Starting phenix.real_space_refine on Fri Feb 16 19:01:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pke_13469/02_2024/7pke_13469_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pke_13469/02_2024/7pke_13469.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pke_13469/02_2024/7pke_13469_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pke_13469/02_2024/7pke_13469_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pke_13469/02_2024/7pke_13469_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pke_13469/02_2024/7pke_13469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pke_13469/02_2024/7pke_13469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pke_13469/02_2024/7pke_13469_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pke_13469/02_2024/7pke_13469_trim_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Ca 10 9.91 5 P 5 5.49 5 S 20 5.16 5 C 5315 2.51 5 N 1310 2.21 5 O 1570 1.98 5 H 7970 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 3": "OD1" <-> "OD2" Residue "E TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E ASP 163": "OD1" <-> "OD2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 193": "OE1" <-> "OE2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 3": "OD1" <-> "OD2" Residue "D ASP 16": "OD1" <-> "OD2" Residue "D TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D ASP 163": "OD1" <-> "OD2" Residue "D ASP 169": "OD1" <-> "OD2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 70": "OD1" <-> "OD2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 3": "OD1" <-> "OD2" Residue "B ASP 16": "OD1" <-> "OD2" Residue "B TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 3": "OD1" <-> "OD2" Residue "A ASP 16": "OD1" <-> "OD2" Residue "A TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A ASP 169": "OD1" <-> "OD2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16200 Number of models: 1 Model: "" Number of chains: 15 Chain: "E" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "D" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "C" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "B" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "A" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 7.56, per 1000 atoms: 0.47 Number of scatterers: 16200 At special positions: 0 Unit cell: (112.86, 114.532, 53.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 10 19.99 S 20 16.00 P 5 15.00 O 1570 8.00 N 1310 7.00 C 5315 6.00 H 7970 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 97 " 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 Time building additional restraints: 13.60 Conformation dependent library (CDL) restraints added in 1.7 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 15 sheets defined 7.8% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 168 through 175 removed outlier: 3.743A pdb=" N THR E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 168 through 175 Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing sheet with id= A, first strand: chain 'E' and resid 199 through 202 Processing sheet with id= B, first strand: chain 'E' and resid 192 through 195 removed outlier: 3.933A pdb=" N ILE E 133 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE E 65 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER E 53 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE E 63 " --> pdb=" O SER E 53 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 34 through 36 Processing sheet with id= D, first strand: chain 'D' and resid 199 through 202 Processing sheet with id= E, first strand: chain 'D' and resid 192 through 195 removed outlier: 3.955A pdb=" N ILE D 133 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE D 65 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER D 53 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE D 63 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 34 through 36 Processing sheet with id= G, first strand: chain 'C' and resid 199 through 202 Processing sheet with id= H, first strand: chain 'C' and resid 192 through 195 removed outlier: 3.932A pdb=" N ILE C 133 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE C 65 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER C 53 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE C 63 " --> pdb=" O SER C 53 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 34 through 36 Processing sheet with id= J, first strand: chain 'B' and resid 199 through 202 Processing sheet with id= K, first strand: chain 'B' and resid 192 through 195 removed outlier: 