Starting phenix.real_space_refine on Sun Jun 15 13:42:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyv_26195/06_2025/7tyv_26195.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyv_26195/06_2025/7tyv_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/cci-nas-00/data/ceres_data/7tyv_26195/06_2025/7tyv_26195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyv_26195/06_2025/7tyv_26195.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyv_26195/06_2025/7tyv_26195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyv_26195/06_2025/7tyv_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. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.62, per 1000 atoms: 0.67 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 - 3.00 Amino acid : True - 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: 4.89 Conformation dependent library (CDL) restraints added in 2.0 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: 2.76 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: 6.30 Time building geometry restraints manager: 5.39 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: 0.00 - 2.01: 23351 2.01 - 4.03: 428 4.03 - 6.04: 100 6.04 - 8.05: 28 8.05 - 10.07: 2 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 3.040 nonbonded pdb=" OG SER L 31 " pdb=" OG SER L 90 " model vdw 2.120 3.040 nonbonded pdb=" NE2 GLN E 121 " pdb=" O THR E 126 " model vdw 2.169 3.120 nonbonded pdb=" O GLN K 121 " pdb=" OG SER K 124 " model vdw 2.224 3.040 nonbonded pdb=" O GLU c 396 " pdb=" OG SER c 400 " model vdw 2.231 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 42.430 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: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 42.190 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:34.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.800 ------------------------------------------------------------------------------- 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 17733 Z= 0.215 Angle : 0.750 15.303 24137 Z= 0.339 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 25) link_NAG-ASN : angle 3.17131 ( 75) link_ALPHA1-6 : bond 0.00505 ( 3) link_ALPHA1-6 : angle 1.27723 ( 9) link_BETA1-4 : bond 0.00690 ( 19) link_BETA1-4 : angle 2.37127 ( 57) link_ALPHA1-2 : bond 0.01140 ( 5) link_ALPHA1-2 : angle 4.20676 ( 15) link_ALPHA1-3 : bond 0.00797 ( 6) link_ALPHA1-3 : angle 1.93948 ( 18) hydrogen bonds : bond 0.14509 ( 664) hydrogen bonds : angle 6.26959 ( 1809) SS BOND : bond 0.00796 ( 27) SS BOND : angle 1.37184 ( 54) covalent geometry : bond 0.00461 (17648) covalent geometry : angle 0.70948 (23909) *********************** 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 to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.834 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: 1.1657 time to fit residues: 406.7441 Evaluate side-chains 270 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 1.761 ------------------------------------------------------------------------------- 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: 0.0570 chunk 154 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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 ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 195 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.163445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.144334 restraints weight = 26156.486| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.23 r_work: 0.3856 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17733 Z= 0.164 Angle : 0.681 15.717 24137 Z= 0.323 Chirality : 0.046 0.680 2875 Planarity : 0.004 0.048 2931 Dihedral : 14.307 113.855 3430 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.49 % Allowed : 11.21 % 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: -0.05 (0.19), residues: 2054 helix: 1.08 (0.30), residues: 343 sheet: 1.32 (0.21), residues: 608 loop : -1.25 (0.18), residues: 1103 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 0.017 0.001 PHE L 115 TYR 0.013 0.001 TYR A 217 ARG 0.007 0.000 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 25) link_NAG-ASN : angle 2.84602 ( 75) link_ALPHA1-6 : bond 0.01310 ( 3) link_ALPHA1-6 : angle 2.05655 ( 9) link_BETA1-4 : bond 0.00727 ( 19) link_BETA1-4 : angle 2.25736 ( 57) link_ALPHA1-2 : bond 0.01476 ( 5) link_ALPHA1-2 : angle 4.75859 ( 15) link_ALPHA1-3 : bond 0.01813 ( 6) link_ALPHA1-3 : angle 1.61106 ( 18) hydrogen bonds : bond 0.03701 ( 664) hydrogen bonds : angle 5.11320 ( 1809) SS BOND : bond 0.00808 ( 27) SS BOND : angle 1.36492 ( 54) covalent geometry : bond 0.00376 (17648) covalent geometry : angle 0.63907 (23909) *********************** 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 320 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 THR cc_start: 0.8420 (p) cc_final: 0.8134 (p) REVERT: B 219 TYR cc_start: 0.6889 (m-80) cc_final: 0.6608 (m-80) REVERT: D 76 LYS cc_start: 0.8243 (mtmm) cc_final: 0.8038 (mtmm) REVERT: E 133 LEU cc_start: 0.7468 (mm) cc_final: 0.7220 (mp) REVERT: L 3 MET cc_start: 0.7782 (mtm) cc_final: 