Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 12:00:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyv_26195/04_2023/7tyv_26195.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyv_26195/04_2023/7tyv_26195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyv_26195/04_2023/7tyv_26195.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyv_26195/04_2023/7tyv_26195.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyv_26195/04_2023/7tyv_26195.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyv_26195/04_2023/7tyv_26195.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 10865 2.51 5 N 2853 2.21 5 O 3480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 81": "OD1" <-> "OD2" Residue "a TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 8.40, per 1000 atoms: 0.49 Number of scatterers: 17306 At special positions: 0 Unit cell: (208.24, 198.376, 88.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 3480 8.00 N 2853 7.00 C 10865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 191 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 148 " - pdb=" SG CYS G 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 131 " - pdb=" SG CYS L 191 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 87 " distance=2.04 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 191 " distance=2.04 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.04 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.04 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.03 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.05 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN Q 4 " - " MAN Q 5 " " MAN Q 5 " - " MAN Q 6 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA N 3 " - " MAN N 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 301 " - " ASN A 89 " " NAG A 302 " - " ASN A 109 " " NAG A 303 " - " ASN A 167 " " NAG B 301 " - " ASN B 89 " " NAG B 302 " - " ASN B 109 " " NAG B 303 " - " ASN B 167 " " NAG C 301 " - " ASN C 89 " " NAG C 302 " - " ASN C 109 " " NAG C 303 " - " ASN C 167 " " NAG F 1 " - " ASN A 79 " " NAG I 1 " - " ASN A 99 " " NAG M 1 " - " ASN a 365 " " NAG N 1 " - " ASN B 79 " " NAG O 1 " - " ASN B 99 " " NAG P 1 " - " ASN B 224 " " NAG Q 1 " - " ASN b 365 " " NAG R 1 " - " ASN C 79 " " NAG S 1 " - " ASN C 99 " " NAG T 1 " - " ASN C 224 " " NAG U 1 " - " ASN c 365 " " NAG V 1 " - " ASN A 224 " " NAG a 501 " - " ASN a 373 " " NAG a 502 " - " ASN a 395 " " NAG b 501 " - " ASN b 373 " " NAG c 501 " - " ASN c 373 " Time building additional restraints: 7.14 Conformation dependent library (CDL) restraints added in 2.3 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: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 75 through 79 removed outlier: 3.515A pdb=" N LEU A 78 " --> pdb=" O MET A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 144 removed outlier: 3.761A pdb=" N ILE A 144 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.645A pdb=" N GLY A 160 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'B' and resid 75 through 79 removed outlier: 3.723A pdb=" N LEU B 78 " --> pdb=" O MET B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 130 through 144 removed outlier: 3.682A pdb=" N ILE B 144 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.512A pdb=" N GLY B 160 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 195 Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.656A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.648A pdb=" N ASN C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'C' and resid 238 through 246 removed outlier: 3.700A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.562A pdb=" N LYS D 31 " --> pdb=" O ASN D 28 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.816A pdb=" N THR D 91 " --> pdb=" O ASP D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 199 removed outlier: 3.528A pdb=" N THR D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 125 removed outlier: 3.526A pdb=" N LEU E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS E 123 " --> pdb=" O ASP E 119 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 184 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.775A pdb=" N LYS G 31 " --> pdb=" O ASN G 28 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.746A pdb=" N THR G 91 " --> pdb=" O ASP G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 166 No H-bonds generated for 'chain 'G' and resid 164 through 166' Processing helix chain 'G' and resid 194 through 199 Processing helix chain 'L' and resid 118 through 124 removed outlier: 3.906A pdb=" N LEU L 122 " --> pdb=" O SER L 118 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 185 removed outlier: 3.919A pdb=" N LYS L 185 " --> pdb=" O ALA L 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.964A pdb=" N THR H 91 " --> pdb=" O ASP H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 199 removed outlier: 3.503A pdb=" N LEU H 197 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR H 199 " --> pdb=" O SER H 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 123 removed outlier: 3.739A pdb=" N LYS K 123 " --> pdb=" O ASP K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 185 removed outlier: 3.985A pdb=" N LYS K 185 " --> pdb=" O ALA K 181 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 300 removed outlier: 3.501A pdb=" N VAL a 298 " --> pdb=" O GLY a 294 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS a 300 " --> pdb=" O THR a 296 " (cutoff:3.500A) Processing helix chain 'a' and resid 301 through 303 No H-bonds generated for 'chain 'a' and resid 301 through 303' Processing helix chain 'a' and resid 307 through 324 removed outlier: 3.919A pdb=" N ASP a 311 " --> pdb=" O GLU a 307 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN a 324 " --> pdb=" O LYS a 320 " (cutoff:3.500A) Processing helix chain 