3.966A pdb=" N ILE B 133 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE B 65 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N SER B 53 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 63 " --> pdb=" O SER B 53 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 34 through 36 Processing sheet with id= M, first strand: chain 'A' and resid 199 through 202 Processing sheet with id= N, first strand: chain 'A' and resid 192 through 195 removed outlier: 3.905A pdb=" N ILE A 133 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 65 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER A 53 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 63 " --> pdb=" O SER A 53 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 34 through 36 290 hydrogen bonds defined for protein. 729 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: 5.73 Time building geometry restraints manager: 14.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7970 1.03 - 1.22: 1 1.22 - 1.42: 3643 1.42 - 1.61: 4766 1.61 - 1.80: 30 Bond restraints: 16410 Sorted by residual: bond pdb=" O4 PC E 303 " pdb=" P1 PC E 303 " ideal model delta sigma weight residual 1.510 1.607 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" O4 PC D 303 " pdb=" P1 PC D 303 " ideal model delta sigma weight residual 1.510 1.606 -0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" O3 PC D 303 " pdb=" P1 PC D 303 " ideal model delta sigma weight residual 1.510 1.605 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" O4 PC B 303 " pdb=" P1 PC B 303 " ideal model delta sigma weight residual 1.510 1.605 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O4 PC A 303 " pdb=" P1 PC A 303 " ideal model delta sigma weight residual 1.510 1.605 -0.095 2.00e-02 2.50e+03 2.23e+01 ... (remaining 16405 not shown) Histogram of bond angle deviations from ideal: 78.28 - 89.44: 27 89.44 - 100.60: 0 100.60 - 111.75: 18310 111.75 - 122.91: 9090 122.91 - 134.07: 2183 Bond angle restraints: 29610 Sorted by residual: angle pdb=" CG2 VAL E 77 " pdb=" CB VAL E 77 " pdb=" HB VAL E 77 " ideal model delta sigma weight residual 108.00 78.28 29.72 3.00e+00 1.11e-01 9.81e+01 angle pdb=" CG2 THR B 46 " pdb=" CB THR B 46 " pdb=" HB THR B 46 " ideal model delta sigma weight residual 108.00 79.35 28.65 3.00e+00 1.11e-01 9.12e+01 angle pdb=" OG1 THR B 46 " pdb=" CB THR B 46 " pdb=" HB THR B 46 " ideal model delta sigma weight residual 109.00 80.70 28.30 3.00e+00 1.11e-01 8.90e+01 angle pdb=" CG1 VAL E 77 " pdb=" CB VAL E 77 " pdb=" HB VAL E 77 " ideal model delta sigma weight residual 108.00 80.46 27.54 3.00e+00 1.11e-01 8.43e+01 angle pdb=" CA THR B 46 " pdb=" CB THR B 46 " pdb=" HB THR B 46 " ideal model delta sigma weight residual 109.00 81.58 27.42 3.00e+00 1.11e-01 8.35e+01 ... (remaining 29605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 6991 16.69 - 33.39: 489 33.39 - 50.08: 154 50.08 - 66.78: 140 66.78 - 83.47: 16 Dihedral angle restraints: 7790 sinusoidal: 4115 harmonic: 3675 Sorted by residual: dihedral pdb=" CA GLU B 62 " pdb=" C GLU B 62 " pdb=" N ILE B 63 " pdb=" CA ILE B 63 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA GLU C 62 " pdb=" C GLU C 62 " pdb=" N ILE C 63 " pdb=" CA ILE C 63 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA GLU D 62 " pdb=" C GLU D 62 " pdb=" N ILE D 63 " pdb=" CA ILE D 63 " ideal model delta harmonic sigma weight residual 180.00 153.93 26.07 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 7787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.344: 1226 0.344 - 0.688: 0 0.688 - 1.032: 0 1.032 - 1.377: 4 1.377 - 1.721: 5 Chirality restraints: 1235 Sorted by residual: chirality pdb=" CG LEU D 83 " pdb=" CB LEU D 83 " pdb=" CD1 LEU D 83 " pdb=" CD2 LEU D 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.40e+01 chirality pdb=" CB VAL B 89 " pdb=" CA VAL B 89 " pdb=" CG1 VAL B 89 " pdb=" CG2 VAL B 89 " both_signs ideal model delta sigma weight residual False -2.63 -1.04 -1.59 2.00e-01 2.50e+01 6.29e+01 chirality pdb=" CB ILE A 82 " pdb=" CA ILE A 82 " pdb=" CG1 ILE A 82 " pdb=" CG2 ILE A 82 " both_signs ideal model delta sigma weight residual False 2.64 1.06 1.58 2.00e-01 2.50e+01 6.24e+01 ... (remaining 1232 not shown) Planarity restraints: 2420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 150 " -0.040 2.00e-02 2.50e+03 4.90e-02 3.60e+01 pdb=" CD GLN E 150 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLN E 150 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN E 150 " 0.077 2.00e-02 2.50e+03 pdb="HE21 GLN