0.7462 (mtm) REVERT: L 185 LYS cc_start: 0.8615 (pttm) cc_final: 0.8257 (ptpp) REVERT: H 34 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7172 (mtp) REVERT: H 120 SER cc_start: 0.8574 (p) cc_final: 0.8184 (t) REVERT: K 105 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7420 (ttm170) REVERT: K 185 LYS cc_start: 0.8475 (pttm) cc_final: 0.8266 (ptpp) REVERT: b 409 ASN cc_start: 0.7731 (m-40) cc_final: 0.7520 (m-40) REVERT: c 279 CYS cc_start: 0.7468 (t) cc_final: 0.7210 (t) outliers start: 28 outliers final: 20 residues processed: 302 average time/residue: 1.0106 time to fit residues: 348.4980 Evaluate side-chains 304 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 282 time to evaluate : 1.885 ------------------------------------------------------------------------------- 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 113 ILE Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 29 SER 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 8 SER Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 105 ARG 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 414 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 125 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 89 optimal weight: 0.0050 chunk 175 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 185 optimal weight: 0.0980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** K 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.164087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.144699 restraints weight = 26378.564| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.32 r_work: 0.3856 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17733 Z= 0.125 Angle : 0.639 15.089 24137 Z= 0.298 Chirality : 0.045 0.657 2875 Planarity : 0.004 0.046 2931 Dihedral : 12.831 114.355 3430 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.35 % Allowed : 13.93 % Favored : 83.72 % 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: 0.06 (0.19), residues: 2054 helix: 1.39 (0.30), residues: 325 sheet: 1.27 (0.20), residues: 635 loop : -1.21 (0.18), residues: 1094 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 0.019 0.001 PHE L 115 TYR 0.013 0.001 TYR H 59 ARG 0.009 0.000 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 25) link_NAG-ASN : angle 2.70640 ( 75) link_ALPHA1-6 : bond 0.01531 ( 3) link_ALPHA1-6 : angle 2.15624 ( 9) link_BETA1-4 : bond 0.00630 ( 19) link_BETA1-4 : angle 2.12458 ( 57) link_ALPHA1-2 : bond 0.01623 ( 5) link_ALPHA1-2 : angle 4.41187 ( 15) link_ALPHA1-3 : bond 0.01713 ( 6) link_ALPHA1-3 : angle 1.70336 ( 18) hydrogen bonds : bond 0.03228 ( 664) hydrogen bonds : angle 4.80451 ( 1809) SS BOND : bond 0.00641 ( 27) SS BOND : angle 1.26709 ( 54) covalent geometry : bond 0.00275 (17648) covalent geometry : angle 0.59939 (23909) *********************** 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 335 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 291 time to evaluate : 1.992 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: 0.8584 (OUTLIER) cc_final: 0.8314 (mtt) REVERT: B 77 THR cc_start: 0.8401 (p) cc_final: 0.8137 (p) REVERT: B 219 TYR cc_start: 0.6918 (m-80) cc_final: 0.6607 (m-80) REVERT: C 96 MET cc_start: 0.7190 (mmt) cc_final: 0.6883 (mmt) REVERT: D 76 LYS cc_start: 0.8314 (mtmm) cc_final: 0.8067 (mtmm) REVERT: D 91 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8325 (t) REVERT: E 133 LEU cc_start: 0.7421 (mm) cc_final: 0.7201 (mp) REVERT: L 3 MET cc_start: 0.7788 (mtm) cc_final: 0.7576 (mtm) REVERT: L 133 LEU cc_start: 0.7550 (mm) cc_final: 0.7288 (tp) REVERT: L 185 LYS cc_start: 0.8618 (pttm) cc_final: 0.8220 (ptpp) REVERT: H 34 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7081 (mtp) REVERT: H 120 SER cc_start: 0.8574 (p) cc_final: 0.8188 (t) REVERT: a 410 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7558 (mtm) REVERT: b 351 MET cc_start: 0.8014 (tpp) cc_final: 0.7765 (tpt) outliers start: 44 outliers final: 24 residues processed: 315 average time/residue: 1.1036 time to fit residues: 396.0034 Evaluate side-chains 305 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 277 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET 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 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 29 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain L residue 8 SER 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 8 SER Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 29 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 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 410 MET 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 198 optimal weight: 0.6980 chunk 165 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 170 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 HIS D 30 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN ** K 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 409 ASN c 324 GLN ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.163538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.144500 