Starting phenix.real_space_refine on Fri Mar 15 19:14:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7h_27230/03_2024/8d7h_27230.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7h_27230/03_2024/8d7h_27230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7h_27230/03_2024/8d7h_27230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7h_27230/03_2024/8d7h_27230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7h_27230/03_2024/8d7h_27230.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7h_27230/03_2024/8d7h_27230.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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 46 5.16 5 C 7970 2.51 5 N 2156 2.21 5 O 2368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 24": "NH1" <-> "NH2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 252": "OD1" <-> "OD2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 45": "OD1" <-> "OD2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A ASP 289": "OD1" <-> "OD2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 37": "NH1" <-> "NH2" Residue "G ASP 41": "OD1" <-> "OD2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "G ASP 63": "OD1" <-> "OD2" Residue "G TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 92": "NH1" <-> "NH2" Residue "G ASP 93": "OD1" <-> "OD2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 157": "OD1" <-> "OD2" Residue "G PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 213": "NH1" <-> "NH2" Residue "G PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 261": "OD1" <-> "OD2" Residue "G TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 45": "OD1" <-> "OD2" Residue "H TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 78": "NH1" <-> "NH2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H ARG 95": "NH1" <-> "NH2" Residue "H ASP 99": "OD1" <-> "OD2" Residue "H TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 118": "NH1" <-> "NH2" Residue "H ARG 122": "NH1" <-> "NH2" Residue "H ARG 131": "NH1" <-> "NH2" Residue "H TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H ARG 204": "NH1" <-> "NH2" Residue "E ASP 120": "OD1" <-> "OD2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 200": "OD1" <-> "OD2" Residue "E PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 221": "NH1" <-> "NH2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E ASP 251": "OD1" <-> "OD2" Residue "E PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E ASP 280": "OD1" <-> "OD2" Residue "E ASP 283": "OD1" <-> "OD2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "E ASP 289": "OD1" <-> "OD2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E ARG 340": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12540 Number of models: 1 Model: "" Number of chains: 22 Chain: "C" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2259 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 24, 'TRANS': 257} Chain: "D" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1432 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "A" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2355 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 280} Chain: "G" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2259 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 24, 'TRANS': 257} Chain: "H" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1432 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "E" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2355 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 280} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.69, per 1000 atoms: 0.53 Number of scatterers: 12540 At special positions: 0 Unit cell: (196.94, 156.52, 101.48, 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 46 16.00 O 2368 8.00 N 2156 7.00 C 7970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 116 " - pdb=" SG CYS G 127 " distance=2.04 Simple disulfide: pdb=" SG CYS G 154 " - pdb=" SG CYS G 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 116 " distance=2.03 Simple disulfide: pdb=" SG CYS E 143 " - pdb=" SG CYS E 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 184 " - pdb=" SG CYS E 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 501 " - " ASN A 168 " " NAG A 502 " - " ASN A 292 " " NAG B 1 " - " ASN C 190 " " NAG E 501 " - " ASN E 168 " " NAG E 502 " - " ASN E 292 " " NAG F 1 " - " ASN C 70 " " NAG I 1 " - " ASN C 60 " " NAG J 1 " - " ASN C 142 " " NAG K 1 " - " ASN A 92 " " NAG L 1 " - " ASN A 104 " " NAG M 1 " - " ASN A 140 " " NAG N 1 " - " ASN G 190 " " NAG O 1 " - " ASN G 70 " " NAG P 1 " - " ASN G 60 " " NAG Q 1 " - " ASN G 142 " " NAG R 1 " - " ASN E 92 " " NAG S 1 " - " ASN E 104 " " NAG T 1 " - " ASN E 140 " Time building additional restraints: 5.03 Conformation dependent library (CDL) restraints added in 2.3 seconds 