E 150 " 0.002 2.00e-02 2.50e+03 pdb="HE22 GLN E 150 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 150 " -0.037 2.00e-02 2.50e+03 4.37e-02 2.86e+01 pdb=" CD GLN C 150 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLN C 150 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN C 150 " 0.067 2.00e-02 2.50e+03 pdb="HE21 GLN C 150 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN C 150 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 150 " -0.033 2.00e-02 2.50e+03 3.96e-02 2.35e+01 pdb=" CD GLN D 150 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN D 150 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN D 150 " 0.062 2.00e-02 2.50e+03 pdb="HE21 GLN D 150 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN D 150 " -0.060 2.00e-02 2.50e+03 ... (remaining 2417 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 635 2.14 - 2.76: 30517 2.76 - 3.37: 45081 3.37 - 3.99: 62784 3.99 - 4.60: 96657 Nonbonded interactions: 235674 Sorted by model distance: nonbonded pdb=" OD1 ASP E 163 " pdb="HD22 ASN E 183 " model vdw 1.529 1.850 nonbonded pdb=" OD1 ASP D 163 " pdb="HD22 ASN D 183 " model vdw 1.546 1.850 nonbonded pdb=" OD2 ASP A 163 " pdb="HD22 ASN A 183 " model vdw 1.594 1.850 nonbonded pdb=" HG SER A 141 " pdb=" OD1 ASN A 145 " model vdw 1.623 1.850 nonbonded pdb=" HG SER D 102 " pdb=" O TYR D 125 " model vdw 1.624 1.850 ... (remaining 235669 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 3.100 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: 0.270 Extract box with map and model: 10.160 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 55.340 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 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 : 0.008 0.097 8440 Z= 0.521 Angle : 0.871 14.288 11480 Z= 0.465 Chirality : 0.132 1.721 1235 Planarity : 0.006 0.115 1450 Dihedral : 13.200 83.470 3005 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.25), residues: 1020 helix: 0.69 (0.69), residues: 50 sheet: -0.06 (0.24), residues: 425 loop : -0.51 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP A 187 HIS 0.006 0.003 HIS D 38 PHE 0.023 0.003 PHE D 66 TYR 0.023 0.006 TYR B 54 ARG 0.058 0.009 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 16 ASP cc_start: 0.8133 (p0) cc_final: 0.7692 (p0) REVERT: D 188 ARG cc_start: 0.8504 (mtm-85) cc_final: 0.8295 (mtm-85) REVERT: B 16 ASP cc_start: 0.8290 (p0) cc_final: 0.7899 (p0) REVERT: A 16 ASP cc_start: 0.8147 (p0) cc_final: 0.7831 (p0) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.6241 time to fit residues: 84.9365 Evaluate side-chains 88 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 HIS E 95 HIS E 172 ASN D 38 HIS D 95 HIS D 195 GLN C 38 HIS C 95 HIS B 38 HIS B 59 GLN B 95 HIS A 38 HIS A 95 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8440 Z= 0.282 Angle : 0.704 15.303 11480 Z= 0.372 Chirality : 0.134 1.685 1235 Planarity : 0.004 0.065 1450 Dihedral : 6.147 32.130 1115 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.89 % Allowed : 3.00 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1020 helix: 2.04 (0.66), residues: 55 sheet: 0.21 (0.24), residues: 425 loop : -0.26 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 162 HIS 0.005 0.003 HIS E 95 PHE 0.014 0.001 PHE D 52 TYR 0.023 0.002 TYR E 54 ARG 0.006 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 LYS cc_start: 0.7992 (ttpt) cc_final: 0.7789 (ttpt) REVERT: B 16 ASP cc_start: 0.8267 (p0) cc_final: 0.7817 (p0) REVERT: B 155 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8271 (m-30) REVERT: A 16 ASP cc_start: 0.8160 (p0) cc_final: 0.7822 (p0) outliers start: 8 outliers final: 7 residues processed: 108 average time/residue: 0.6289 time to fit residues: 85.9702 Evaluate side-chains 101 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 HIS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain A residue 38 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 HIS ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS C 38 HIS B 38 HIS A 38 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8440 Z= 0.237 Angle : 0.666 15.681 11480 Z= 0.351 Chirality : 0.133 1.690 1235 Planarity : 0.004 0.068 1450 Dihedral : 5.805 31.808 1115 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.78 % Allowed : 3.78 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1020 helix: 2.43 (0.66), residues: 55 sheet: 0.35 (0.22), residues: 445 loop : -0.39 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 162 HIS 0.012 0.006 HIS E 38 PHE 0.011 0.001 PHE D 52 