restraints weight = 26091.287| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.24 r_work: 0.3850 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17733 Z= 0.155 Angle : 0.665 15.191 24137 Z= 0.310 Chirality : 0.046 0.685 2875 Planarity : 0.004 0.046 2931 Dihedral : 11.970 113.035 3430 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.20 % Allowed : 15.37 % Favored : 81.43 % 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: 0.03 (0.19), residues: 2054 helix: 1.23 (0.30), residues: 343 sheet: 1.36 (0.21), residues: 612 loop : -1.24 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 162 HIS 0.014 0.001 HIS c 354 PHE 0.018 0.001 PHE L 115 TYR 0.012 0.001 TYR H 202 ARG 0.009 0.000 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 25) link_NAG-ASN : angle 2.80227 ( 75) link_ALPHA1-6 : bond 0.01722 ( 3) link_ALPHA1-6 : angle 2.47236 ( 9) link_BETA1-4 : bond 0.00615 ( 19) link_BETA1-4 : angle 2.08778 ( 57) link_ALPHA1-2 : bond 0.01596 ( 5) link_ALPHA1-2 : angle 4.46676 ( 15) link_ALPHA1-3 : bond 0.01610 ( 6) link_ALPHA1-3 : angle 1.78957 ( 18) hydrogen bonds : bond 0.03328 ( 664) hydrogen bonds : angle 4.77300 ( 1809) SS BOND : bond 0.00752 ( 27) SS BOND : angle 1.57666 ( 54) covalent geometry : bond 0.00360 (17648) covalent geometry : angle 0.62293 (23909) *********************** 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 347 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 287 time to evaluate : 2.109 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: 0.8576 (OUTLIER) cc_final: 0.8311 (mtt) REVERT: A 96 MET cc_start: 0.6898 (mmp) cc_final: 0.6686 (mmt) REVERT: B 219 TYR cc_start: 0.6951 (m-80) cc_final: 0.6611 (m-80) REVERT: C 96 MET cc_start: 0.7209 (mmt) cc_final: 0.6905 (mmt) REVERT: D 76 LYS cc_start: 0.8314 (mtmm) cc_final: 0.8065 (mtmm) REVERT: E 133 LEU cc_start: 0.7350 (mm) cc_final: 0.7145 (mp) REVERT: G 83 MET cc_start: 0.6035 (OUTLIER) cc_final: 0.5639 (mtm) REVERT: L 3 MET cc_start: 0.7787 (mtm) cc_final: 0.7549 (mtm) REVERT: H 34 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7151 (mtp) REVERT: a 410 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7547 (mtm) REVERT: b 351 MET cc_start: 0.7991 (tpp) cc_final: 0.7751 (tpt) REVERT: c 321 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7472 (mp10) outliers start: 60 outliers final: 35 residues processed: 318 average time/residue: 1.2543 time to fit residues: 459.0434 Evaluate side-chains 321 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 281 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 87 THR 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 101 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 E residue 8 SER Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 77 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 104 SER Chi-restraints excluded: chain G residue 105 THR 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 203 THR Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 29 SER 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 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 410 MET 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 39 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 HIS D 30 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN ** K 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 HIS b 409 ASN c 324 GLN ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.163501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.144317 restraints weight = 26365.560| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.26 r_work: 0.3846 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17733 Z= 0.155 Angle : 0.664 15.223 24137 Z= 0.310 Chirality : 0.046 0.672 2875 Planarity : 0.004 0.046 2931 Dihedral : 11.568 112.034 3430 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.31 % Allowed : 16.86 % Favored : 79.83 % 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: 0.03 (0.19), residues: 2054 helix: 1.40 (0.31), residues: 325 sheet: 1.24 (0.21), residues: 639 loop : -1.23 (0.18), residues: 1090 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 0.011 0.001 TYR H 202 ARG 0.008 0.000 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 25) link_NAG-ASN : angle 2.76914 ( 75) link_ALPHA1-6 : bond 0.01795 ( 3) link_ALPHA1-6 : angle 2.61232 ( 9) link_BETA1-4 : bond 0.00589 ( 19) link_BETA1-4 : angle 1.99408 ( 57) link_ALPHA1-2 : bond 0.01565 ( 5) link_ALPHA1-2 : angle 4.46804 ( 15) link_ALPHA1-3 : bond 0.01597 ( 6) link_ALPHA1-3 : angle 1.81413 ( 18) hydrogen bonds : bond 0.03245 ( 664) hydrogen bonds : angle 4.76438 ( 1809) SS BOND : bond 0.00731 ( 27) SS BOND : angle 1.68547 ( 54) covalent geometry : bond 0.00360 (17648) covalent geometry : angle 0.62236 (23909) *********************** 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 344 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 282 time to evaluate : 1.646 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: 0.8589 (OUTLIER) cc_final: 0.8296 (mtt) REVERT: A 96 MET cc_start: 0.6906 (mmp) cc_final: 0.6682 (mmt) REVERT: B 219 TYR cc_start: 0.6975 (m-80) cc_final: 0.6629 (m-80) REVERT: C 96 MET cc_start: 0.7186 (mmt) cc_final: 0.6881 (mmt) REVERT: D 34 MET cc_start: 0.7557 (mmt) cc_final: 0.6867 (mtt) REVERT: D 76 LYS cc_start: 0.8324 (mtmm) cc_final: 0.8063 (mtmm) REVERT: D 91 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8340 (t) REVERT: E 123 LYS cc_start: 0.6770 (mtmm) cc_final: 0.6467 (mmmt) REVERT: E 133 LEU cc_start: 0.7360 (mm) cc_final: 0.7157 (mp) REVERT: G 83 MET cc_start: 0.6041 (OUTLIER) cc_final: 0.5642 (mtm) REVERT: L 3 MET cc_start: 0.7771 (mtm) cc_final: 0.7429 (mtm) REVERT: L 105 ARG cc_start: 0.7293 (ttt90) cc_final: 0.7085 (ttt90) REVERT: L 133 LEU cc_start: 0.7588 (mm) cc_final: 0.7321 (tp) REVERT: H 34 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7157 (mtp) REVERT: H 120 SER cc_start: 0.8673 (p) cc_final: 0.8294 (t) REVERT: K 3 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.5690 (mtt) REVERT: a 410 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7574 (mtm) REVERT: b 351 MET cc_start: 0.7989 (tpp) cc_final: 0.7755 (tpt) outliers start: 62 outliers final: 38 residues processed: 310 average time/residue: 1.0006 time to fit residues: 355.7021 Evaluate side-chains 320 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 276 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 87 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 67 GLU 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 8 SER Chi-restraints excluded: chain E residue 29 SER 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 G residue 83 MET Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 105 THR 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 129 VAL Chi-restraints excluded: chain L residue 203 THR 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 27 SER Chi-restraints excluded: chain K residue 29 SER 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 304 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 0.0030 chunk 101 optimal weight: 0.4980 chunk 151 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 115 optimal weight: 0.3980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 HIS D 30 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN ** L 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN ** K 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 409 ASN c 324 GLN ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.162864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.143710 restraints weight = 26324.655| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.26 r_work: 0.3842 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17733 Z= 0.173 Angle : 0.687 15.299 24137 Z= 0.320 Chirality : 0.046 0.673 2875 Planarity : 0.004 0.046 2931 Dihedral : 11.322 111.787 3430 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.74 % Allowed : 17.72 % Favored : 78.55 % 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: 1.16 (0.30), residues: 343 sheet: 1.12 (0.21), residues: 648 loop : -1.43 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 162 HIS 0.011 0.001 HIS c 354 PHE 0.019 0.001 PHE L 115 TYR 0.012 0.002 TYR H 202 ARG 0.008 0.000 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 25) link_NAG-ASN : angle 2.83515 ( 75) link_ALPHA1-6 : bond 0.01821 ( 3) link_ALPHA1-6 : angle 2.79912 ( 9) link_BETA1-4 : bond 0.00586 ( 19) link_BETA1-4 : angle 1.96281 ( 57) link_ALPHA1-2 : bond 0.01461 ( 5) link_ALPHA1-2 : angle 4.48902 ( 15) link_ALPHA1-3 : bond 0.01519 ( 6) link_ALPHA1-3 : angle 1.85051 ( 18) hydrogen bonds : bond 0.03344 ( 664) hydrogen bonds : angle 4.78230 ( 1809) SS BOND : bond 0.00788 ( 27) SS BOND : angle 1.77285 ( 54) covalent geometry : bond 0.00408 (17648) covalent geometry : angle 0.64591 (23909) *********************** 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 347 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 277 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8295 (mtt) REVERT: A 96 MET cc_start: 0.6925 (mmp) cc_final: 0.6700 (mmt) REVERT: B 219 TYR cc_start: 0.7019 (m-80) cc_final: 0.6766 (m-80) REVERT: C 244 LEU cc_start: 0.8268 (tt) cc_final: 0.8037 (tt) REVERT: D 34 MET cc_start: 0.7564 (mmt) cc_final: 0.6872 (mtt) REVERT: D 76 LYS cc_start: 0.8327 (mtmm) cc_final: 0.8067 (mtmm) REVERT: D 91 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8364 (t) REVERT: E 123 LYS cc_start: 0.6700 (mtmm) cc_final: 0.6480 (mmmt) REVERT: E 133 LEU cc_start: 0.7385 (mm) cc_final: 0.7136 (mt) REVERT: G 83 MET cc_start: 0.6112 (OUTLIER) cc_final: 0.5561 (mtm) REVERT: L 3 MET cc_start: 0.7800 (mtm) cc_final: 0.7481 (mtm) REVERT: L 133 LEU cc_start: 0.7617 (mm) cc_final: 0.7343 (tp) REVERT: H 34 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7160 (mtp) REVERT: H 120 SER cc_start: 0.8657 (p) cc_final: 0.8288 (t) REVERT: K 3 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.5702 (mtt) REVERT: a 410 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7576 (mtm) REVERT: b 351 MET cc_start: 0.8005 (tpp) cc_final: 0.7765 (tpt) REVERT: c 325 