Starting phenix.real_space_refine on Mon Jul 22 07:24:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyv_26195/07_2024/7tyv_26195.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyv_26195/07_2024/7tyv_26195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyv_26195/07_2024/7tyv_26195.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyv_26195/07_2024/7tyv_26195.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyv_26195/07_2024/7tyv_26195.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyv_26195/07_2024/7tyv_26195.cif" } resolution = 2.8 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= 0.001 sd= 0.019 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 108 5.16 5 C 10865 2.51 5 N 2853 2.21 5 O 3480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 81": "OD1" <-> "OD2" Residue "a TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17306 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1172 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain breaks: 3 Chain: "B" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1178 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 3, 'TRANS': 144} Chain breaks: 3 Chain: "C" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1178 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 3, 'TRANS': 144} Chain breaks: 3 Chain: "D" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1580 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain breaks: 1 Chain: "E" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1603 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 198} Chain: "G" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1580 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain breaks: 1 Chain: "L" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1603 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 198} Chain: "H" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1580 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain breaks: 1 Chain: "K" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1603 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 198} Chain: "a" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1160 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain breaks: 2 Chain: "b" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1160 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain breaks: 2 Chain: "c" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1160 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain breaks: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.18, per 1000 atoms: 0.59 Number of scatterers: 17306 At special positions: 0 Unit cell: (208.24, 198.376, 88.776, 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 108 16.00 O 3480 8.00 N 2853 7.00 C 10865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 191 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 148 " - pdb=" SG CYS G 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 131 " - pdb=" SG CYS L 191 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 87 " distance=2.04 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 191 " distance=2.04 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.04 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.04 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.03 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.05 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN Q 4 " - " MAN Q 5 " " MAN Q 5 " - " MAN Q 6 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA N 3 " - " MAN N 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 301 " - " ASN A 89 " " NAG A 302 " - " ASN A 109 " " NAG A 303 " - " ASN A 167 " " NAG B 301 " - " ASN B 89 " " NAG B 302 " - " ASN B 109 " " NAG B 303 " - " ASN B 167 " " NAG C 301 " - " ASN C 89 " " NAG C 302 " - " ASN C 109 " " NAG C 303 " - " ASN C 167 " " NAG F 1 " - " ASN A 79 " " NAG I 1 " - " ASN A 99 " " NAG M 1 " - " ASN a 365 " " NAG N 1 " - " ASN B 79 " " NAG O 1 " - " ASN B 99 " " NAG P 1 " - " ASN B 224 " " NAG Q 1 " - " ASN b 365 " " NAG R 1 " - " ASN C 79 " " NAG S 1 " - " ASN C 99 " " NAG T 1 " - " ASN C 224 " " NAG U 1 " - " ASN c 365 " " NAG V 1 " - " ASN A 224 " " NAG a 501 " - " ASN a 373 " " NAG a 502 " - " ASN a 395 " " NAG b 501 " - " ASN b 373 " " NAG c 501 " - " ASN c 373 " Time building additional restraints: 6.92 Conformation dependent library (CDL) restraints added in 2.9 seconds 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3976 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 44 sheets defined 21.6% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 75 through 79 removed outlier: 3.515A pdb=" N LEU A 78 " --> pdb=" O MET A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 144 removed outlier: 3.761A pdb=" N ILE A 144 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.645A pdb=" N GLY A 160 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'B' and resid 75 through 79 removed outlier: 3.723A pdb=" N LEU B 78 " --> pdb=" O MET B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 130 through 144 removed outlier: 3.682A pdb=" N ILE B 144 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.512A pdb=" N GLY B 160 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 195 Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.656A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.648A pdb=" N ASN C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'C' and resid 238 through 246 removed outlier: 3.700A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.562A pdb=" N LYS D 31 " --> pdb=" O ASN D 28 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.816A pdb=" N THR D 91 " --> pdb=" O ASP D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 199 removed outlier: 3.528A pdb=" N THR