'a' and resid 335 through 341 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.832A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 417 removed outlier: 3.650A pdb=" N LYS a 417 " --> pdb=" O GLU a 413 " (cutoff:3.500A) Processing helix chain 'b' and resid 294 through 300 removed outlier: 3.650A pdb=" N VAL b 298 " --> pdb=" O GLY b 294 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS b 300 " --> pdb=" O THR b 296 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 325 removed outlier: 3.718A pdb=" N ASP b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) Processing helix chain 'b' and resid 335 through 341 Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.763A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 417 removed outlier: 3.559A pdb=" N ILE b 403 " --> pdb=" O PHE b 399 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU b 404 " --> pdb=" O SER b 400 " (cutoff:3.500A) Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 removed outlier: 4.092A pdb=" N ASP c 311 " --> pdb=" O GLU c 307 " (cutoff:3.500A) Processing helix chain 'c' and resid 335 through 341 Processing helix chain 'c' and resid 342 through 344 No H-bonds generated for 'chain 'c' and resid 342 through 344' Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.788A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 417 removed outlier: 3.777A pdb=" N ILE c 403 " --> pdb=" O PHE c 399 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 89 removed outlier: 3.507A pdb=" N LYS A 88 " --> pdb=" O HIS A 92 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.829A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 89 removed outlier: 6.840A pdb=" N HIS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR C 225 " --> pdb=" O GLY C 102 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 108 " --> pdb=" O TYR C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.172A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN D 33 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.172A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ARG D 98 " --> pdb=" O ASP D 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.117A pdb=" N TYR D 184 " --> pdb=" O ASP D 152 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS D 172 " --> pdb=" O VAL D 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.117A pdb=" N TYR D 184 " --> pdb=" O ASP D 152 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER D 185 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 159 through 162 removed outlier: 4.599A pdb=" N TYR D 202 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.593A pdb=" N LEU E 10 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP E 102 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP E 34 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.593A pdb=" N LEU E 10 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP E 102 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR E 94 " --> pdb=" O GLN E 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 111 through 115 removed outlier: 6.048A pdb=" N TYR E 170 " --> pdb=" O ASN E 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 141 through 147 removed outlier: 3.625A pdb=" N VAL E 202 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.055A pdb=" N GLY G 10 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN G 33 " --> pdb=" O GLU G 99 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET G 34 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.055A pdb=" N GLY G 10 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG G 98 " --> pdb=" O ASP G 109 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 128 through 131 removed outlier: 6.136A pdb=" N TYR G 184 " --> pdb=" O ASP G 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS G 172 " --> pdb=" O VAL G 189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 128 through 131 removed outlier: 6.136A pdb=" N TYR G 184 " --> pdb=" O ASP G 152 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER G 185 " --> pdb=" O VAL G 177 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 159 through 162 Processing sheet with id=AC6, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'L' and resid 9 through 11 removed outlier: 7.007A pdb=" N LEU L 10 " --> pdb=" O ASP L 102 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP L 34 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 111 through 112 removed outlier: 5.989A pdb=" N TYR L 170 " --> pdb=" O ASN L 135 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 111 through 112 removed outlier: 5.989A pdb=" N TYR L 170 " --> pdb=" O ASN L 135 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 141 through 147 Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.033A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN H 33 " --> pdb=" O GLU H 99 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.033A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE H 100 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA H 108 " --> pdb=" O ILE H 100 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 128 through 131 removed outlier: 6.133A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS H 172 " --> pdb=" O VAL H 189 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 128 through 131 removed outlier: 6.133A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER H 185 " --> pdb=" O VAL H 177 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 159 through 162 Processing sheet with id=AD8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AD9, first strand: chain 'K' and resid 9 through 11 removed outlier: 7.146A pdb=" N LEU K 10 " --> pdb=" O ASP K 102 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP K 34 " --> pdb=" O LEU K 46 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 111 through 112 removed outlier: 