109 (pttt) cc_final: 0.8700 (tttp) REVERT: I 213 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8880 (tp) REVERT: J 614 TRP cc_start: 0.6504 (OUTLIER) cc_final: 0.5943 (m-10) REVERT: K 218 LYS cc_start: 0.9070 (pttt) cc_final: 0.8646 (tptt) REVERT: L 108 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8595 (mtpp) outliers start: 36 outliers final: 18 residues processed: 90 average time/residue: 0.3774 time to fit residues: 57.2311 Evaluate side-chains 79 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 56 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 614 TRP Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain L residue 108 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.4980 chunk 167 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 252 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 350 GLN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25587 Z= 0.295 Angle : 0.670 10.373 34811 Z= 0.339 Chirality : 0.045 0.211 4119 Planarity : 0.004 0.059 4376 Dihedral : 8.691 75.631 4775 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.37 % Favored : 93.34 % Rotamer: Outliers : 1.51 % Allowed : 9.61 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.59 (0.16), residues: 3078 helix: 1.03 (0.25), residues: 465 sheet: -0.59 (0.16), residues: 999 loop : -0.59 (0.17), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 112 HIS 0.006 0.001 HIS E 374 PHE 0.021 0.002 PHE E 376 TYR 0.022 0.002 TYR E 61 ARG 0.003 0.000 ARG I 480 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 56 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 LYS cc_start: 0.9563 (mmtt) cc_final: 0.9198 (mppt) REVERT: E 135 THR cc_start: 0.3950 (OUTLIER) cc_final: 0.3743 (p) REVERT: E 417 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8164 (mp10) REVERT: F 530 MET cc_start: 0.8465 (mtp) cc_final: 0.7995 (mtp) REVERT: G 213 LYS cc_start: 0.9474 (mmtt) cc_final: 0.9085 (mmtm) REVERT: G 218 LYS cc_start: 0.9116 (pttt) cc_final: 0.8716 (tttp) REVERT: I 213 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8882 (tp) REVERT: J 614 TRP cc_start: 0.6483 (OUTLIER) cc_final: 0.5957 (m-10) REVERT: K 218 LYS cc_start: 0.9107 (pttt) cc_final: 0.8659 (tptt) REVERT: L 108 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8508 (mtpp) outliers start: 41 outliers final: 28 residues processed: 96 average time/residue: 0.3489 time to fit residues: 56.5056 Evaluate side-chains 88 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 55 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 614 TRP Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 106 TRP Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 195 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 8.9990 chunk 266 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 296 optimal weight: 40.0000 chunk 245 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 155 optimal weight: 0.0770 overall best weight: 5.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 651 ASN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 25587 Z= 0.372 Angle : 0.706 10.342 34811 Z= 0.355 Chirality : 0.046 0.210 4119 Planarity : 0.004 0.052 4376 Dihedral : 8.693 80.908 4775 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.47 % Favored : 93.24 % Rotamer: Outliers : 1.66 % Allowed : 10.64 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.68 (0.16), residues: 3078 helix: 0.89 (0.25), residues: 468 sheet: -0.66 (0.16), residues: 1008 loop : -0.62 (0.17), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 112 HIS 0.007 0.002 HIS I 330 PHE 0.023 0.002 PHE E 376 TYR 0.024 0.002 TYR E 61 ARG 0.004 0.000 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 54 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 LYS cc_start: 0.9564 (mmtt) cc_final: 0.9185 (mppt) REVERT: E 135 THR cc_start: 0.3621 (OUTLIER) cc_final: 0.3388 (p) REVERT: E 417 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8255 (mp10) REVERT: F 530 MET cc_start: 0.8496 (mtp) cc_final: 0.8054 (mtp) REVERT: I 213 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8947 (tp) REVERT: I 467 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.7822 (p) REVERT: K 218 LYS cc_start: 0.9107 (pttt) cc_final: 0.8661 (tptt) outliers start: 45 outliers final: 26 residues processed: 96 average time/residue: 0.3578 time to fit residues: 58.4299 Evaluate side-chains 84 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 54 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 106 TRP Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain L residue 108 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 