D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 125 removed outlier: 3.526A pdb=" N LEU E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS E 123 " --> pdb=" O ASP E 119 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 184 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.775A pdb=" N LYS G 31 " --> pdb=" O ASN G 28 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.746A pdb=" N THR G 91 " --> pdb=" O ASP G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 166 No H-bonds generated for 'chain 'G' and resid 164 through 166' Processing helix chain 'G' and resid 194 through 199 Processing helix chain 'L' and resid 118 through 124 removed outlier: 3.906A pdb=" N LEU L 122 " --> pdb=" O SER L 118 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 185 removed outlier: 3.919A pdb=" N LYS L 185 " --> pdb=" O ALA L 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.964A pdb=" N THR H 91 " --> pdb=" O ASP H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 199 removed outlier: 3.503A pdb=" N LEU H 197 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR H 199 " --> pdb=" O SER H 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 123 removed outlier: 3.739A pdb=" N LYS K 123 " --> pdb=" O ASP K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 185 removed outlier: 3.985A pdb=" N LYS K 185 " --> pdb=" O ALA K 181 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 300 removed outlier: 3.501A pdb=" N VAL a 298 " --> pdb=" O GLY a 294 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS a 300 " --> pdb=" O THR a 296 " (cutoff:3.500A) Processing helix chain 'a' and resid 301 through 303 No H-bonds generated for 'chain 'a' and resid 301 through 303' Processing helix chain 'a' and resid 307 through 324 removed outlier: 3.919A pdb=" N ASP a 311 " --> pdb=" O GLU a 307 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN a 324 " --> pdb=" O LYS a 320 " (cutoff:3.500A) Processing helix chain 'a' and resid 335 through 341 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.832A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 417 removed outlier: 3.650A pdb=" N LYS a 417 " --> pdb=" O GLU a 413 " (cutoff:3.500A) Processing helix chain 'b' and resid 294 through 300 removed outlier: 3.650A pdb=" N VAL b 298 " --> pdb=" O GLY b 294 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS b 300 " --> pdb=" O THR b 296 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 325 removed outlier: 3.718A pdb=" N ASP b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) Processing helix chain 'b' and resid 335 through 341 Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.763A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 417 removed outlier: 3.559A pdb=" N ILE b 403 " --> pdb=" O PHE b 399 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU b 404 " --> pdb=" O SER b 400 " (cutoff:3.500A) Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 removed outlier: 4.092A pdb=" N ASP c 311 " --> pdb=" O GLU c 307 " (cutoff:3.500A) Processing helix chain 'c' and resid 335 through 341 Processing helix chain 'c' and resid 342 through 344 No H-bonds generated for 'chain 'c' and resid 342 through 344' Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.788A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 417 removed outlier: 3.777A pdb=" N ILE c 403 " --> pdb=" O PHE c 399 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 89 removed outlier: 3.507A pdb=" N LYS A 88 " --> pdb=" O HIS A 92 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.829A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 89 removed outlier: 6.840A pdb=" N HIS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR C 225 " --> pdb=" O GLY C 102 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 108 " --> pdb=" O TYR C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.172A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN D 33 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.172A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ARG D 98 " --> pdb=" O ASP D 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.117A pdb=" N TYR D 184 " --> pdb=" O ASP D 152 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS D 172 " --> pdb=" O VAL D 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.117A pdb=" N TYR D 184 " --> pdb=" O ASP D 152 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER D 185 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 159 through 162 removed outlier: 4.599A pdb=" N TYR D 202 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.593A pdb=" N LEU E 10 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP E 102 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP E 34 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.593A pdb=" N LEU E 10 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP E 102 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR E 94 " --> pdb=" O GLN E 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 111 through 115 removed outlier: 6.048A pdb=" N TYR E 170 " --> pdb=" O ASN E 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 141 through 147 removed outlier: 3.625A pdb=" N VAL E 202 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.055A pdb=" N GLY G 10 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN G 33 " --> pdb=" O GLU G 99 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET G 34 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.055A pdb=" N GLY G 10 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG G 98 " --> pdb=" O ASP G 109 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 128 through 131 removed outlier: 6.136A pdb=" N TYR G 184 " --> pdb=" O ASP G 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS G 172 " --> pdb=" O