Starting phenix.real_space_refine on Tue Aug 6 12:00:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wv5_37865/08_2024/8wv5_37865.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wv5_37865/08_2024/8wv5_37865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wv5_37865/08_2024/8wv5_37865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wv5_37865/08_2024/8wv5_37865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wv5_37865/08_2024/8wv5_37865.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wv5_37865/08_2024/8wv5_37865.cif" } resolution = 3.5 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= 0.005 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: 5 Type Number sf(0) Gaussians Ca 20 9.91 5 S 40 5.16 5 C 10580 2.51 5 N 2610 2.21 5 O 3090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 16": "OD1" <-> "OD2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E ASP 169": "OD1" <-> "OD2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ASP 169": "OD1" <-> "OD2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B ASP 16": "OD1" <-> "OD2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 70": "OD1" <-> "OD2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "F PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 163": "OD1" <-> "OD2" Residue "F TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 16": "OD1" <-> "OD2" Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "I ASP 16": "OD1" <-> "OD2" Residue "I PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 42": "OE1" <-> "OE2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 112": "OD1" <-> "OD2" Residue "I GLU 170": "OE1" <-> "OE2" Residue "I TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 14": "OE1" <-> "OE2" Residue "J ASP 16": "OD1" <-> "OD2" Residue "J PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "J ASP 70": "OD1" <-> "OD2" Residue "J GLU 85": "OE1" <-> "OE2" Residue "J GLU 108": "OE1" <-> "OE2" Residue "J PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 112": "OD1" <-> "OD2" Residue "J GLU 147": "OE1" <-> "OE2" Residue "J TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "H ASP 16": "OD1" <-> "OD2" Residue "H PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 112": "OD1" <-> "OD2" Residue "H TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 193": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16340 Number of models: 1 Model: "" Number of chains: 20 Chain: "E" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "A" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "B" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "C" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "D" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "F" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "G" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "I" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "J" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "H" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.29, per 1000 atoms: 0.57 Number of scatterers: 16340 At special positions: 0 Unit cell: (118.77, 155.15, 109.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 20 19.99 S 40 16.00 O 3090 8.00 N 2610 7.00 C 10580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 97 " distance=2.04 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 97 " distance=2.04 Simple disulfide: pdb=" SG CYS F 36 " - pdb=" SG CYS F 97 " distance=2.04 Simple disulfide: pdb=" SG CYS G 36 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 36 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS J 36 " - pdb=" SG CYS J 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 36 " - pdb=" SG CYS H 97 " distance=2.04 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: 6.33 Conformation dependent library (CDL) restraints added in 2.8 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 42 sheets defined 7.3% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'E' and resid 43 through 46 removed outlier: 3.538A pdb=" N THR E 46 " --> pdb=" O LEU E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 43 through 46' Processing helix chain 'E' and resid 167 through 177 Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.873A pdb=" N SER A 45 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'B' and resid 43 through 46 removed outlier: 3.579A pdb=" N THR B 46 " --> pdb=" O LEU B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 46' Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'C' and resid 43 through 46 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'D' and resid 43 through 46 Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'F' and resid 43 through 46 removed outlier: 3.535A pdb=" N THR F 46 " --> pdb=" O LEU F 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 43 through 46' Processing helix chain 'F' and resid 167 through 177 Processing helix chain 'G' and resid 43 through 46 Processing helix chain 'G' and resid 167 through 177 Processing helix chain 'I' and resid 43 through 46 Processing helix chain 'I' and resid 167 through 177 Processing helix chain 'J' and resid 43 through 46 Processing helix chain 'J' and resid 167 through 177 Processing helix chain 'H' and resid 43 through 46 Processing helix chain 'H' and resid 167 through 177 Processing sheet with id=AA1, first strand: chain 'E' and resid 114 through 115 removed outlier: 3.937A pdb=" N THR E 34 " --> pdb=" O TRP E 162 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N HIS E 38 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASN E 158 " --> pdb=" O HIS E 38 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N TYR E 40 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE E 156 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN E 158 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N LYS E 7 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE E 199 " --> pdb=" O VAL E 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 80 through 85 removed outlier: 3.655A pdb=" N SER E 80 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR E 73 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE E 66 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR E 76 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 64 