216 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 294 optimal weight: 5.9990 chunk 184 optimal weight: 30.0000 chunk 179 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 463 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25587 Z= 0.320 Angle : 0.668 9.239 34811 Z= 0.337 Chirality : 0.045 0.210 4119 Planarity : 0.004 0.055 4376 Dihedral : 8.393 57.378 4772 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.34 % Favored : 93.34 % Rotamer: Outliers : 1.55 % Allowed : 11.16 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.64 (0.16), residues: 3078 helix: 0.99 (0.26), residues: 468 sheet: -0.65 (0.16), residues: 1035 loop : -0.60 (0.17), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 112 HIS 0.007 0.001 HIS I 374 PHE 0.022 0.002 PHE E 376 TYR 0.021 0.002 TYR E 61 ARG 0.003 0.000 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 55 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 LYS cc_start: 0.9568 (mmtt) cc_final: 0.9178 (mppt) REVERT: C 218 LYS cc_start: 0.9033 (pttt) cc_final: 0.8547 (tptt) REVERT: E 417 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8267 (mp10) REVERT: F 530 MET cc_start: 0.8490 (mtp) cc_final: 0.8048 (mtp) REVERT: I 104 MET cc_start: 0.8897 (ttt) cc_final: 0.8531 (ttp) REVERT: I 213 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8984 (tp) REVERT: I 467 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.7951 (p) REVERT: K 218 LYS cc_start: 0.9111 (pttt) cc_final: 0.8669 (tptt) outliers start: 42 outliers final: 29 residues processed: 95 average time/residue: 0.3465 time to fit residues: 56.0640 Evaluate side-chains 85 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 53 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 106 TRP Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 195 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 145 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 231 optimal weight: 0.8980 chunk 268 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25587 Z= 0.242 Angle : 0.625 9.422 34811 Z= 0.316 Chirality : 0.044 0.210 4119 Planarity : 0.004 0.045 4376 Dihedral : 8.117 57.653 4772 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.17 % Favored : 93.50 % Rotamer: Outliers : 1.29 % Allowed : 11.79 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.59 (0.16), residues: 3078 helix: 1.14 (0.26), residues: 468 sheet: -0.59 (0.15), residues: 1095 loop : -0.62 (0.17), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 112 HIS 0.006 0.001 HIS I 374 PHE 0.019 0.002 PHE E 376 TYR 0.020 0.001 TYR E 61 ARG 0.002 0.000 ARG J 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 53 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 LYS cc_start: 0.9562 (mmtt) cc_final: 0.9155 (mppt) REVERT: C 218 LYS cc_start: 0.9023 (pttt) cc_final: 0.8538 (tptt) REVERT: E 417 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8197 (mp10) REVERT: F 530 MET cc_start: 0.8474 (mtp) cc_final: 0.8056 (mtp) REVERT: G 218 LYS cc_start: 0.9099 (pttt) cc_final: 0.8594 (tptt) REVERT: I 95 MET cc_start: 0.8008 (ttp) cc_final: 0.7388 (ttm) REVERT: I 213 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8909 (tp) REVERT: I 467 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7953 (p) REVERT: K 218 LYS cc_start: 0.9098 (pttt) cc_final: 0.8656 (tptt) REVERT: L 108 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8358 (mmmm) outliers start: 35 outliers final: 25 residues processed: 86 average time/residue: 0.3507 time to fit residues: 51.3182 Evaluate side-chains 82 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 53 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 108 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 20.0000 chunk 257 optimal weight: 0.4980 chunk 274 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 248 optimal weight: 0.7980 chunk 259 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 404 ASN J 540 GLN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25587 Z= 0.164 Angle : 0.586 9.271 34811 Z= 0.296 Chirality : 0.043 0.202 4119 Planarity : 0.004 0.048 4376 Dihedral : 7.768 58.847 4772 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.88 % Favored : 93.79 % Rotamer: Outliers : 1.07 % Allowed : 12.04 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.42 (0.16), residues: 3078 helix: 1.39 (0.26), residues: 468 sheet: -0.48 (0.16), residues: 1095 loop : -0.55 (0.17), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 112 HIS 0.005 0.001 HIS I 374 PHE 0.017 0.001 PHE A 376 TYR 0.018 0.001 TYR E 61 ARG 0.005 0.000 ARG I 476 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 54 