TYR 0.017 0.001 TYR E 54 ARG 0.008 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 ASP cc_start: 0.8127 (p0) cc_final: 0.7838 (p0) REVERT: B 16 ASP cc_start: 0.8267 (p0) cc_final: 0.7812 (p0) REVERT: B 155 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8219 (m-30) REVERT: A 16 ASP cc_start: 0.8145 (p0) cc_final: 0.7829 (p0) outliers start: 7 outliers final: 2 residues processed: 103 average time/residue: 0.6210 time to fit residues: 80.9565 Evaluate side-chains 97 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain B residue 155 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 0.0970 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8440 Z= 0.226 Angle : 0.643 15.750 11480 Z= 0.336 Chirality : 0.133 1.689 1235 Planarity : 0.004 0.072 1450 Dihedral : 5.425 32.257 1115 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.56 % Allowed : 5.22 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1020 helix: 2.53 (0.65), residues: 55 sheet: 0.37 (0.23), residues: 445 loop : -0.34 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 162 HIS 0.009 0.003 HIS D 38 PHE 0.010 0.001 PHE D 52 TYR 0.034 0.001 TYR B 125 ARG 0.007 0.000 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 16 ASP cc_start: 0.8177 (p0) cc_final: 0.7898 (p0) REVERT: B 16 ASP cc_start: 0.8224 (p0) cc_final: 0.7773 (p0) REVERT: A 16 ASP cc_start: 0.8153 (p0) cc_final: 0.7832 (p0) outliers start: 5 outliers final: 4 residues processed: 107 average time/residue: 0.6459 time to fit residues: 87.9256 Evaluate side-chains 99 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 147 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 0.0670 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8440 Z= 0.203 Angle : 0.630 15.743 11480 Z= 0.328 Chirality : 0.133 1.690 1235 Planarity : 0.004 0.080 1450 Dihedral : 5.185 35.992 1115 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.56 % Allowed : 5.89 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1020 helix: 2.37 (0.64), residues: 55 sheet: 0.32 (0.23), residues: 445 loop : -0.29 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 162 HIS 0.007 0.002 HIS E 38 PHE 0.010 0.001 PHE D 52 TYR 0.020 0.001 TYR B 125 ARG 0.008 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 ASP cc_start: 0.8210 (p0) cc_final: 0.7919 (p0) REVERT: B 16 ASP cc_start: 0.8254 (p0) cc_final: 0.7787 (p0) outliers start: 5 outliers final: 5 residues processed: 109 average time/residue: 0.6369 time to fit residues: 87.3996 Evaluate side-chains 102 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 147 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8440 Z= 0.234 Angle : 0.631 15.750 11480 Z= 0.329 Chirality : 0.133 1.690 1235 Planarity : 0.004 0.089 1450 Dihedral : 5.250 45.528 1115 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.89 % Allowed : 5.78 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1020 helix: 2.30 (0.62), residues: 55 sheet: 0.33 (0.23), residues: 445 loop : -0.35 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 162 HIS 0.007 0.002 HIS E 38 PHE 0.018 0.001 PHE E 180 TYR 0.017 0.001 TYR B 125 ARG 0.011 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 16 ASP cc_start: 0.8124 (p0) cc_final: 0.7628 (p0) REVERT: D 16 ASP cc_start: 0.8220 (p0) cc_final: 0.7947 (p0) REVERT: B 16 ASP cc_start: 0.8256 (p0) cc_final: 0.7801 (p0) REVERT: B 155 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8147 (m-30) outliers start: 8 outliers final: 4 residues processed: 111 average time/residue: 0.6409 time to fit residues: 90.7027 Evaluate side-chains 103 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 147 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.0770 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8440 Z= 0.226 Angle : 0.627 15.718 11480 Z= 0.326 Chirality : 0.133 1.693 1235 Planarity : 0.003 0.046 1450 Dihedral : 5.343 58.446 1115 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.78 % Allowed : 6.11 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.26), residues: 1020 helix: 2.34 (0.61), residues: 55 sheet: 0.37 (0.23), residues: 445 loop : -0.37 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 162 HIS 0.007 0.002 HIS E 38 PHE 0.010 0.001 PHE D 52 TYR 0.014 0.001 TYR B 125 ARG 0.003 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 ASP cc_start: 0.8224 (p0) cc_final: 0.7963 (p0) REVERT: B 16 ASP cc_start: 0.8222 (p0) cc_final: 0.7786 (p0) REVERT: B 155 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8159 (m-30) outliers start: 7 outliers final: 4 residues