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7117 (mtt90) REVERT: c 409 ASN cc_start: 0.7503 (m-40) cc_final: 0.7251 (m-40) outliers start: 70 outliers final: 43 residues processed: 312 average time/residue: 1.1117 time to fit residues: 397.4366 Evaluate side-chains 324 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 274 time to evaluate : 1.735 ------------------------------------------------------------------------------- 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 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 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 160 VAL 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 29 SER 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 23 THR Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 105 THR 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 129 VAL Chi-restraints excluded: chain L residue 203 THR 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 27 SER Chi-restraints excluded: chain K residue 29 SER 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 304 LYS Chi-restraints excluded: chain c residue 324 GLN Chi-restraints excluded: chain c residue 325 ARG 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 68 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 152 optimal weight: 0.0570 chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 203 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 HIS D 30 ASN ** E 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN ** L 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 409 ASN c 324 GLN ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.163002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.143693 restraints weight = 26138.831| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.30 r_work: 0.3841 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17733 Z= 0.160 Angle : 0.685 15.241 24137 Z= 0.316 Chirality : 0.046 0.671 2875 Planarity : 0.004 0.048 2931 Dihedral : 11.118 112.206 3430 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.68 % Allowed : 18.20 % Favored : 78.12 % 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: -0.21 (0.18), residues: 2054 helix: 1.17 (0.30), residues: 343 sheet: 1.12 (0.21), residues: 636 loop : -1.44 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 162 HIS 0.010 0.001 HIS c 354 PHE 0.020 0.001 PHE L 115 TYR 0.011 0.001 TYR H 202 ARG 0.010 0.000 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 25) link_NAG-ASN : angle 2.83268 ( 75) link_ALPHA1-6 : bond 0.01842 ( 3) link_ALPHA1-6 : angle 2.75631 ( 9) link_BETA1-4 : bond 0.00561 ( 19) link_BETA1-4 : angle 1.89239 ( 57) link_ALPHA1-2 : bond 0.01523 ( 5) link_ALPHA1-2 : angle 4.48113 ( 15) link_ALPHA1-3 : bond 0.01521 ( 6) link_ALPHA1-3 : angle 1.87416 ( 18) hydrogen bonds : bond 0.03251 ( 664) hydrogen bonds : angle 4.74492 ( 1809) SS BOND : bond 0.00762 ( 27) SS BOND : angle 1.73167 ( 54) covalent geometry : bond 0.00377 (17648) covalent geometry : angle 0.64438 (23909) *********************** 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 346 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 277 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8289 (mtt) REVERT: A 96 MET cc_start: 0.6898 (mmp) cc_final: 0.6670 (mmt) REVERT: B 219 TYR cc_start: 0.7027 (m-80) cc_final: 0.6752 (m-80) REVERT: D 34 MET cc_start: 0.7582 (mmt) cc_final: 0.6912 (mtt) REVERT: D 76 LYS cc_start: 0.8339 (mtmm) cc_final: 0.8062 (mtmm) REVERT: D 91 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8343 (t) REVERT: E 105 ARG cc_start: 0.7166 (tmt90) cc_final: 0.6920 (tmt90) REVERT: E 123 LYS cc_start: 0.6781 (mtmm) cc_final: 0.6495 (mmmt) REVERT: E 133 LEU cc_start: 0.7361 (mm) cc_final: 0.7127 (mt) REVERT: G 83 MET cc_start: 0.6041 (OUTLIER) cc_final: 0.5479 (mtm) REVERT: G 206 VAL cc_start: 0.7282 (t) cc_final: 0.7028 (m) REVERT: L 3 MET cc_start: 0.7813 (mtm) cc_final: 0.7515 (mtm) REVERT: L 133 LEU cc_start: 0.7593 (mm) cc_final: 0.7330 (tp) REVERT: H 34 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7152 (mtp) REVERT: H 116 LEU cc_start: 0.6347 (tp) cc_final: 0.6092 (tt) REVERT: H 120 SER cc_start: 0.8664 (p) cc_final: 0.8291 (t) REVERT: K 3 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.5719 (mtt) REVERT: a 410 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7484 (mtm) REVERT: b 279 CYS cc_start: 0.7328 (t) cc_final: 0.7126 (m) REVERT: b 351 MET cc_start: 0.7997 (tpp) cc_final: 0.7766 (tpt) REVERT: c 321 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7568 (mp10) REVERT: c 325 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7130 (mtt90) REVERT: c 409 ASN cc_start: 0.7424 (m-40) cc_final: 0.7171 (m-40) outliers start: 69 outliers final: 49 residues processed: 310 average time/residue: 1.1119 time to fit residues: 391.8887 Evaluate side-chains 331 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 274 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 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 101 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 134 MET 