6.051A pdb=" N TYR K 170 " --> pdb=" O ASN K 135 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 111 through 112 removed outlier: 6.051A pdb=" N TYR K 170 " --> pdb=" O ASN K 135 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 141 through 147 Processing sheet with id=AE4, first strand: chain 'a' and resid 279 through 280 removed outlier: 3.583A pdb=" N LEU a 280 " --> pdb=" O LYS a 291 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS a 291 " --> pdb=" O LEU a 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AE6, first strand: chain 'b' and resid 279 through 280 removed outlier: 3.550A pdb=" N LYS b 291 " --> pdb=" O LEU b 280 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 279 through 280 removed outlier: 3.806A pdb=" N LYS c 291 " --> pdb=" O LEU c 280 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'c' and resid 388 through 389 715 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.57 Time building geometry restraints manager: 7.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5388 1.35 - 1.47: 4626 1.47 - 1.59: 7475 1.59 - 1.72: 0 1.72 - 1.84: 159 Bond restraints: 17648 Sorted by residual: bond pdb=" C2 MAN M 4 " pdb=" O2 MAN M 4 " ideal model delta sigma weight residual 1.407 1.494 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C1 MAN M 4 " pdb=" C2 MAN M 4 " ideal model delta sigma weight residual 1.526 1.590 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C1 BMA M 3 " pdb=" C2 BMA M 3 " ideal model delta sigma weight residual 1.519 1.565 -0.046 2.00e-02 2.50e+03 5.26e+00 bond pdb=" C5 MAN N 5 " pdb=" O5 MAN N 5 " ideal model delta sigma weight residual 1.418 1.463 -0.045 2.00e-02 2.50e+03 4.98e+00 bond pdb=" C5 MAN R 4 " pdb=" O5 MAN R 4 " ideal model delta sigma weight residual 1.418 1.463 -0.045 2.00e-02 2.50e+03 4.97e+00 ... (remaining 17643 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.29: 400 106.29 - 113.23: 10089 113.23 - 120.18: 5637 120.18 - 127.12: 7606 127.12 - 134.07: 177 Bond angle restraints: 23909 Sorted by residual: angle pdb=" CA CYS c 292 " pdb=" CB CYS c 292 " pdb=" SG CYS c 292 " ideal model delta sigma weight residual 114.40 122.76 -8.36 2.30e+00 1.89e-01 1.32e+01 angle pdb=" C1 MAN M 4 " pdb=" C2 MAN M 4 " pdb=" O2 MAN M 4 " ideal model delta sigma weight residual 106.80 116.87 -10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CA CYS a 292 " pdb=" CB CYS a 292 " pdb=" SG CYS a 292 " ideal model delta sigma weight residual 114.40 121.90 -7.50 2.30e+00 1.89e-01 1.06e+01 angle pdb=" CA CYS b 292 " pdb=" CB CYS b 292 " pdb=" SG CYS b 292 " ideal model delta sigma weight residual 114.40 121.77 -7.37 2.30e+00 1.89e-01 1.03e+01 angle pdb=" C3 MAN U 4 " pdb=" C2 MAN U 4 " pdb=" O2 MAN U 4 " ideal model delta sigma weight residual 111.77 103.90 7.87 3.00e+00 1.11e-01 6.88e+00 ... (remaining 23904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 9063 16.19 - 32.39: 835 32.39 - 48.58: 210 48.58 - 64.78: 28 64.78 - 80.97: 15 Dihedral angle restraints: 10151 sinusoidal: 3998 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 10148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 2864 0.188 - 0.375: 10 0.375 - 0.563: 0 0.563 - 0.750: 0 0.750 - 0.938: 1 Chirality restraints: 2875 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN c 365 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" C5 BMA T 3 " pdb=" C4 BMA T 3 " pdb=" C6 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2872 not shown) Planarity restraints: 2956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN a 365 " -0.030 2.00e-02 2.50e+03 2.85e-02 1.02e+01 pdb=" CG ASN a 365 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN a 365 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN a 365 " 0.032 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE b 361 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO b 362 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO b 362 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO b 362 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE c 411 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.22e+00 pdb=" C ILE c 411 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE c 411 " -0.012 2.00e-02 2.50e+03 pdb=" N THR c 412 " -0.010 2.00e-02 2.50e+03 ... (remaining 2953 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 206 2.65 - 3.21: 14827 3.21 - 3.77: 24366 3.77 - 4.34: 33574 4.34 - 4.90: 57445 Nonbonded interactions: 130418 Sorted by model distance: nonbonded pdb=" OE1 GLU E 192 " pdb=" OG1 THR E 203 " model vdw 2.081 2.440 nonbonded pdb=" OG SER L 31 " pdb=" OG SER L 90 " model vdw 2.120 2.440 nonbonded pdb=" NE2 GLN E 121 " pdb=" O THR E 126 " model vdw 2.169 2.520 nonbonded pdb=" O GLN K 121 " pdb=" OG SER K 124 " model vdw 2.224 2.440 nonbonded pdb=" O GLU c 396 " pdb=" OG SER c 400 " model vdw 2.231 2.440 ... (remaining 130413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 60 through 168 or resid 183 through 246 or resid 301 throu \ gh 303)) selection = (chain 'C' and (resid 60 through 168 or resid 183 through 246 or resid 301 throu \ gh 303)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'M' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'I' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'Q' selection = chain 'U' } ncs_group { reference = (chain 'a' and (resid 260 through 417 or resid 501)) selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 8.520 Check model and map are aligned: 0.240 Set scattering table: 0.130 Process input model: 43.200 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 17648 Z= 0.303 Angle : 0.709 10.066 23909 Z= 0.329 Chirality : 0.049 0.938 2875 Planarity : 0.004 0.047 2931 Dihedral : 13.450 80.972 6094 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 % 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 