processed: 111 average time/residue: 0.6775 time to fit residues: 95.2683 Evaluate side-chains 105 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 147 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.0270 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8440 Z= 0.187 Angle : 0.621 15.688 11480 Z= 0.322 Chirality : 0.133 1.694 1235 Planarity : 0.004 0.087 1450 Dihedral : 5.166 51.300 1115 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.78 % Allowed : 6.11 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1020 helix: 2.42 (0.61), residues: 55 sheet: 0.38 (0.23), residues: 445 loop : -0.34 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 162 HIS 0.006 0.002 HIS E 38 PHE 0.010 0.001 PHE D 52 TYR 0.013 0.001 TYR B 125 ARG 0.011 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: E 16 ASP cc_start: 0.8141 (p0) cc_final: 0.7680 (p0) REVERT: D 16 ASP cc_start: 0.8216 (p0) cc_final: 0.7973 (p0) REVERT: B 16 ASP cc_start: 0.8222 (p0) cc_final: 0.7789 (p0) REVERT: B 155 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: B 163 ASP cc_start: 0.8255 (p0) cc_final: 0.7964 (p0) outliers start: 7 outliers final: 4 residues processed: 117 average time/residue: 0.6230 time to fit residues: 94.1441 Evaluate side-chains 111 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 147 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 94 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 GLN ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8440 Z= 0.222 Angle : 0.626 15.720 11480 Z= 0.325 Chirality : 0.133 1.696 1235 Planarity : 0.004 0.090 1450 Dihedral : 5.116 39.277 1115 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.89 % Allowed : 6.00 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.26), residues: 1020 helix: 2.44 (0.61), residues: 55 sheet: 0.37 (0.23), residues: 445 loop : -0.37 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 162 HIS 0.006 0.002 HIS E 38 PHE 0.010 0.001 PHE D 52 TYR 0.014 0.001 TYR D 125 ARG 0.012 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: E 1 GLN cc_start: 0.7920 (mp10) cc_final: 0.7710 (mm110) REVERT: D 16 ASP cc_start: 0.8224 (p0) cc_final: 0.7973 (p0) REVERT: B 16 ASP cc_start: 0.8211 (p0) cc_final: 0.7791 (p0) outliers start: 8 outliers final: 6 residues processed: 116 average time/residue: 0.6159 time to fit residues: 90.8912 Evaluate side-chains 113 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 147 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8440 Z= 0.215 Angle : 0.623 15.718 11480 Z= 0.323 Chirality : 0.133 1.698 1235 Planarity : 0.004 0.094 1450 Dihedral : 5.160 45.690 1115 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.78 % Allowed : 6.11 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.26), residues: 1020 helix: 2.47 (0.61), residues: 55 sheet: 0.37 (0.23), residues: 445 loop : -0.39 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 162 HIS 0.006 0.002 HIS D 38 PHE 0.010 0.001 PHE D 52 TYR 0.013 0.001 TYR B 125 ARG 0.013 0.001 ARG C 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 16 ASP cc_start: 0.8195 (p0) cc_final: 0.7753 (p0) REVERT: D 16 ASP cc_start: 0.8211 (p0) cc_final: 0.7967 (p0) REVERT: B 16 ASP cc_start: 0.8167 (p0) cc_final: 0.7761 (p0) outliers start: 7 outliers final: 6 residues processed: 113 average time/residue: 0.6282 time to fit residues: 90.3932 Evaluate side-chains 115 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 147 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.074372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2419 r_free = 0.2419 target = 0.061242 restraints weight = 37789.058| |-----------------------------------------------------------------------------| r_work (start): 0.2422 rms_B_bonded: 2.16 r_work: 0.2316 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2179 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8440 Z= 0.182 Angle : 0.618 15.691 11480 Z= 0.320 Chirality : 0.133 1.698 1235 Planarity : 0.004 0.090 1450 Dihedral : 5.020 47.778 1115 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.89 % Allowed : 6.11 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.26), residues: 1020 helix: 2.52 (0.61), residues: 55 sheet: 0.37 (0.23), residues: 445 loop : -0.34 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 162 HIS 0.005 0.002 HIS A 38 PHE 0.010 0.001 PHE D 52 TYR 0.013 0.001 TYR B 125 ARG 0.012 0.001 ARG C 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4232.71 seconds wall clock time: 75 minutes 18.56 seconds (4518.56 seconds total)