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 160 VAL 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 29 SER 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 23 THR Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 105 THR 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 46 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 203 THR 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 29 SER Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 398 HIS 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 304 LYS Chi-restraints excluded: chain c residue 321 GLN Chi-restraints excluded: chain c residue 324 GLN Chi-restraints excluded: chain c residue 325 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 155 optimal weight: 0.6980 chunk 169 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 0.0570 chunk 165 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN E 186 HIS ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 321 GLN b 409 ASN c 324 GLN c 354 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.163496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.144270 restraints weight = 26139.559| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.30 r_work: 0.3851 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17733 Z= 0.132 Angle : 0.660 15.200 24137 Z= 0.305 Chirality : 0.045 0.661 2875 Planarity : 0.004 0.048 2931 Dihedral : 10.902 112.123 3430 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.63 % Allowed : 18.78 % Favored : 77.59 % 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: 0.02 (0.19), residues: 2054 helix: 1.48 (0.31), residues: 325 sheet: 1.31 (0.21), residues: 594 loop : -1.21 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 162 HIS 0.011 0.001 HIS c 354 PHE 0.021 0.001 PHE L 115 TYR 0.010 0.001 TYR H 202 ARG 0.009 0.000 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 25) link_NAG-ASN : angle 2.81286 ( 75) link_ALPHA1-6 : bond 0.01817 ( 3) link_ALPHA1-6 : angle 2.64097 ( 9) link_BETA1-4 : bond 0.00547 ( 19) link_BETA1-4 : angle 1.81318 ( 57) link_ALPHA1-2 : bond 0.01540 ( 5) link_ALPHA1-2 : angle 4.45956 ( 15) link_ALPHA1-3 : bond 0.01541 ( 6) link_ALPHA1-3 : angle 1.91263 ( 18) hydrogen bonds : bond 0.03038 ( 664) hydrogen bonds : angle 4.65041 ( 1809) SS BOND : bond 0.00656 ( 27) SS BOND : angle 1.41880 ( 54) covalent geometry : bond 0.00301 (17648) covalent geometry : angle 0.62033 (23909) *********************** 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 344 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 276 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8291 (mtt) REVERT: A 96 MET cc_start: 0.6894 (mmp) cc_final: 0.6679 (mmt) REVERT: A 139 THR cc_start: 0.8303 (t) cc_final: 0.7809 (p) REVERT: B 219 TYR cc_start: 0.6999 (m-80) cc_final: 0.6726 (m-80) REVERT: D 34 MET cc_start: 0.7540 (mmt) cc_final: 0.6896 (mtt) REVERT: D 76 LYS cc_start: 0.8311 (mtmm) cc_final: 0.8041 (mtmm) REVERT: D 91 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8336 (t) REVERT: E 105 ARG cc_start: 0.7132 (tmt90) cc_final: 0.6884 (tmt90) REVERT: E 123 LYS cc_start: 0.6771 (mtmm) cc_final: 0.6543 (mmmt) REVERT: E 133 LEU cc_start: 0.7359 (mm) cc_final: 0.7130 (mt) REVERT: G 83 MET cc_start: 0.6044 (OUTLIER) cc_final: 0.5637 (mtm) REVERT: G 206 VAL cc_start: 0.7304 (t) cc_final: 0.7056 (m) REVERT: L 3 MET cc_start: 0.7821 (mtm) cc_final: 0.7529 (mtm) REVERT: L 133 LEU cc_start: 0.7584 (mm) cc_final: 0.7332 (tp) REVERT: L 180 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6717 (tptt) REVERT: H 34 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7129 (mtp) REVERT: H 116 LEU cc_start: 0.6379 (tp) cc_final: 0.6133 (tt) REVERT: H 120 SER cc_start: 0.8563 (p) cc_final: 0.8198 (t) REVERT: K 3 MET cc_start: 0.6520 (OUTLIER) cc_final: 0.5716 (mtt) REVERT: a 410 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7438 (mtm) REVERT: b 351 MET cc_start: 0.7984 (tpp) cc_final: 0.7777 (tpt) REVERT: b 409 ASN cc_start: 0.7650 (m-40) cc_final: 0.7429 (m-40) REVERT: c 321 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7533 (mp10) REVERT: c 325 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7064 (mtt90) REVERT: c 409 ASN cc_start: 0.7411 (m-40) cc_final: 0.7149 (m-40) outliers start: 68 outliers final: 44 residues processed: 310 average time/residue: 1.0498 time to fit residues: 373.1209 Evaluate side-chains 327 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 274 time to evaluate : 1.829 ------------------------------------------------------------------------------- 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 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 101 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 134 MET 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 8 SER Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 29 SER 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 23 THR Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 180 LYS Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain K residue 3 MET Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 