VAL G 189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 128 through 131 removed outlier: 6.136A pdb=" N TYR G 184 " --> pdb=" O ASP G 152 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER G 185 " --> pdb=" O VAL G 177 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 159 through 162 Processing sheet with id=AC6, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'L' and resid 9 through 11 removed outlier: 7.007A pdb=" N LEU L 10 " --> pdb=" O ASP L 102 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP L 34 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 111 through 112 removed outlier: 5.989A pdb=" N TYR L 170 " --> pdb=" O ASN L 135 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 111 through 112 removed outlier: 5.989A pdb=" N TYR L 170 " --> pdb=" O ASN L 135 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 141 through 147 Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.033A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN H 33 " --> pdb=" O GLU H 99 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.033A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE H 100 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA H 108 " --> pdb=" O ILE H 100 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 128 through 131 removed outlier: 6.133A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS H 172 " --> pdb=" O VAL H 189 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 128 through 131 removed outlier: 6.133A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER H 185 " --> pdb=" O VAL H 177 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 159 through 162 Processing sheet with id=AD8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AD9, first strand: chain 'K' and resid 9 through 11 removed outlier: 7.146A pdb=" N LEU K 10 " --> pdb=" O ASP K 102 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP K 34 " --> pdb=" O LEU K 46 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 111 through 112 removed outlier: 6.051A pdb=" N TYR K 170 " --> pdb=" O ASN K 135 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 111 through 112 removed outlier: 6.051A pdb=" N TYR K 170 " --> pdb=" O ASN K 135 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 141 through 147 Processing sheet with id=AE4, first strand: chain 'a' and resid 279 through 280 removed outlier: 3.583A pdb=" N LEU a 280 " --> pdb=" O LYS a 291 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS a 291 " --> pdb=" O LEU a 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AE6, first strand: chain 'b' and resid 279 through 280 removed outlier: 3.550A pdb=" N LYS b 291 " --> pdb=" O LEU b 280 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 279 through 280 removed outlier: 3.806A pdb=" N LYS c 291 " --> pdb=" O LEU c 280 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'c' and resid 388 through 389 715 hydrogen bonds defined for protein. 1809 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: 5.59 Time building geometry restraints manager: 7.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5388 1.35 - 1.47: 4626 1.47 - 1.59: 7475 1.59 - 1.72: 0 1.72 - 1.84: 159 Bond restraints: 17648 Sorted by residual: bond pdb=" C2 MAN M 4 " pdb=" O2 MAN M 4 " ideal model delta sigma weight residual 1.407 1.494 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C1 MAN M 4 " pdb=" C2 MAN M 4 " ideal model delta sigma weight residual 1.526 1.590 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C1 BMA M 3 " pdb=" C2 BMA M 3 " ideal model delta sigma weight residual 1.519 1.565 -0.046 2.00e-02 2.50e+03 5.26e+00 bond pdb=" C5 MAN N 5 " pdb=" O5 MAN N 5 " ideal model delta sigma weight residual 1.418 1.463 -0.045 2.00e-02 2.50e+03 4.98e+00 bond pdb=" C5 MAN R 4 " pdb=" O5 MAN R 4 " ideal model delta sigma weight residual 1.418 1.463 -0.045 2.00e-02 2.50e+03 4.97e+00 ... (remaining 17643 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.29: 400 106.29 - 113.23: 10089 113.23 - 120.18: 5637 120.18 - 127.12: 7606 127.12 - 134.07: 177 Bond angle restraints: 23909 Sorted by residual: angle pdb=" CA CYS c 292 " pdb=" CB CYS c 292 " pdb=" SG CYS c 292 " ideal model delta sigma weight residual 114.40 122.76 -8.36 2.30e+00 1.89e-01 1.32e+01 angle pdb=" C1 MAN M 4 " pdb=" C2 MAN M 4 " pdb=" O2 MAN M 4 " ideal model delta sigma weight residual 106.80 116.87 -10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CA CYS a 292 " pdb=" CB CYS a 292 " pdb=" SG CYS a 292 " ideal model delta sigma weight residual 114.40 121.90 -7.50 2.30e+00 1.89e-01 1.06e+01 angle pdb=" CA CYS b 292 " pdb=" CB CYS b 292 " pdb=" SG CYS b 292 " ideal model delta sigma weight residual 114.40 121.77 -7.37 2.30e+00 1.89e-01 1.03e+01 angle pdb=" C3 MAN U 4 " pdb=" C2 MAN U 4 " pdb=" O2 MAN U 4 " ideal model delta sigma weight residual 111.77 103.90 7.87 3.00e+00 1.11e-01 6.88e+00 ... (remaining 23904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.67: 10618 24.67 - 49.34: 543 49.34 - 74.01: 78 74.01 - 98.68: 53 98.68 - 123.36: 35 Dihedral angle restraints: 11327 sinusoidal: 5174 harmonic: 6153 Sorted by residual: dihedral pdb=" CA CYS c 292 " pdb=" C CYS c 292 " pdb=" N PHE c 293 " pdb=" CA PHE c 293 " ideal model delta harmonic sigma weight residual 180.00 -152.63 -27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CB CYS K 131 " pdb=" SG CYS K 131 " pdb=" SG CYS K 191 " pdb=" CB CYS K 191 " ideal model delta sinusoidal sigma weight residual 93.00 132.85 -39.85 1 1.00e+01 1.00e-02 2.23e+01 dihedral pdb=" CA CYS a 292 " pdb=" C CYS a 292 " pdb=" N PHE a 293 " pdb=" CA PHE a 293 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 11324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 2864 0.188 - 0.375: 10 0.375 - 0.563: 0 0.563 - 0.750: 0 0.750 - 0.938: 1 Chirality restraints: 2875 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN c 365 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" C5 BMA T 3 " pdb=" C4 BMA T 3 " pdb=" C6 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2872 not shown) Planarity restraints: 2956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN a 365 " -0.030 2.00e-02 2.50e+03 2.85e-02 1.02e+01 pdb=" CG ASN a 365 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN a 365 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN a 365 " 0.032 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE b 361 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO b 362 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO b 362 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO b 362 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE c 411 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.22e+00 pdb=" C ILE c 411 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE c 411 " -0.012 2.00e-02 2.50e+03 pdb=" N THR c 412 " -0.010 2.00e-02 2.50e+03 ... (remaining 2953 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 206 2.65 - 3.21: 14827 3.21 - 3.77: 24366 3.77 - 4.34: 33574 4.34 - 4.90: 57445 Nonbonded interactions: 130418 Sorted by model distance: nonbonded pdb=" OE1 GLU E 192 " pdb=" OG1 THR E 203 " model vdw 2.081 2.440 nonbonded pdb=" OG SER L 31 " pdb=" OG SER L 90 " model vdw 2.120 2.440 nonbonded pdb=" NE2 GLN E 121 " pdb=" O THR E 126 " model vdw 2.169 2.520 nonbonded pdb=" O GLN K 121 " pdb=" OG SER K 124 " model vdw 2.224 2.440 nonbonded pdb=" O GLU c 396 " pdb=" OG SER c 400 " model vdw 2.231 2.440 ... (remaining 130413 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 'B' and (resid 60 through 168 or resid 183 through 246 or resid 301 throu \ gh 303)) selection = (chain 'C' and (resid 60 through 168 or resid 183 through 246 or resid 301 throu \ gh 303)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'M' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'I' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'Q' selection = chain 'U' } ncs_group { reference = (chain 'a' and (resid 260 through 417 or resid 501)) selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.530 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: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 46.580 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 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 : 0.005 0.087 17648 Z= 0.303 Angle : 0.709 10.066 23909 Z= 0.329 Chirality : 0.049 0.938 2875 Planarity : 0.004 0.047 2931 Dihedral : 17.124 123.355 7270 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2054 helix: 0.97 (0.30), residues: 340 sheet: 1.25 (0.21), residues: 612 loop : -1.36 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 162 HIS 0.004 0.001 HIS C 141 PHE 0.012 0.001 PHE H 80 TYR 0.015 0.001 TYR A 217 ARG 0.005 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 THR cc_start: 0.8246 (p) cc_final: 0.8037 (p) REVERT: B 219 TYR cc_start: 0.6320 (m-80) cc_final: 0.6060 (m-80) REVERT: C 87 THR cc_start: 0.8363 (p) cc_final: 0.7986 (p) REVERT: D 76 LYS cc_start: 0.7732 (mtmm) cc_final: 0.7514 (mtmm) REVERT: L 185 LYS cc_start: 0.8512 (pttm) cc_final: 0.8134 (ptpp) REVERT: K 185 LYS cc_start: 0.8308 (pttm) cc_final: 0.8092 (ptpp) outliers start: 0 outliers final: 1 residues processed: 305 average time/residue: 1.0005 time to fit residues: 348.1788 Evaluate side-chains 270 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.0770 chunk 154 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN E 89 GLN c 324 GLN ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17648 Z= 0.239 Angle : 0.624 7.764 23909 Z= 0.305 Chirality : 0.046 0.672 2875 Planarity : 0.004 0.048 2931 Dihedral : 14.326 113.705 3430 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.44 % Allowed : 11.26 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.18), residues: 2054 helix: 0.97 (0.29), residues: 361 sheet: 1.34 (0.21), residues: 608 loop : -1.38 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 162 HIS 0.015 0.001 HIS c 354 PHE 0.018 0.001 PHE L 115 TYR 0.012 0.001 TYR A 217 ARG 0.008 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 289 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 THR cc_start: 0.8078 (p) cc_final: 0.7829 (p) REVERT: D 76 LYS cc_start: 0.7741 (mtmm) cc_final: 0.7498 (mtmm) REVERT: E 133 LEU cc_start: 0.7221 (mm) cc_final: 0.6983 (mp) REVERT: L 3 MET cc_start: 0.7595 (mtm) cc_final: 0.7281 (mtm) REVERT: L 185 LYS cc_start: 0.8546 (pttm) cc_final: 0.8132 (ptpp) REVERT: H 34 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6769 (mtp) REVERT: H 120 SER cc_start: 0.8536 (p) cc_final: 0.8148 (t) REVERT: K 105 ARG cc_start: 0.7356 (ttm170) cc_final: 0.7150 (ttm170) REVERT: K 185 LYS cc_start: 0.8357 (pttm) cc_final: 0.8148 (ptpp) REVERT: c 375 THR cc_start: 0.7680 (p) cc_final: 0.7461 (p) outliers start: 27 outliers final: 18 residues processed: 295 average time/residue: 1.0441 time to fit residues: 350.5504 Evaluate side-chains 300 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 281 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain K residue 171 SER Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain b residue 414 MET Chi-restraints excluded: chain c residue 324 GLN Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 414 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 185 optimal weight: 0.6980 chunk 200 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN G 30 ASN H 30 ASN H 74 ASN ** K 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 354 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 17648 Z= 0.458 Angle : 0.752 8.973 23909 Z= 0.367 Chirality : 