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TRP E 67 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N SER E 50 " --> pdb=" O TRP E 67 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE E 133 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER E 21 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 106 through 107 Processing sheet with id=AA4, first strand: chain 'E' and resid 139 through 141 removed outlier: 6.251A pdb=" N ASN E 145 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.770A pdb=" N THR A 34 " --> pdb=" O TRP A 162 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N HIS A 38 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ASN A 158 " --> pdb=" O HIS A 38 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N TYR A 40 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE A 156 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN A 158 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N LYS A 7 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE A 199 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 80 through 85 removed outlier: 3.541A pdb=" N TYR A 73 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 64 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 52 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TRP A 67 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER A 50 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 133 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 21 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 193 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA8, first strand: chain 'A' and resid 139 through 141 removed outlier: 6.267A pdb=" N ASN A 145 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 101 removed outlier: 6.309A pdb=" N THR B 34 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N MET B 161 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N CYS B 36 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL B 159 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASN B 158 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N LYS B 7 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 199 " --> pdb=" O VAL B 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 85 removed outlier: 3.655A pdb=" N TYR B 73 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 76 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 64 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TRP B 67 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N SER B 50 " --> pdb=" O TRP B 67 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE B 133 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 20 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER B 21 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 193 " --> pdb=" O SER B 21 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.021A pdb=" N VAL B 107 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ARG B 118 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B 109 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 139 through 141 removed outlier: 6.375A pdb=" N ASN B 145 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 115 removed outlier: 4.375A pdb=" N ILE C 96 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU C 37 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR C 98 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 35 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR C 34 " --> pdb=" O MET C 161 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET C 161 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N CYS C 36 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL C 159 " --> pdb=" O CYS C 36 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASN C 158 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N LYS C 7 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE C 199 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 80 through 85 removed outlier: 3.595A pdb=" N THR C 76 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 64 " --> pdb=" O THR C 76 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TRP C 67 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER C 50 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 133 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 20 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 195 " --> pdb=" O TYR C 19 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 21 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AB7, first strand: chain 'C' and resid 139 through 141 removed outlier: 6.392A pdb=" N ASN C 145 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB9, first strand: chain 'D' and resid 114 through 115 removed outlier: 3.765A pdb=" N ILE D 106 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE D 96 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU D 37 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR D 98 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR D 34 " --> pdb=" O MET D 161 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N MET D 161 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N CYS D 36 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL D 159 " --> pdb=" O CYS D 36 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASN D 158 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N LYS D 7 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE D 199 " --> pdb=" O VAL D 10 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.689A pdb=" N TYR D 73 " --> pdb=" O PHE D 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.659A pdb=" N THR D 76 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D 64 " --> pdb=" O THR D 76 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE D 52 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TRP D 67 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N SER D 50 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE D 133 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D 21 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 139 through 141 removed outlier: 6.393A pdb=" N ASN D 145 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 114 through 115 removed outlier: 4.239A pdb=" N ILE F 96 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU F 37 