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 LYS cc_start: 0.9557 (mmtt) cc_final: 0.9147 (mppt) REVERT: C 218 LYS cc_start: 0.9016 (pttt) cc_final: 0.8560 (tptt) REVERT: E 417 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8151 (mp10) REVERT: F 530 MET cc_start: 0.8483 (mtp) cc_final: 0.8047 (mtp) REVERT: G 218 LYS cc_start: 0.9097 (pttt) cc_final: 0.8604 (tptt) REVERT: I 95 MET cc_start: 0.7997 (ttp) cc_final: 0.7396 (ttm) REVERT: I 213 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8932 (tp) REVERT: I 467 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7928 (p) REVERT: K 34 MET cc_start: 0.9035 (mmm) cc_final: 0.8777 (mmm) REVERT: K 218 LYS cc_start: 0.9127 (pttt) cc_final: 0.8634 (tptt) REVERT: L 108 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8381 (mmmm) outliers start: 29 outliers final: 23 residues processed: 82 average time/residue: 0.3677 time to fit residues: 51.0461 Evaluate side-chains 81 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 54 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 540 GLN Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain L residue 108 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.6980 chunk 177 optimal weight: 0.4980 chunk 137 optimal weight: 0.6980 chunk 202 optimal weight: 30.0000 chunk 304 optimal weight: 30.0000 chunk 280 optimal weight: 8.9990 chunk 242 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 540 GLN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25587 Z= 0.194 Angle : 0.586 9.388 34811 Z= 0.296 Chirality : 0.043 0.206 4119 Planarity : 0.004 0.044 4376 Dihedral : 7.707 59.013 4772 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.62 % Favored : 94.05 % Rotamer: Outliers : 1.10 % Allowed : 11.93 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.39 (0.16), residues: 3078 helix: 1.43 (0.26), residues: 468 sheet: -0.47 (0.16), residues: 1101 loop : -0.53 (0.18), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 112 HIS 0.005 0.001 HIS I 374 PHE 0.016 0.001 PHE A 376 TYR 0.018 0.001 TYR E 61 ARG 0.004 0.000 ARG J 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 54 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 LYS cc_start: 0.9556 (mmtt) cc_final: 0.9147 (mppt) REVERT: C 218 LYS cc_start: 0.9024 (pttt) cc_final: 0.8565 (tptt) REVERT: E 369 MET cc_start: 0.7645 (mtt) cc_final: 0.6980 (mtp) REVERT: E 417 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8165 (mp10) REVERT: F 530 MET cc_start: 0.8478 (mtp) cc_final: 0.8030 (mtp) REVERT: G 218 LYS cc_start: 0.9097 (pttt) cc_final: 0.8607 (tptt) REVERT: I 95 MET cc_start: 0.8087 (ttp) cc_final: 0.7520 (ttm) REVERT: I 213 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8922 (tp) REVERT: I 467 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.7926 (p) REVERT: K 34 MET cc_start: 0.9042 (mmm) cc_final: 0.8784 (mmm) REVERT: K 218 LYS cc_start: 0.9121 (pttt) cc_final: 0.8632 (tptt) REVERT: L 108 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8377 (mmmm) outliers start: 30 outliers final: 24 residues processed: 83 average time/residue: 0.3552 time to fit residues: 50.1492 Evaluate side-chains 82 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 54 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 108 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.0000 chunk 74 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 243 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 249 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 540 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.040527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.030696 restraints weight = 252008.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.031498 restraints weight = 144155.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.031993 restraints weight = 104472.425| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 25587 Z= 0.131 Angle : 0.555 9.074 34811 Z= 0.280 Chirality : 0.043 0.204 4119 Planarity : 0.004 0.043 4376 Dihedral : 7.293 59.790 4772 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.26 % Favored : 94.41 % Rotamer: Outliers : 0.81 % Allowed : 12.19 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 (0.16), residues: 3078 helix: 1.65 (0.26), residues: 468 sheet: -0.44 (0.16), residues: 1101 loop : -0.45 (0.17), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP I 427 HIS 0.007 0.001 HIS A 105 PHE 0.017 0.001 PHE A 376 TYR 0.016 0.001 TYR E 61 ARG 0.005 0.000 ARG I 476 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3557.76 seconds wall clock time: 68 minutes 26.58 seconds (4106.58 seconds total)