0.051 0.704 2875 Planarity : 0.005 0.050 2931 Dihedral : 13.498 120.135 3430 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.36 % Allowed : 14.94 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2054 helix: 0.72 (0.29), residues: 343 sheet: 0.80 (0.20), residues: 701 loop : -1.56 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP H 162 HIS 0.011 0.002 HIS c 354 PHE 0.020 0.003 PHE L 115 TYR 0.021 0.003 TYR a 363 ARG 0.009 0.001 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 285 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7531 (mtt) REVERT: A 139 THR cc_start: 0.8196 (t) cc_final: 0.7979 (m) REVERT: B 219 TYR cc_start: 0.6540 (m-80) cc_final: 0.6227 (m-80) REVERT: D 76 LYS cc_start: 0.7773 (mtmm) cc_final: 0.7517 (mtmm) REVERT: D 105 THR cc_start: 0.7404 (OUTLIER) cc_final: 0.7178 (m) REVERT: E 133 LEU cc_start: 0.7383 (mm) cc_final: 0.7126 (mt) REVERT: G 83 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5857 (mtm) REVERT: L 105 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6880 (tmt90) REVERT: L 185 LYS cc_start: 0.8618 (pttm) cc_final: 0.8317 (ptpp) REVERT: H 34 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6864 (mtp) REVERT: H 120 SER cc_start: 0.8571 (p) cc_final: 0.8231 (t) REVERT: K 3 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.6916 (mtt) REVERT: K 139 ARG cc_start: 0.6686 (tpt90) cc_final: 0.6435 (tpt90) REVERT: K 185 LYS cc_start: 0.8385 (pttm) cc_final: 0.8062 (ptpp) REVERT: a 368 LYS cc_start: 0.8237 (tttp) cc_final: 0.7815 (tttp) REVERT: b 351 MET cc_start: 0.7465 (tpp) cc_final: 0.7196 (tpt) outliers start: 63 outliers final: 39 residues processed: 316 average time/residue: 0.9673 time to fit residues: 350.6575 Evaluate side-chains 321 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 276 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 105 ARG Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain K residue 3 MET Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain b residue 414 MET Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 414 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 96 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 186 optimal weight: 0.9980 chunk 197 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN G 30 ASN H 30 ASN K 195 HIS c 324 GLN ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17648 Z= 0.236 Angle : 0.637 9.873 23909 Z= 0.308 Chirality : 0.046 0.705 2875 Planarity : 0.004 0.050 2931 Dihedral : 12.413 114.585 3430 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.99 % Allowed : 17.66 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.18), residues: 2054 helix: 0.79 (0.29), residues: 361 sheet: 1.01 (0.20), residues: 642 loop : -1.66 (0.17), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 162 HIS 0.013 0.001 HIS c 354 PHE 0.019 0.001 PHE L 115 TYR 0.017 0.001 TYR c 393 ARG 0.010 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 282 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7458 (mtt) REVERT: A 87 THR cc_start: 0.8293 (t) cc_final: 0.8021 (p) REVERT: A 139 THR cc_start: 0.8157 (t) cc_final: 0.7874 (m) REVERT: D 34 MET cc_start: 0.6934 (mmt) cc_final: 0.6224 (mtt) REVERT: D 76 LYS cc_start: 0.7740 (mtmm) cc_final: 0.7468 (mtmm) REVERT: D 91 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8306 (t) REVERT: E 133 LEU cc_start: 0.7264 (mm) cc_final: 0.7005 (mt) REVERT: E 139 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.6509 (ttt90) REVERT: E 185 LYS cc_start: 0.8692 (pptt) cc_final: 0.8490 (pptt) REVERT: G 109 ASP cc_start: 0.7105 (p0) cc_final: 0.6892 (p0) REVERT: L 133 LEU cc_start: 0.7222 (mm) cc_final: 0.7000 (mt) REVERT: L 185 LYS cc_start: 0.8666 (pttm) cc_final: 0.8416 (ptpp) REVERT: H 34 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6770 (mtp) REVERT: H 120 SER cc_start: 0.8441 (p) cc_final: 0.8090 (t) REVERT: K 3 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7168 (mtp) REVERT: K 139 ARG cc_start: 0.6610 (tpt90) cc_final: 0.6407 (tpt90) REVERT: K 185 LYS cc_start: 0.8331 (pttm) cc_final: 0.8088 (ptpp) REVERT: b 351 MET cc_start: 0.7466 (tpp) cc_final: 0.7122 (tpt) REVERT: c 321 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6947 (mp10) REVERT: c 368 LYS cc_start: 0.8229 (tttm) cc_final: 0.8028 (tttp) outliers start: 56 outliers final: 31 residues processed: 314 average time/residue: 1.0734 time to fit residues: 384.1000 Evaluate side-chains 314 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 277 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain K residue 3 MET Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 410 MET Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain b residue 414 MET Chi-restraints excluded: chain c residue 321 GLN Chi-restraints excluded: chain c residue 324 GLN Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 404 GLU Chi-restraints excluded: chain c residue 414 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.0570 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 146 optimal weight: 0.4980 chunk 81 optimal weight: 0.0980 chunk 168 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN G 30 ASN H 30 ASN K 52 ASN c 324 GLN ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17648 Z= 0.175 Angle : 0.599 9.028 23909 Z= 0.288 Chirality : 0.045 0.680 2875 Planarity : 0.004 0.048 2931 Dihedral : 11.585 112.662 3430 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.93 % Allowed : 19.05 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2054 helix: 1.19 (0.30), residues: 343 sheet: 1.13 (0.21), residues: 628 loop : -1.46 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 162 HIS 0.012 0.001 HIS c 354 PHE 0.021 0.001 PHE L 115 TYR 0.018 0.001 TYR B 219 ARG 0.009 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 