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 305 average time/residue: 1.0105 time to fit residues: 353.7888 Evaluate side-chains 271 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 1.793 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1961 time to fit residues: 2.8915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.0770 chunk 154 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN E 89 GLN c 324 GLN ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 17648 Z= 0.238 Angle : 0.610 7.981 23909 Z= 0.302 Chirality : 0.044 0.606 2875 Planarity : 0.004 0.047 2931 Dihedral : 4.539 20.780 2252 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 1.55 % 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: -0.14 (0.18), residues: 2054 helix: 0.96 (0.29), residues: 361 sheet: 1.33 (0.21), residues: 608 loop : -1.38 (0.18), residues: 1085 *********************** 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 318 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 289 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 19 residues processed: 295 average time/residue: 1.0400 time to fit residues: 351.9422 Evaluate side-chains 299 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 280 time to evaluate : 1.941 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 4 residues processed: 16 average time/residue: 0.5700 time to fit residues: 13.8374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 185 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 G 30 ASN H 74 ASN ** K 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 354 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 17648 Z= 0.384 Angle : 0.700 8.590 23909 Z= 0.343 Chirality : 0.048 0.608 2875 Planarity : 0.005 0.050 2931 Dihedral : 4.915 18.557 2252 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 3.52 % 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: -0.36 (0.19), residues: 2054 helix: 0.87 (0.29), residues: 343 sheet: 0.84 (0.20), residues: 701 loop : -1.48 (0.19), residues: 1010 *********************** 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 342 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 276 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 40 residues processed: 305 average time/residue: 1.0446 time to fit residues: 365.0693 Evaluate side-chains 308 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 268 time to evaluate : 1.910 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 17 residues processed: 23 average time/residue: 0.3889 time to fit residues: 14.8908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 H 30 ASN K 195 HIS ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 17648 Z= 0.290 Angle : 0.647 10.473 23909 Z= 0.316 Chirality : 0.045 0.600 2875 Planarity : 0.004 0.049 2931 Dihedral : 4.758 16.822 2252 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 3.26 % 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: -0.50 (0.18), residues: 2054 helix: 0.77 (0.29), residues: 361 sheet: 1.01 (0.20), residues: 642 loop : -1.68 (0.17), residues: 1051 *********************** 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 345 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 284 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 34 residues processed: 323 average time/residue: 1.0373 time to fit residues: 386.4321 Evaluate side-chains 309 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 275 time to evaluate : 1.843 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 19 residues processed: 15 average time/residue: 0.3571 time to fit residues: 10.2206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.0980 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 146 optimal weight: 0.2980 chunk 81 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN H 30 ASN c 324 GLN ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 17648 Z= 0.190 Angle : 0.597 8.990 23909 Z= 0.290 Chirality : 0.043 0.579 2875 Planarity : 0.004 0.048 2931 Dihedral : 4.517 15.272 2252 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 3.47 % 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: -0.34 (0.18), residues: 2054 helix: 1.15 (0.30), residues: 343 sheet: 0.96 (0.20), residues: 669 loop : -1.58 (0.18), residues: 1042 *********************** 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 352 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 287 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 41 residues processed: 326 average time/residue: 1.0055 time to fit residues: 377.4462 Evaluate side-chains 322 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 281 time to evaluate : 1.672 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 25 residues processed: 16 average time/residue: 0.4607 time to fit residues: 11.8696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 0.0980 chunk 48 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN D 74 ASN H 30 ASN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 17648 Z= 0.245 Angle : 0.623 8.887 23909 Z= 0.301 Chirality : 0.044 0.576 2875 Planarity : 0.004 0.047 2931 Dihedral : 4.554 16.231 2252 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 3.74 % 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: -0.33 (0.18), residues: 2054 helix: 1.11 (0.30), residues: 343 sheet: 1.12 (0.21), residues: 630 loop : -1.58 (0.17), residues: 1081 *********************** 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 353 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 283 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 48 residues processed: 320 average time/residue: 1.0176 time to fit residues: 375.5159 Evaluate side-chains 331 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 283 time to evaluate : 1.745 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 28 residues processed: 