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2860 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 26 sheets defined 19.5% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.560A pdb=" N HIS C 83 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER C 84 " --> pdb=" O LEU C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 84' Processing helix chain 'D' and resid 35 through 66 removed outlier: 4.252A pdb=" N SER D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE D 40 " --> pdb=" O PRO D 36 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.625A pdb=" N LEU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 126 through 154 Processing helix chain 'D' and resid 176 through 208 Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.819A pdb=" N LEU A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.526A pdb=" N HIS G 83 " --> pdb=" O GLU G 80 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER G 84 " --> pdb=" O LEU G 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 80 through 84' Processing helix chain 'H' and resid 35 through 66 removed outlier: 4.251A pdb=" N SER H 39 " --> pdb=" O GLY H 35 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 40 " --> pdb=" O PRO H 36 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN H 41 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'H' and resid 90 through 97 removed outlier: 3.637A pdb=" N LEU H 97 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'H' and resid 121 through 123 No H-bonds generated for 'chain 'H' and resid 121 through 123' Processing helix chain 'H' and resid 126 through 154 Processing helix chain 'H' and resid 176 through 208 Processing helix chain 'E' and resid 69 through 74 removed outlier: 3.948A pdb=" N LEU E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 231 Processing sheet with id=AA1, first strand: chain 'C' and resid 32 through 36 removed outlier: 6.379A pdb=" N HIS C 32 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N HIS C 104 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN C 34 " --> pdb=" O HIS C 104 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU C 97 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N HIS C 91 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS C 99 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS C 89 " --> pdb=" O HIS C 99 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 101 " --> pdb=" O TYR C 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 45 removed outlier: 3.602A pdb=" N VAL C 42 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 113 through 114 removed outlier: 3.758A pdb=" N HIS C 130 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 140 through 145 removed outlier: 3.684A pdb=" N THR C 144 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 190 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 211 through 214 removed outlier: 3.657A pdb=" N VAL C 224 " --> pdb=" O HIS C 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 255 through 258 removed outlier: 3.544A pdb=" N GLN C 255 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR C 246 " --> pdb=" O GLN C 255 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE C 243 " --> pdb=" O ALA C 281 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.589A pdb=" N VAL A 42 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 61 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 91 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.665A pdb=" N GLY A 132 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 125 " --> pdb=" O CYS A 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 186 through 187 removed outlier: 4.008A pdb=" N GLU A 186 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR A 156 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASN A 140 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N THR A 234 " --> pdb=" O CYS A 143 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER A 145 " --> pdb=" O THR A 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AB2, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AB3, first strand: chain 'A' and resid 242 through 244 Processing sheet with id=AB4, first strand: chain 'A' and resid 284 through 286 removed outlier: 3.540A pdb=" N PHE A 308 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 32 through 36 removed outlier: 6.402A pdb=" N HIS G 32 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N HIS G 104 " --> pdb=" O HIS G 32 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN G 34 " --> pdb=" O HIS G 104 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU G 97 " --> pdb=" O HIS G 91 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS G 91 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS G 99 " --> pdb=" O CYS G 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 41 through 45 