288 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7427 (mtt) REVERT: B 63 LYS cc_start: 0.8603 (mmmm) cc_final: 0.8351 (mptt) REVERT: D 34 MET cc_start: 0.6870 (mmt) cc_final: 0.6236 (mtt) REVERT: D 76 LYS cc_start: 0.7720 (mtmm) cc_final: 0.7451 (mtmm) REVERT: D 91 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8270 (t) REVERT: E 133 LEU cc_start: 0.7146 (mm) cc_final: 0.6914 (mt) REVERT: E 139 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.6482 (ttt90) REVERT: G 109 ASP cc_start: 0.7049 (p0) cc_final: 0.6827 (p0) REVERT: L 133 LEU cc_start: 0.7221 (mm) cc_final: 0.7017 (tp) REVERT: L 185 LYS cc_start: 0.8653 (pttm) cc_final: 0.8412 (ptpp) REVERT: H 34 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6676 (mtp) REVERT: H 120 SER cc_start: 0.8403 (p) cc_final: 0.8039 (t) REVERT: K 3 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7252 (mtp) REVERT: b 278 TYR cc_start: 0.8058 (t80) cc_final: 0.7454 (t80) REVERT: b 351 MET cc_start: 0.7488 (tpp) cc_final: 0.7217 (tpt) REVERT: c 368 LYS cc_start: 0.8206 (tttm) cc_final: 0.7992 (tttp) REVERT: c 375 THR cc_start: 0.7916 (p) cc_final: 0.7661 (p) outliers start: 55 outliers final: 33 residues processed: 315 average time/residue: 1.0276 time to fit residues: 369.7751 Evaluate side-chains 319 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 281 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain K residue 3 MET Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 410 MET Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain b residue 293 PHE Chi-restraints excluded: chain b residue 414 MET Chi-restraints excluded: chain c residue 324 GLN Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 404 GLU Chi-restraints excluded: chain c residue 414 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.9980 chunk 177 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 0.0870 chunk 48 optimal weight: 0.5980 chunk 197 optimal weight: 1.9990 chunk 163 optimal weight: 0.0570 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN G 30 ASN H 30 ASN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 321 GLN c 324 GLN c 353 ASN ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 17648 Z= 0.160 Angle : 0.587 9.425 23909 Z= 0.279 Chirality : 0.044 0.663 2875 Planarity : 0.004 0.046 2931 Dihedral : 11.013 111.994 3430 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.67 % Allowed : 20.12 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.19), residues: 2054 helix: 1.35 (0.30), residues: 343 sheet: 0.97 (0.20), residues: 655 loop : -1.34 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 162 HIS 0.011 0.001 HIS c 354 PHE 0.018 0.001 PHE L 115 TYR 0.017 0.001 TYR B 219 ARG 0.008 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 293 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8119 (t) cc_final: 0.7719 (p) REVERT: D 34 MET cc_start: 0.6799 (mmt) cc_final: 0.6256 (mtt) REVERT: D 76 LYS cc_start: 0.7698 (mtmm) cc_final: 0.7423 (mtmm) REVERT: D 91 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.8268 (t) REVERT: H 34 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6655 (mtp) REVERT: H 116 LEU cc_start: 0.5777 (tp) cc_final: 0.5512 (tt) REVERT: H 120 SER cc_start: 0.8405 (p) cc_final: 0.8044 (t) REVERT: K 3 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7329 (mtp) REVERT: K 166 LYS cc_start: 0.7681 (mmtm) cc_final: 0.7380 (mmtm) REVERT: a 409 ASN cc_start: 0.7259 (m-40) cc_final: 0.6971 (m-40) REVERT: b 278 TYR cc_start: 0.7995 (t80) cc_final: 0.7429 (t80) REVERT: b 351 MET cc_start: 0.7480 (tpp) cc_final: 0.7122 (tpt) REVERT: c 321 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7132 (mp10) REVERT: c 368 LYS cc_start: 0.8204 (tttm) cc_final: 0.7974 (tttp) REVERT: c 375 THR cc_start: 0.7908 (p) cc_final: 0.7633 (p) outliers start: 50 outliers final: 29 residues processed: 313 average time/residue: 1.0057 time to fit residues: 358.7865 Evaluate side-chains 319 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 286 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 3 MET Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 398 HIS Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain b residue 293 PHE Chi-restraints excluded: chain c residue 304 LYS Chi-restraints excluded: chain c residue 321 GLN Chi-restraints excluded: chain c residue 324 GLN Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 404 GLU Chi-restraints excluded: chain c residue 414 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.0000 chunk 22 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 144 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 196 optimal weight: 0.6980 chunk 123 optimal weight: 0.0060 chunk 119 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS C 93 HIS D 30 ASN G 30 ASN H 30 ASN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 324 GLN c 353 ASN ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17648 Z= 0.172 Angle : 0.589 9.723 23909 Z= 0.280 Chirality : 0.044 0.656 2875 Planarity : 0.004 0.047 2931 Dihedral : 10.689 111.685 3430 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.15 % Allowed : 20.28 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.19), residues: 2054 helix: 1.36 (0.30), residues: 343 sheet: 1.02 (0.20), residues: 655 loop : -1.29 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 162 HIS 0.011 0.001 HIS c 354 PHE 0.020 0.001 PHE L 115 TYR 0.016 0.001 TYR B 219 ARG 0.008 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 284 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 THR cc_start: 0.8123 (t) cc_final: 0.7683 (p) REVERT: C 96 MET cc_start: 0.6838 (mmt) cc_final: 0.6489 (mmt) REVERT: D 76 LYS cc_start: 0.7698 (mtmm) cc_final: 0.7428 (mtmm) REVERT: D 91 