398 HIS 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 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 325 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 192 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.162354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.143493 restraints weight = 26441.760| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.20 r_work: 0.3847 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17733 Z= 0.173 Angle : 0.696 15.275 24137 Z= 0.323 Chirality : 0.046 0.669 2875 Planarity : 0.004 0.049 2931 Dihedral : 10.882 112.459 3430 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.31 % Allowed : 19.69 % Favored : 77.00 % 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: -0.21 (0.19), residues: 2054 helix: 1.17 (0.30), residues: 343 sheet: 1.08 (0.21), residues: 648 loop : -1.45 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 162 HIS 0.012 0.001 HIS c 354 PHE 0.021 0.001 PHE L 115 TYR 0.012 0.002 TYR H 202 ARG 0.010 0.000 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 25) link_NAG-ASN : angle 2.86785 ( 75) link_ALPHA1-6 : bond 0.01817 ( 3) link_ALPHA1-6 : angle 2.71657 ( 9) link_BETA1-4 : bond 0.00583 ( 19) link_BETA1-4 : angle 1.89521 ( 57) link_ALPHA1-2 : bond 0.01512 ( 5) link_ALPHA1-2 : angle 4.48947 ( 15) link_ALPHA1-3 : bond 0.01442 ( 6) link_ALPHA1-3 : angle 1.87959 ( 18) hydrogen bonds : bond 0.03318 ( 664) hydrogen bonds : angle 4.74247 ( 1809) SS BOND : bond 0.00792 ( 27) SS BOND : angle 1.91572 ( 54) covalent geometry : bond 0.00408 (17648) covalent geometry : angle 0.65420 (23909) *********************** 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 335 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 273 time to evaluate : 1.696 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: 0.8550 (OUTLIER) cc_final: 0.8285 (mtt) REVERT: A 96 MET cc_start: 0.6897 (mmp) cc_final: 0.6691 (mmt) REVERT: B 219 TYR cc_start: 0.7011 (m-80) cc_final: 0.6767 (m-80) REVERT: D 34 MET cc_start: 0.7491 (mmt) cc_final: 0.6841 (mtt) REVERT: D 76 LYS cc_start: 0.8274 (mtmm) cc_final: 0.8038 (mtmm) REVERT: E 89 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.6845 (tt0) REVERT: E 105 ARG cc_start: 0.7236 (tmt90) cc_final: 0.6949 (tmt90) REVERT: E 123 LYS cc_start: 0.6760 (mtmm) cc_final: 0.6545 (mmmt) REVERT: E 133 LEU cc_start: 0.7411 (mm) cc_final: 0.7178 (mt) REVERT: G 83 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5629 (mtm) REVERT: G 206 VAL cc_start: 0.7402 (t) cc_final: 0.7161 (m) REVERT: L 3 MET cc_start: 0.7778 (mtm) cc_final: 0.7514 (mtm) REVERT: L 133 LEU cc_start: 0.7652 (mm) cc_final: 0.7382 (tp) REVERT: H 34 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7139 (mtp) REVERT: H 116 LEU cc_start: 0.6336 (tp) cc_final: 0.6094 (tt) REVERT: H 120 SER cc_start: 0.8640 (p) cc_final: 0.8279 (t) REVERT: K 3 MET cc_start: 0.6520 (OUTLIER) cc_final: 0.5661 (mtt) REVERT: b 351 MET cc_start: 0.7992 (tpp) cc_final: 0.7749 (tpt) REVERT: c 321 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7595 (mp10) REVERT: c 325 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7054 (mtt90) REVERT: c 409 ASN cc_start: 0.7517 (m-40) cc_final: 0.7255 (m-40) outliers start: 62 outliers final: 46 residues processed: 304 average time/residue: 1.0764 time to fit residues: 372.2482 Evaluate side-chains 323 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 270 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 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 101 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain D residue 70 VAL 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 29 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 203 THR 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 G residue 104 SER Chi-restraints excluded: chain G residue 105 THR 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 77 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 203 THR 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 27 SER Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 398 HIS 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 304 LYS Chi-restraints excluded: chain c residue 321 GLN Chi-restraints excluded: chain c residue 324 GLN Chi-restraints excluded: chain c residue 325 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 135 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 184 optimal weight: 0.3980 chunk 194 optimal weight: 0.1980 chunk 43 optimal weight: 0.0170 chunk 195 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 409 ASN c 324 GLN ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.162592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.143559 restraints weight = 26070.007| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.25 r_work: 0.3843 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17733 Z= 0.122 Angle : 0.657 15.159 24137 Z= 0.304 Chirality : 0.044 0.653 2875 Planarity : 0.004 0.050 2931 Dihedral : 10.688 111.970 3430 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.67 % Allowed : 20.49 % Favored : 76.84 % 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: 0.05 (0.19), residues: 2054 helix: 1.51 (0.30), residues: 325 sheet: 1.32 (0.21), residues: 594 loop : -1.20 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 162 HIS 0.011 0.001 HIS c 354 PHE 0.022 0.001 PHE L 115 TYR 0.010 0.001 TYR A 219 ARG 0.009 0.000 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 25) link_NAG-ASN : angle 2.69820 ( 75) link_ALPHA1-6 : bond 0.01792 ( 3) link_ALPHA1-6 : angle 2.51344 ( 9) link_BETA1-4 : bond 0.00543 ( 19) link_BETA1-4 : angle 1.76789 ( 57) link_ALPHA1-2 : bond 0.01486 ( 5) link_ALPHA1-2 : angle 4.44694 ( 15) link_ALPHA1-3 : bond 0.01509 ( 6) link_ALPHA1-3 : angle 1.94336 ( 18) hydrogen bonds : bond 0.02936 ( 664) hydrogen bonds : angle 4.59417 ( 1809) SS BOND : bond 0.00708 ( 27) SS BOND : angle 1.31453 ( 54) covalent geometry : bond 0.00276 (17648) covalent geometry : angle 0.61933 (23909) ********************** 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 324 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 274 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8281 (mtt) REVERT: A 80 MET cc_start: 0.7384 (mtp) cc_final: 0.7000 (mtm) REVERT: A 139 THR cc_start: 0.8315 (t) cc_final: 0.7848 (p) REVERT: B 219 TYR cc_start: 0.6960 (m-80) cc_final: 0.6707 (m-80) REVERT: D 34 MET cc_start: 0.7488 (mmt) cc_final: 0.6966 (mtt) REVERT: D 76 LYS cc_start: 0.8264 (mtmm) cc_final: 0.8027 (mtmm) REVERT: E 105 ARG cc_start: 0.7176 (tmt90) cc_final: 0.6911 (tmt90) REVERT: E 133 LEU cc_start: 0.7380 (mm) cc_final: 0.7163 (mt) REVERT: G 206 VAL cc_start: 0.7342 (t) cc_final: 0.7097 (m) REVERT: L 3 MET cc_start: 0.7850 (mtm) cc_final: 0.7491 (mtm) REVERT: L 133 LEU cc_start: 0.7606 (mm) cc_final: 0.7359 (tp) REVERT: H 116 LEU cc_start: 0.6382 (tp) cc_final: 0.6150 (tt) REVERT: H 120 SER cc_start: 0.8663 (p) cc_final: 0.8293 (t) REVERT: K 3 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.5695 (mtt) REVERT: a 339 LYS cc_start: 0.8149 (ptpp) cc_final: 0.7831 (mtmm) REVERT: a 410 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7449 (mtm) REVERT: c 321 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: c 325 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7215 (mtt90) outliers start: 50 outliers final: 41 residues processed: 300 average time/residue: 1.0617 time to fit residues: 362.7439 Evaluate side-chains 319 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 273 time to evaluate : 1.669 ------------------------------------------------------------------------------- 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 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 70 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 29 SER 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 23 THR Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 105 THR 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 112 VAL Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain K residue 3 MET Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 398 HIS 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 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 325 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 0 optimal weight: 2.9990 chunk 89 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 162 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 187 optimal weight: 0.5980 chunk 83 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 HIS ** 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 = 0.4187 r_free = 0.4187 target = 0.162584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.143569 restraints weight = 25971.814| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.24 r_work: 0.3844 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17733 Z= 0.129 Angle : 0.662 15.193 24137 Z= 0.306 Chirality : 0.045 0.647 2875 Planarity : 0.004 0.050 2931 Dihedral : 10.598 111.632 3430 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.56 % Allowed : 20.81 % Favored : 76.63 % 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: -0.06 (0.19), residues: 2054 helix: 1.30 (0.30), residues: 343 sheet: 1.33 (0.21), residues: 594 loop : -1.32 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 162 HIS 0.012 0.001 HIS c 354 PHE 0.019 0.001 PHE L 115 TYR 0.009 0.001 TYR H 202 ARG 0.010 0.000 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 25) link_NAG-ASN : angle 2.68491 ( 75) link_ALPHA1-6 : bond 0.01759 ( 3) link_ALPHA1-6 : angle 2.50879 ( 9) link_BETA1-4 : bond 0.00540 ( 19) link_BETA1-4 : angle 1.74885 ( 57) link_ALPHA1-2 : bond 0.01518 ( 5) link_ALPHA1-2 : angle 4.45337 ( 15) link_ALPHA1-3 : bond 0.01480 ( 6) link_ALPHA1-3 : angle 1.94799 ( 18) hydrogen bonds : bond 0.02961 ( 664) hydrogen bonds : angle 4.59208 ( 1809) SS BOND : bond 0.00673 ( 27) SS BOND : angle 1.78306 ( 54) covalent geometry : bond 0.00296 (17648) covalent geometry : angle 0.62251 (23909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18549.06 seconds wall clock time: 325 minutes 54.51 seconds (19554.51 seconds total)