removed outlier: 3.508A pdb=" N VAL G 42 " --> pdb=" O LEU G 76 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 113 through 114 removed outlier: 3.756A pdb=" N HIS G 130 " --> pdb=" O VAL G 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 140 through 145 removed outlier: 3.685A pdb=" N THR G 144 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN G 190 " --> pdb=" O VAL G 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 211 through 214 removed outlier: 3.731A pdb=" N VAL G 224 " --> pdb=" O HIS G 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 255 through 258 removed outlier: 3.689A pdb=" N GLN G 255 " --> pdb=" O TYR G 246 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR G 246 " --> pdb=" O GLN G 255 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL G 257 " --> pdb=" O LEU G 244 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE G 243 " --> pdb=" O ALA G 281 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 42 through 44 removed outlier: 3.572A pdb=" N VAL E 42 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER E 61 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 91 " --> pdb=" O THR E 95 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 49 through 51 removed outlier: 3.665A pdb=" N GLY E 132 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA E 125 " --> pdb=" O CYS E 116 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 186 through 187 removed outlier: 4.002A pdb=" N GLU E 186 " --> pdb=" O HIS E 196 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR E 156 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASN E 140 " --> pdb=" O THR E 156 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N THR E 234 " --> pdb=" O CYS E 143 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER E 145 " --> pdb=" O THR E 234 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 182 through 183 Processing sheet with id=AC6, first strand: chain 'E' and resid 182 through 183 Processing sheet with id=AC7, first strand: chain 'E' and resid 242 through 244 Processing sheet with id=AC8, first strand: chain 'E' and resid 284 through 286 removed outlier: 3.538A pdb=" N PHE E 308 " --> pdb=" O ARG E 277 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1167 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: 3.55 Time building geometry restraints manager: 5.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4000 1.35 - 1.47: 3228 1.47 - 1.59: 5630 1.59 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 12916 Sorted by residual: bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.88e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 ... (remaining 12911 not shown) Histogram of bond angle deviations from ideal: 100.72 - 107.37: 760 107.37 - 114.02: 7397 114.02 - 120.67: 4663 120.67 - 127.33: 4598 127.33 - 133.98: 246 Bond angle restraints: 17664 Sorted by residual: angle pdb=" C GLY H 164 " pdb=" N THR H 165 " pdb=" CA THR H 165 " ideal model delta sigma weight residual 121.54 126.74 -5.20 1.91e+00 2.74e-01 7.41e+00 angle pdb=" C GLY D 164 " pdb=" N THR D 165 " pdb=" CA THR D 165 " ideal model delta sigma weight residual 121.54 126.71 -5.17 1.91e+00 2.74e-01 7.33e+00 angle pdb=" C HIS C 25 " pdb=" N SER C 26 " pdb=" CA SER C 26 " ideal model delta sigma weight residual 120.51 123.74 -3.23 1.45e+00 4.76e-01 4.95e+00 angle pdb=" C LEU C 251 " pdb=" N ASP C 252 " pdb=" CA ASP C 252 " ideal model delta sigma weight residual 122.46 125.52 -3.06 1.41e+00 5.03e-01 4.70e+00 angle pdb=" C LEU G 251 " pdb=" N ASP G 252 " pdb=" CA ASP G 252 " ideal model delta sigma weight residual 121.54 125.27 -3.73 1.91e+00 2.74e-01 3.81e+00 ... (remaining 17659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 7488 17.59 - 35.18: 438 35.18 - 52.76: 116 52.76 - 70.35: 23 70.35 - 87.94: 15 Dihedral angle restraints: 8080 sinusoidal: 3642 harmonic: 4438 Sorted by residual: dihedral pdb=" CB CYS G 46 " pdb=" SG CYS G 46 " pdb=" SG CYS G 89 " pdb=" CB CYS G 89 " ideal model delta sinusoidal sigma weight residual 93.00 43.91 49.09 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CB CYS C 46 " pdb=" SG CYS C 46 " pdb=" SG CYS C 89 " pdb=" CB CYS C 89 " ideal model delta sinusoidal sigma weight residual 93.00 45.65 47.35 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CB CYS C 116 " pdb=" SG CYS C 116 " pdb=" SG CYS C 127 " pdb=" CB CYS C 127 " ideal model delta sinusoidal sigma weight residual 93.00 54.73 38.27 1 1.00e+01 1.00e-02 2.06e+01 ... (remaining 8077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1627 0.046 - 0.091: 254 0.091 - 0.137: 139 0.137 - 0.182: 0 0.182 - 0.228: 2 Chirality restraints: 2022 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN E 104 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN A 104 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA VAL E 290 " pdb=" N VAL E 290 " pdb=" C VAL E 290 " pdb=" CB VAL E 290 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 2019 not shown) Planarity restraints: 2246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 66 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO D 67 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 66 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO H 67 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 67 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 67 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 66 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO E 67 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " -0.020 5.00e-02 4.00e+02 ... (remaining 2243 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3481 2.81 - 3.33: 10249 3.33 - 3.86: 19416 3.86 - 4.38: 20534 4.38 - 4.90: 37340 Nonbonded interactions: 91020 Sorted by model distance: nonbonded pdb=" OD1 ASP A 120 " pdb=" OG SER A 122 " model vdw 2.291 2.440 nonbonded pdb=" OD1 ASP G 197 " pdb=" OG1 THR G 200 " model vdw 2.329 2.440 nonbonded pdb=" OD1 ASP E 120 " pdb=" OG SER E 122 " model vdw 2.334 2.440 nonbonded pdb=" NH2 ARG C 245 " pdb=" OE1 GLN C 279 " model vdw 2.359 2.520 nonbonded pdb=" NH2 ARG G 245 " pdb=" OE1 GLN G 279 " model vdw 2.360 2.520 ... (remaining 91015 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' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.370 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: 0.010 Extract box with map and model: 12.030 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 34.390 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 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 : 0.003 0.044 12916 Z= 0.209 Angle : 0.528 6.910 17664 Z= 0.266 Chirality : 0.041 0.228 2022 Planarity : 0.004 0.047 2228 Dihedral : 12.375 87.938 5184 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.06 % Allowed : 8.45 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.21), residues: 1514 helix: 2.16 (0.30), residues: 250 sheet: -0.29 (0.25), residues: 456 loop : -2.42 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 254 HIS 0.004 0.000 HIS G 83 PHE 0.004 0.000 PHE H 74 TYR 0.005 0.000 TYR C 136 ARG 0.001 0.000 ARG G 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 206 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 HIS cc_start: 0.4518 (m-70) cc_final: 0.4266 (m-70) REVERT: C 104 HIS cc_start: 0.7099 (m-70) cc_final: 0.6777 (m-70) REVERT: C 226 TRP cc_start: 0.8827 (p90) cc_final: 0.8561 (p90) REVERT: D 117 LEU cc_start: 0.7648 (tt) cc_final: 0.7446 (tt) REVERT: D 209 MET cc_start: 0.5983 (tpp) cc_final: 0.5263 (mtt) REVERT: A 57 LEU cc_start: 0.7672 (tp) cc_final: 0.7432 (mp) REVERT: G 83 HIS cc_start: 0.4061 (m170) cc_final: 0.3807 (m-70) REVERT: G 226 TRP cc_start: 0.8708 (p90) cc_final: 0.8409 (p90) REVERT: H 209 MET cc_start: 0.6323 (tpp) cc_final: 0.5666 (mtt) REVERT: E 57 LEU cc_start: 0.7761 (tp) cc_final: 0.7393 (mp) outliers start: 14 outliers final: 6 residues processed: 217 average time/residue: 0.2645 time to fit residues: 79.7733 Evaluate side-chains 142 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 60 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 0.0170 chunk 71 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 136 optimal weight: 0.0370 overall best weight: 0.8898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 265 HIS C 285 ASN D 105 GLN A 113 ASN A 196 HIS ** G 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS G 285 ASN H 105 GLN H 106 ASN H 175 HIS E 113 ASN E 196 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12916 Z= 0.215 Angle : 0.590 13.142 17664 Z= 0.284 Chirality : 0.044 0.348 2022 Planarity : 0.005 0.050 2228 Dihedral : 5.298 56.282 2342 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.17 % Allowed : 13.73 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.22), residues: 1514 helix: 3.05 (0.32), residues: 252 sheet: 0.28 (0.25), residues: 456 loop : -1.90 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 57 HIS 0.004 0.001 HIS C 265 PHE 0.013 0.002 PHE H 185 TYR 0.016 0.001 TYR H 49 ARG 0.007 0.000 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 137 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7302 (m-70) cc_final: 0.7019 (m-70) REVERT: C 226 TRP cc_start: 0.8885 (p90) cc_final: 0.8509 (p90) REVERT: D 201 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.6987 (m-30) REVERT: D 209 MET cc_start: 0.6061 (tpp) cc_final: 0.5528 (mtt) REVERT: A 57 LEU cc_start: 0.7981 (tp) cc_final: 0.7749 (mp) REVERT: G 103 LEU cc_start: 0.5101 (pp) cc_final: 0.4539 (mm) REVERT: G 104 HIS cc_start: 0.7154 (m-70) cc_final: 0.6733 (m-70) REVERT: G 226 TRP cc_start: 0.8745 (p90) cc_final: 0.8330 (p90) REVERT: H 201 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.6990 (m-30) REVERT: H 209 MET cc_start: 0.6243 (tpp) cc_final: 0.5917 (mtt) REVERT: E 57 LEU cc_start: 0.8062 (tp) cc_final: 0.7704 (mp) outliers start: 42 outliers final: 20 residues processed: 168 average time/residue: 0.1506 time to fit residues: 40.3138 Evaluate side-chains 144 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 189 HIS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 285 ASN Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 40.0000 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 ASN D 203 ASN ** G 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 HIS G 100 GLN H 53 GLN H 203 ASN E 113 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12916 Z= 0.289 Angle : 0.639 10.282 17664 Z= 0.312 Chirality : 0.047 0.341 2022 Planarity : 0.005 0.063 2228 Dihedral : 5.446 59.955 2340 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.32 % Allowed : 16.06 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1514 helix: 3.09 (0.31), residues: 246 sheet: 0.47 (0.25), residues: 450 loop : -1.64 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 210 HIS 0.006 0.001 HIS A 193 PHE 0.022 0.002 PHE E 266 TYR 0.014 0.002 TYR D 110 ARG 0.003 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 113 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7258 (m-70) cc_final: 0.7027 (m-70) REVERT: C 117 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7777 (ptt-90) REVERT: D 209 MET cc_start: 0.6286 (tpp) cc_final: 0.5935 (mtt) REVERT: A 57 LEU cc_start: 0.8185 (tp) cc_final: 0.7924 (mp) REVERT: G 44 LEU cc_start: 0.5695 (OUTLIER) cc_final: 0.4820 (mm) REVERT: G 74 LEU cc_start: 0.7190 (mt) cc_final: 0.6880 (mp) REVERT: G 246 TYR cc_start: 0.5865 (p90) cc_final: 0.5359 (p90) REVERT: H 201 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7431 (m-30) REVERT: E 57 LEU cc_start: 0.8225 (tp) cc_final: 0.7829 (mp) outliers start: 44 outliers final: 29 residues processed: 144 average time/residue: 0.1896 time to fit residues: 43.1669 Evaluate side-chains 133 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.7980 chunk 102 optimal weight: 30.0000 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 203 ASN ** G 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 HIS H 53 GLN H 203 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12916 Z= 0.194 Angle : 0.560 9.651 17664 Z= 0.272 Chirality : 0.044 0.408 2022 Planarity : 0.004 0.061 2228 Dihedral : 5.275 59.857 2340 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.24 % Allowed : 17.80 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: 0.07 (0.22), residues: 1514 helix: 3.47 (0.31), residues: 244 sheet: 0.48 (0.24), residues: 482 loop : -1.43 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 196 HIS 0.003 0.001 HIS G 83 PHE 0.020 0.002 PHE E 266 TYR 0.009 0.001 TYR E 75 ARG 0.003 0.000 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 100 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7861 (ptt-90) REVERT: D 201 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7309 (m-30) REVERT: D 209 MET cc_start: 0.6303 (tpp) cc_final: 0.6013 (mtt) REVERT: A 57 LEU cc_start: 0.8197 (tp) cc_final: 0.7925 (mp) REVERT: G 246 TYR cc_start: 0.5903 (p90) cc_final: 0.5400 (p90) REVERT: H 201 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: E 57 LEU cc_start: 0.8241 (tp) cc_final: 0.7866 (mp) outliers start: 43 outliers final: 23 residues processed: 133 average time/residue: 0.1855 time to fit residues: 38.7341 Evaluate side-chains 121 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.0030 chunk 82 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 107 optimal weight: 0.0770 chunk 59 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 25 HIS G 28 GLN G 83 HIS H 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12916 Z= 0.191 Angle : 0.562 10.108 17664 Z= 0.273 Chirality : 0.045 0.396 2022 Planarity : 0.004 0.059 2228 Dihedral : 5.282 56.498 2340 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.54 % Allowed : 18.02 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: 0.23 (0.22), residues: 1514 helix: 3.59 (0.31), residues: 244 sheet: 0.56 (0.24), residues: 482 loop : -1.31 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 196 HIS 0.003 0.001 HIS D 52 PHE 0.016 0.002 PHE E 266 TYR 0.008 0.001 TYR H 110 ARG 0.002 0.000 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 107 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7892 (ptt-90) REVERT: D 201 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7336 (m-30) REVERT: D 209 MET cc_start: 0.6391 (tpp) cc_final: 0.6092 (mtt) REVERT: A 57 LEU cc_start: 0.8238 (tp) cc_final: 0.7966 (mp) REVERT: G 103 LEU cc_start: 0.4943 (pp) cc_final: 0.4354 (mm) REVERT: G 246 TYR cc_start: 0.5828 (p90) cc_final: 0.5382 (p90) REVERT: H 201 