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8279 (t) REVERT: G 83 MET cc_start: 0.6147 (OUTLIER) cc_final: 0.5898 (mtm) REVERT: H 34 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6681 (mtp) REVERT: H 116 LEU cc_start: 0.5842 (tp) cc_final: 0.5583 (tt) REVERT: H 120 SER cc_start: 0.8403 (p) cc_final: 0.8049 (t) REVERT: K 3 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7385 (mtp) REVERT: K 166 LYS cc_start: 0.7689 (mmtm) cc_final: 0.7388 (mmtm) REVERT: a 359 MET cc_start: 0.8011 (mtp) cc_final: 0.7810 (mtp) REVERT: b 278 TYR cc_start: 0.7979 (t80) cc_final: 0.7430 (t80) REVERT: b 351 MET cc_start: 0.7481 (tpp) cc_final: 0.7121 (tpt) REVERT: c 321 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.6973 (mp10) REVERT: c 368 LYS cc_start: 0.8231 (tttm) cc_final: 0.8017 (tttp) REVERT: c 375 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7646 (p) outliers start: 59 outliers final: 41 residues processed: 314 average time/residue: 1.0299 time to fit residues: 368.9565 Evaluate side-chains 324 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 277 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 3 MET Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain a residue 315 LEU Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 398 HIS Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain b residue 293 PHE Chi-restraints excluded: chain b residue 414 MET Chi-restraints excluded: chain c residue 292 CYS Chi-restraints excluded: chain c residue 304 LYS Chi-restraints excluded: chain c residue 321 GLN Chi-restraints excluded: chain c residue 324 GLN Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 375 THR Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 404 GLU Chi-restraints excluded: chain c residue 414 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 178 optimal weight: 0.0010 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN ** L 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 324 GLN c 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17648 Z= 0.307 Angle : 0.666 11.615 23909 Z= 0.317 Chirality : 0.047 0.688 2875 Planarity : 0.004 0.048 2931 Dihedral : 10.777 112.798 3430 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.47 % Allowed : 20.49 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.19), residues: 2054 helix: 1.37 (0.30), residues: 325 sheet: 1.10 (0.21), residues: 642 loop : -1.39 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 162 HIS 0.011 0.001 HIS c 354 PHE 0.018 0.002 PHE L 115 TYR 0.015 0.002 TYR B 219 ARG 0.007 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 283 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7468 (mtt) REVERT: D 34 MET cc_start: 0.6852 (mmm) cc_final: 0.6175 (mtm) REVERT: D 76 LYS cc_start: 0.7736 (mtmm) cc_final: 0.7453 (mtmm) REVERT: D 91 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8259 (t) REVERT: G 83 MET cc_start: 0.6147 (OUTLIER) cc_final: 0.5926 (mtm) REVERT: H 34 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6810 (mtp) REVERT: H 116 LEU cc_start: 0.5851 (tp) cc_final: 0.5605 (tt) REVERT: H 120 SER cc_start: 0.8531 (p) cc_final: 0.8184 (t) REVERT: K 3 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.6418 (mmm) REVERT: K 166 LYS cc_start: 0.7743 (mmtm) cc_final: 0.7439 (mmtm) REVERT: a 359 MET cc_start: 0.8070 (mtp) cc_final: 0.7864 (mtp) REVERT: b 278 TYR cc_start: 0.8082 (t80) cc_final: 0.7476 (t80) REVERT: b 321 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: b 351 MET cc_start: 0.7482 (tpp) cc_final: 0.7181 (tpt) REVERT: c 321 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.6976 (mp10) REVERT: c 375 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7740 (p) outliers start: 65 outliers final: 43 residues processed: 319 average time/residue: 0.9929 time to fit residues: 362.2107 Evaluate side-chains 332 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 281 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain K residue 3 MET Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain a residue 315 LEU Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 398 HIS Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain b residue 293 PHE Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 414 MET Chi-restraints excluded: chain c residue 304 LYS Chi-restraints excluded: chain c residue 321 GLN Chi-restraints excluded: chain c residue 324 GLN Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 375 THR Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 404 GLU Chi-restraints excluded: chain c residue 414 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 183 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN ** L 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 324 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17648 Z= 0.257 Angle : 0.646 9.892 23909 Z= 0.309 Chirality : 0.046 0.716 2875 Planarity : 0.004 0.049 2931 Dihedral : 10.688 113.176 3430 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.09 % Allowed : 21.45 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.19), residues: 2054 helix: 1.36 (0.30), residues: 325 sheet: 1.07 (0.21), residues: 642 loop : -1.40 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 162 HIS 0.004 0.001 HIS E 186 PHE 0.022 0.001 PHE L 115 TYR 0.018 0.002 TYR c 393 ARG 0.009 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 279 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7466 (mtt) REVERT: A 139 THR cc_start: 0.8149 (t) cc_final: 0.7717 (p) REVERT: B 82 MET cc_start: 0.8040 (ptp) cc_final: 0.7839 (ptp) REVERT: D 34 MET cc_start: 0.6913 (mmm) cc_final: 0.6184 (mtm) REVERT: D 76 LYS cc_start: 0.7728 (mtmm) cc_final: 0.7447 (mtmm) REVERT: D 91 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8318 (t) REVERT: G 83 MET cc_start: 