20 average time/residue: 0.5396 time to fit residues: 16.0648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 166 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 123 optimal weight: 0.4980 chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN H 30 ASN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 17648 Z= 0.222 Angle : 0.619 12.020 23909 Z= 0.298 Chirality : 0.044 0.549 2875 Planarity : 0.004 0.046 2931 Dihedral : 4.516 15.630 2252 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 3.42 % 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: -0.32 (0.18), residues: 2054 helix: 1.13 (0.30), residues: 343 sheet: 0.96 (0.21), residues: 657 loop : -1.52 (0.18), residues: 1054 *********************** 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 345 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 281 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 46 residues processed: 320 average time/residue: 1.0288 time to fit residues: 379.1561 Evaluate side-chains 323 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 277 time to evaluate : 1.858 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 29 residues processed: 17 average time/residue: 0.4412 time to fit residues: 12.6951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 133 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN G 30 ASN H 30 ASN K 88 GLN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 17648 Z= 0.255 Angle : 0.635 9.653 23909 Z= 0.307 Chirality : 0.044 0.555 2875 Planarity : 0.004 0.046 2931 Dihedral : 4.574 15.743 2252 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer Outliers : 2.93 % 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: -0.37 (0.18), residues: 2054 helix: 1.10 (0.30), residues: 343 sheet: 0.90 (0.21), residues: 657 loop : -1.54 (0.18), residues: 1054 *********************** 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 337 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 282 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 43 residues processed: 317 average time/residue: 1.0035 time to fit residues: 365.5476 Evaluate side-chains 321 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 278 time to evaluate : 1.860 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 30 residues processed: 13 average time/residue: 0.3316 time to fit residues: 8.6940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.0980 chunk 171 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN G 30 ASN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 17648 Z= 0.257 Angle : 0.648 11.902 23909 Z= 0.310 Chirality : 0.044 0.556 2875 Planarity : 0.004 0.046 2931 Dihedral : 4.586 15.530 2252 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 2.24 % 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: -0.40 (0.18), residues: 2054 helix: 1.09 (0.30), residues: 343 sheet: 0.84 (0.20), residues: 663 loop : -1.54 (0.18), residues: 1048 *********************** 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 325 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 283 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 38 residues processed: 315 average time/residue: 1.0089 time to fit residues: 367.4597 Evaluate side-chains 316 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 278 time to evaluate : 1.905 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 31 residues processed: 8 average time/residue: 0.3095 time to fit residues: 6.3566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 125 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 128 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: D 30 ASN G 30 ASN H 30 ASN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 17648 Z= 0.238 Angle : 0.653 12.585 23909 Z= 0.313 Chirality : 0.044 0.547 2875 Planarity : 0.004 0.048 2931 Dihedral : 4.601 29.816 2252 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 2.40 % 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: -0.39 (0.18), residues: 2054 helix: 1.12 (0.30), residues: 343 sheet: 0.84 (0.20), residues: 663 loop : -1.53 (0.18), residues: 1048 ********************** 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 325 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 280 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 38 residues processed: 313 average time/residue: 1.0346 time to fit residues: 373.5707 Evaluate side-chains 315 residues out of total 1874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 277 time to evaluate : 1.939 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 31 residues processed: 8 average time/residue: 0.4715 time to fit residues: 7.7027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 49 optimal weight: 0.0370 chunk 149 optimal weight: 1.9990 chunk 23 optimal weight: 0.0370 chunk 44 optimal weight: 0.7980 chunk 162 optimal weight: 0.0470 chunk 67 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.2434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN G 30 ASN H 30 ASN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 353 ASN ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.165000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.145952 restraints weight = 26405.202| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.25 r_work: 0.3868 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 17648 Z= 0.155 Angle : 0.592 10.509 23909 Z= 0.283 Chirality : 0.042 0.514 2875 Planarity : 0.004 0.049 2931 Dihedral : 4.295 28.624 2252 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 2054 helix: 1.34 (0.30), residues: 343 sheet: 1.09 (0.21), residues: 622 loop : -1.34 (0.18), residues: 1089 =============================================================================== Job complete usr+sys time: 6406.44 seconds wall clock time: 114 minutes 56.46 seconds (6896.46 seconds total)