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7375 (m-30) REVERT: E 57 LEU cc_start: 0.8248 (tp) cc_final: 0.7872 (mp) outliers start: 47 outliers final: 29 residues processed: 145 average time/residue: 0.1848 time to fit residues: 43.1119 Evaluate side-chains 135 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.0670 chunk 130 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 120 optimal weight: 0.2980 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 chunk 76 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 HIS H 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12916 Z= 0.146 Angle : 0.541 8.778 17664 Z= 0.262 Chirality : 0.045 0.517 2022 Planarity : 0.004 0.054 2228 Dihedral : 5.120 55.859 2340 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.17 % Allowed : 18.85 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: 0.44 (0.22), residues: 1514 helix: 3.82 (0.31), residues: 244 sheet: 0.67 (0.25), residues: 460 loop : -1.12 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 196 HIS 0.002 0.000 HIS G 83 PHE 0.014 0.001 PHE E 266 TYR 0.009 0.001 TYR C 87 ARG 0.002 0.000 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 109 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8114 (ptt-90) REVERT: D 201 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7198 (m-30) REVERT: D 209 MET cc_start: 0.6318 (tpp) cc_final: 0.6013 (mtt) REVERT: A 57 LEU cc_start: 0.8224 (tp) cc_final: 0.7930 (mp) REVERT: A 150 ASP cc_start: 0.8581 (p0) cc_final: 0.8320 (p0) REVERT: G 103 LEU cc_start: 0.5272 (pp) cc_final: 0.4664 (mm) REVERT: G 246 TYR cc_start: 0.5814 (p90) cc_final: 0.5399 (p90) REVERT: H 201 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7276 (m-30) REVERT: E 57 LEU cc_start: 0.8246 (tp) cc_final: 0.7860 (mp) outliers start: 42 outliers final: 25 residues processed: 141 average time/residue: 0.1955 time to fit residues: 44.2788 Evaluate side-chains 128 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 50.0000 chunk 105 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 90 optimal weight: 0.2980 chunk 88 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 HIS ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 12916 Z= 0.417 Angle : 0.717 9.151 17664 Z= 0.361 Chirality : 0.051 0.501 2022 Planarity : 0.005 0.076 2228 Dihedral : 5.596 49.694 2340 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.07 % Allowed : 19.00 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: -0.22 (0.22), residues: 1514 helix: 2.62 (0.31), residues: 256 sheet: 0.49 (0.24), residues: 478 loop : -1.60 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 196 HIS 0.007 0.001 HIS D 52 PHE 0.024 0.003 PHE G 243 TYR 0.021 0.002 TYR H 110 ARG 0.005 0.001 ARG H 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 96 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7940 (ptt-90) REVERT: C 260 SER cc_start: 0.8269 (p) cc_final: 0.8014 (t) REVERT: D 63 ASN cc_start: 0.8241 (t0) cc_final: 0.7915 (t0) REVERT: D 209 MET cc_start: 0.6533 (tpp) cc_final: 0.6175 (mtt) REVERT: A 57 LEU cc_start: 0.8204 (tp) cc_final: 0.8001 (mp) REVERT: A 268 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7515 (p90) REVERT: G 246 TYR cc_start: 0.5853 (p90) cc_final: 0.5406 (p90) REVERT: E 57 LEU cc_start: 0.8271 (tp) cc_final: 0.7978 (mp) REVERT: E 268 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7612 (p90) outliers start: 54 outliers final: 38 residues processed: 143 average time/residue: 0.2023 time to fit residues: 45.5744 Evaluate side-chains 129 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 88 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 139 ASN Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 268 PHE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12916 Z= 0.188 Angle : 0.592 8.500 17664 Z= 0.292 Chirality : 0.048 0.690 2022 Planarity : 0.004 0.064 2228 Dihedral : 5.600 58.995 2340 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.94 % Allowed : 20.21 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: 0.09 (0.22), residues: 1514 helix: 3.10 (0.32), residues: 256 sheet: 0.64 (0.24), residues: 476 loop : -1.45 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 196 HIS 0.003 0.001 HIS D 175 PHE 0.015 0.002 PHE E 266 TYR 0.011 0.001 TYR A 187 ARG 0.003 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 96 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7613 (ptt-90) REVERT: C 146 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8384 (tp) REVERT: D 201 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: D 209 MET cc_start: 0.6445 (tpp) cc_final: 0.6223 (mtt) REVERT: A 57 LEU cc_start: 0.8215 (tp) cc_final: 0.8006 (mp) REVERT: G 103 LEU cc_start: 0.5288 (pp) cc_final: 0.4590 (mm) REVERT: G 246 TYR cc_start: 0.5809 (p90) cc_final: 0.5440 (p90) REVERT: H 201 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7416 (m-30) REVERT: E 57 LEU cc_start: 0.8290 (tp) cc_final: 0.7965 (mp) outliers start: 39 outliers final: 30 residues processed: 130 average time/residue: 0.1925 time to fit residues: 39.7689 Evaluate side-chains 123 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 89 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 81 optimal weight: 30.0000 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 142 optimal weight: 0.0060 chunk 86 optimal weight: 4.