0.6130 (OUTLIER) cc_final: 0.5901 (mtm) REVERT: L 133 LEU cc_start: 0.7202 (mm) cc_final: 0.6898 (tp) REVERT: H 34 MET cc_start: 0.7036 (OUTLIER) cc_final: 0.6757 (mtp) REVERT: H 116 LEU cc_start: 0.5912 (tp) cc_final: 0.5694 (tt) REVERT: H 120 SER cc_start: 0.8522 (p) cc_final: 0.8169 (t) REVERT: K 3 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.6435 (mmm) REVERT: K 166 LYS cc_start: 0.7735 (mmtm) cc_final: 0.7432 (mmtm) REVERT: a 339 LYS cc_start: 0.7693 (ptpp) cc_final: 0.7374 (mtmm) REVERT: b 351 MET cc_start: 0.7484 (tpp) cc_final: 0.7188 (tpt) REVERT: c 321 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.7148 (mp10) REVERT: c 368 LYS cc_start: 0.8326 (tttp) cc_final: 0.7911 (tttp) REVERT: c 375 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7727 (p) outliers start: 58 outliers final: 45 residues processed: 306 average time/residue: 1.0157 time to fit residues: 355.2864 Evaluate side-chains 327 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 275 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain K residue 3 MET Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain a residue 315 LEU Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 398 HIS Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain b residue 293 PHE Chi-restraints excluded: chain b residue 304 LYS Chi-restraints excluded: chain b residue 414 MET Chi-restraints excluded: chain c residue 292 CYS Chi-restraints excluded: chain c residue 304 LYS Chi-restraints excluded: chain c residue 321 GLN Chi-restraints excluded: chain c residue 324 GLN Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 375 THR Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 404 GLU Chi-restraints excluded: chain c residue 414 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 187 optimal weight: 0.0570 chunk 161 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 125 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN ** L 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 324 GLN ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17648 Z= 0.223 Angle : 0.636 11.763 23909 Z= 0.302 Chirality : 0.045 0.710 2875 Planarity : 0.004 0.049 2931 Dihedral : 10.540 112.917 3430 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.99 % Allowed : 22.09 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 2054 helix: 1.40 (0.30), residues: 325 sheet: 1.19 (0.21), residues: 609 loop : -1.30 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 162 HIS 0.012 0.001 HIS c 354 PHE 0.021 0.001 PHE L 115 TYR 0.015 0.001 TYR B 219 ARG 0.009 0.000 ARG E 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 276 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7457 (mtt) REVERT: A 139 THR cc_start: 0.8137 (t) cc_final: 0.7700 (p) REVERT: B 82 MET cc_start: 0.8039 (ptp) cc_final: 0.7832 (ptp) REVERT: D 34 MET cc_start: 0.6877 (mmm) cc_final: 0.6213 (mtm) REVERT: D 76 LYS cc_start: 0.7721 (mtmm) cc_final: 0.7438 (mtmm) REVERT: D 91 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8316 (t) REVERT: G 83 MET cc_start: 0.6126 (OUTLIER) cc_final: 0.5892 (mtm) REVERT: G 206 VAL cc_start: 0.7265 (t) cc_final: 0.7006 (m) REVERT: L 133 LEU cc_start: 0.7192 (mm) cc_final: 0.6900 (tp) REVERT: H 116 LEU cc_start: 0.5912 (tp) cc_final: 0.5705 (tt) REVERT: H 120 SER cc_start: 0.8514 (p) cc_final: 0.8162 (t) REVERT: K 3 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.6480 (mmm) REVERT: K 166 LYS cc_start: 0.7724 (mmtm) cc_final: 0.7422 (mmtm) REVERT: a 339 LYS cc_start: 0.7677 (ptpp) cc_final: 0.7368 (mtmm) REVERT: b 351 MET cc_start: 0.7487 (tpp) cc_final: 0.7219 (tpt) REVERT: c 321 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7137 (mp10) REVERT: c 375 THR cc_start: 0.7918 (OUTLIER) cc_final: 0.7695 (p) outliers start: 56 outliers final: 43 residues processed: 301 average time/residue: 1.0240 time to fit residues: 352.4285 Evaluate side-chains 322 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 273 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain K residue 3 MET Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain a residue 315 LEU Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 398 HIS Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain b residue 293 PHE Chi-restraints excluded: chain b residue 414 MET Chi-restraints excluded: chain c residue 292 CYS Chi-restraints excluded: chain c residue 304 LYS Chi-restraints excluded: chain c residue 321 GLN Chi-restraints excluded: chain c residue 324 GLN Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 375 THR Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 404 GLU Chi-restraints excluded: chain c residue 414 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 149 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN ** L 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 324 GLN ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.161765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.142508 restraints weight = 26244.895| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.29 r_work: 0.3841 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17648 Z= 0.229 Angle : 0.634 10.509 23909 Z= 0.302 Chirality : 0.045 0.699 2875 Planarity : 0.004 0.049 2931 Dihedral : 10.459 112.889 3430 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.83 % Allowed : 22.20 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 2054 helix: 1.41 (0.30), residues: 325 sheet: 0.96 (0.21), residues: 636 loop : -1.26 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 162 HIS 0.012 0.001 HIS c 354 PHE 0.020 0.001 PHE L 115 TYR 0.015 0.001 TYR B 219 ARG 0.009 0.000 ARG H 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6676.19 seconds wall clock time: 118 minutes 15.95 seconds (7095.95 seconds total)