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 HIS ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12916 Z= 0.285 Angle : 0.625 8.576 17664 Z= 0.313 Chirality : 0.049 0.598 2022 Planarity : 0.005 0.067 2228 Dihedral : 5.659 59.854 2340 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.09 % Allowed : 20.21 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: 0.02 (0.22), residues: 1514 helix: 2.98 (0.31), residues: 258 sheet: 0.58 (0.24), residues: 474 loop : -1.47 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 196 HIS 0.004 0.001 HIS H 52 PHE 0.017 0.002 PHE A 266 TYR 0.013 0.002 TYR H 110 ARG 0.003 0.000 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 94 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8064 (ptt-90) REVERT: D 209 MET cc_start: 0.6544 (tpp) cc_final: 0.6295 (mtt) REVERT: A 57 LEU cc_start: 0.8248 (tp) cc_final: 0.8032 (mp) REVERT: G 246 TYR cc_start: 0.5660 (p90) cc_final: 0.5397 (p90) REVERT: H 201 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7498 (m-30) REVERT: E 57 LEU cc_start: 0.8319 (tp) cc_final: 0.8007 (mp) outliers start: 41 outliers final: 34 residues processed: 130 average time/residue: 0.2022 time to fit residues: 41.1943 Evaluate side-chains 129 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 93 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 139 ASN Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.0070 chunk 99 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 94 optimal weight: 0.0010 chunk 126 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 HIS ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 HIS ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12916 Z= 0.160 Angle : 0.574 12.011 17664 Z= 0.282 Chirality : 0.046 0.509 2022 Planarity : 0.004 0.057 2228 Dihedral : 5.415 59.602 2340 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.64 % Allowed : 20.97 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: 0.24 (0.22), residues: 1514 helix: 3.34 (0.31), residues: 254 sheet: 0.73 (0.24), residues: 474 loop : -1.37 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 196 HIS 0.002 0.000 HIS D 175 PHE 0.017 0.001 PHE A 266 TYR 0.012 0.001 TYR H 49 ARG 0.002 0.000 ARG G 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 100 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7755 (ptt-90) REVERT: C 123 LYS cc_start: 0.7073 (mmmm) cc_final: 0.6813 (mppt) REVERT: C 260 SER cc_start: 0.8232 (p) cc_final: 0.7959 (t) REVERT: D 201 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: D 209 MET cc_start: 0.6386 (tpp) cc_final: 0.5743 (mtt) REVERT: A 150 ASP cc_start: 0.8588 (p0) cc_final: 0.8343 (p0) REVERT: G 103 LEU cc_start: 0.4820 (pt) cc_final: 0.4354 (mm) REVERT: G 246 TYR cc_start: 0.5632 (p90) cc_final: 0.5392 (p90) REVERT: H 201 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7342 (m-30) REVERT: E 57 LEU cc_start: 0.8322 (tp) cc_final: 0.7986 (mp) outliers start: 35 outliers final: 29 residues processed: 131 average time/residue: 0.1969 time to fit residues: 40.5980 Evaluate side-chains 126 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 94 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.4980 chunk 17 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 HIS ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 175 HIS ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.180028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124105 restraints weight = 17586.373| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.08 r_work: 0.3362 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12916 Z= 0.181 Angle : 0.588 9.450 17664 Z= 0.288 Chirality : 0.050 0.740 2022 Planarity : 0.004 0.057 2228 Dihedral : 5.499 55.240 2340 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.71 % Allowed : 20.66 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % 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: 0.28 (0.22), residues: 1514 helix: 3.39 (0.31), residues: 254 sheet: 0.76 (0.24), residues: 474 loop : -1.37 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 196 HIS 0.003 0.001 HIS H 52 PHE 0.014 0.001 PHE A 266 TYR 0.013 0.001 TYR H 49 ARG 0.002 0.000 ARG G 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2770.51 seconds wall clock time: 51 minutes 51.41 seconds (3111.41 seconds total)