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR F 98 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL F 35 " --> pdb=" O THR F 98 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS F 38 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASN F 158 " --> pdb=" O HIS F 38 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR F 40 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE F 156 " --> pdb=" O TYR F 40 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASN F 158 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N LYS F 7 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE F 199 " --> pdb=" O VAL F 10 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 80 through 85 removed outlier: 3.674A pdb=" N TYR F 73 " --> pdb=" O PHE F 84 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR F 76 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU F 64 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE F 52 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TRP F 67 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER F 50 " --> pdb=" O TRP F 67 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE F 133 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL F 20 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER F 21 " --> pdb=" O GLU F 193 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU F 193 " --> pdb=" O SER F 21 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 106 through 107 Processing sheet with id=AC7, first strand: chain 'F' and resid 139 through 141 removed outlier: 6.321A pdb=" N ASN F 145 " --> pdb=" O ASP F 140 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 114 through 115 Processing sheet with id=AC9, first strand: chain 'G' and resid 114 through 115 removed outlier: 3.941A pdb=" N ILE G 106 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR G 34 " --> pdb=" O TRP G 162 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS G 38 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASN G 158 " --> pdb=" O HIS G 38 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR G 40 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE G 156 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN G 158 " --> pdb=" O LYS G 7 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N LYS G 7 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE G 199 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 80 through 85 removed outlier: 3.614A pdb=" N TYR G 73 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR G 76 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU G 64 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TRP G 67 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N SER G 50 " --> pdb=" O TRP G 67 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE G 133 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL G 20 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN G 195 " --> pdb=" O TYR G 19 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER G 21 " --> pdb=" O GLU G 193 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 139 through 141 removed outlier: 6.357A pdb=" N ASN G 145 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 100 through 101 removed outlier: 6.833A pdb=" N THR I 34 " --> pdb=" O MET I 161 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET I 161 " --> pdb=" O THR I 34 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N CYS I 36 " --> pdb=" O VAL I 159 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL I 159 " --> pdb=" O CYS I 36 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASN I 158 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N LYS I 7 " --> pdb=" O ASN I 158 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE I 199 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 80 through 83 removed outlier: 3.626A pdb=" N SER I 80 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE I 66 " --> pdb=" O SER I 74 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR I 76 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU I 64 " --> pdb=" O THR I 76 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TRP I 67 " --> pdb=" O SER I 50 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N SER I 50 " --> pdb=" O TRP I 67 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE I 133 " --> pdb=" O LEU I 22 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL I 20 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER I 21 " --> pdb=" O GLU I 193 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 96 through 97 Processing sheet with id=AD6, first strand: chain 'I' and resid 106 through 107 Processing sheet with id=AD7, first strand: chain 'J' and resid 114 through 115 removed outlier: 4.282A pdb=" N ILE J 96 " --> pdb=" O LEU J 37 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU J 37 " --> pdb=" O ILE J 96 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR J 98 " --> pdb=" O VAL J 35 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL J 35 " --> pdb=" O THR J 98 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR J 34 " --> pdb=" O TRP J 162 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS J 38 " --> pdb=" O ASN J 158 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASN J 158 " --> pdb=" O HIS J 38 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR J 40 " --> pdb=" O ILE J 156 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE J 156 " --> pdb=" O TYR J 40 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASN J 158 " --> pdb=" O LYS J 7 " (cutoff:3.500A) removed outlier: 10.083A pdb=" N LYS J 7 " --> pdb=" O ASN J 158 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE J 199 " --> pdb=" O VAL J 10 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 80 through 85 removed outlier: 3.592A pdb=" N TYR J 73 " --> pdb=" O PHE J 84 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE J 66 " --> pdb=" O SER J 74 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR J 76 " --> pdb=" O LEU J 64 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU J 64 " --> pdb=" O THR J 76 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TRP J 67 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER J 50 " --> pdb=" O TRP J 67 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE J 133 " --> pdb=" O LEU J 22 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL J 20 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER J 21 " --> pdb=" O GLU J 193 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU J 193 " --> pdb=" O SER J 21 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 106 through 107 Processing sheet with id=AE1, first strand: chain 'J' and resid 139 through 141 removed outlier: 6.312A pdb=" N ASN J 145 " --> pdb=" O ASP J 140 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 114 through 115 removed outlier: 4.264A pdb=" N ILE H 96 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU H 37 " --> pdb=" O ILE H 96 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR H 98 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL H 35 " --> pdb=" O THR H 98 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR H 34 " --> pdb=" O MET H 161 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N MET H 161 " --> pdb=" O THR H 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N CYS H 36 " --> pdb=" O VAL H 159 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL H 159 " --> pdb=" O CYS H 36 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN H 158 " --> pdb=" O LYS H 7 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N LYS H 7 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE H 199 " --> pdb=" O VAL H 10 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 80 through 81 removed outlier: 3.597A pdb=" N SER H 80 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR H 73 " --> pdb=" O PHE H 84 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 80 through 81 removed outlier: 3.597A pdb=" N SER H 80 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE H 66 " --> pdb=" O SER H 74 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR H 76 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU H 64 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TRP H 67 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N SER H 50 " --> pdb=" O TRP H 67 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE H 133 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL H 20 " --> pdb=" O LEU H 135 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 106 through 107 Processing sheet with id=AE6, first strand: chain 'H' and resid 139 through 141 removed outlier: 6.338A pdb=" N ASN H 145 " --> pdb=" O ASP H 140 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1224 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: 5.12 Time building geometry restraints manager: 6.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5080 1.35 - 1.47: 4492 1.47 - 1.59: 7148 1.59 - 1.71: 0 1.71 - 1.83: 60 Bond restraints: 16780 Sorted by residual: bond pdb=" N VAL F 86 " pdb=" CA VAL F 86 " ideal model delta sigma weight residual 1.454 1.462 -0.007 7.70e-03 1.69e+04 9.32e-01 bond pdb=" N VAL C 86 " pdb=" CA VAL C 86 " ideal model delta sigma weight residual 1.454 1.461 -0.007 7.70e-03 1.69e+04 7.71e-01 bond pdb=" N GLY I 178 " pdb=" CA GLY I 178 " ideal model delta sigma weight residual 1.434 1.444 -0.010 1.22e-02 6.72e+03 6.92e-01 bond pdb=" N SER C 181 " pdb=" CA SER C 181 " ideal model delta sigma weight residual 1.463 1.455 0.007 8.80e-03 1.29e+04 6.87e-01 bond pdb=" C VAL E 153 " pdb=" N GLY E 154 " ideal model delta sigma weight residual 1.331 1.318 0.012 1.46e-02 4.69e+03 6.85e-01 ... (remaining 16775 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.21: 625 107.21 - 113.91: 9131 113.91 - 120.60: 6051 120.60 - 127.30: 6779 127.30 - 133.99: 224 Bond angle restraints: 22810 Sorted by residual: angle pdb=" N THR G 17 " pdb=" CA THR G 17 " pdb=" C THR G 17 " ideal model delta sigma weight residual 114.31 109.95 4.36 1.29e+00 6.01e-01 1.14e+01 angle pdb=" N THR E 17 " pdb=" CA THR E 17 " pdb=" C THR E 17 " ideal model delta sigma weight residual 114.31 110.46 3.85 1.29e+00 6.01e-01 8.91e+00 angle pdb=" N THR D 17 " pdb=" CA THR D 17 " pdb=" C THR D 17 " ideal model delta sigma weight residual 114.31 110.55 3.76 1.29e+00 6.01e-01 8.49e+00 angle pdb=" N THR H 17 " pdb=" CA THR H 17 " pdb=" C THR H 17 " ideal model delta sigma weight residual 114.31 110.65 3.66 1.29e+00 6.01e-01 8.06e+00 angle pdb=" N THR A 17 " pdb=" CA THR A 17 " pdb=" C THR A 17 " ideal model delta sigma weight residual 114.56 110.95 3.61 1.27e+00 6.20e-01 8.06e+00 ... (remaining 22805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 9084 17.80 - 35.59: 573 35.59 - 53.39: 90 53.39 - 71.19: 33 71.19 - 88.98: 10 Dihedral angle restraints: 9790 sinusoidal: 3880 harmonic: 5910 Sorted by residual: dihedral pdb=" CB CYS I 36 " pdb=" SG CYS I 36 " pdb=" SG CYS I 97 " pdb=" CB CYS I 97 " ideal model delta sinusoidal sigma weight residual 93.00 14.18 78.82 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS D 36 " pdb=" SG CYS D 36 " pdb=" SG CYS D 97 " pdb=" CB CYS D 97 " ideal model delta sinusoidal sigma weight residual -86.00 -40.91 -45.09 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS E 36 " pdb=" SG CYS E 36 " pdb=" SG CYS E 97 " pdb=" CB CYS E 97 " ideal model delta sinusoidal sigma weight residual -86.00 -44.00 -42.00 1 1.00e+01 1.00e-02 2.47e+01 ... (remaining 9787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1400 0.026 - 0.051: 610 0.051 - 0.077: 182 0.077 - 0.103: 160 0.103 - 0.129: 118 Chirality restraints: 2470 Sorted by residual: chirality pdb=" CA ILE A 63 " pdb=" N ILE A 63 " pdb=" C ILE A 63 " pdb=" CB ILE A 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE F 63 " pdb=" N ILE F 63 " pdb=" C ILE F 63 " pdb=" CB ILE F 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE C 63 " pdb=" N ILE C 63 " pdb=" C ILE C 63 " pdb=" CB ILE C 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 2467 not shown) Planarity restraints: 2900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 167 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO D 168 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 168 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 168 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 35 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.39e+00 pdb=" C VAL C 35 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL C 35 " 0.008 2.00e-02 2.50e+03 pdb=" N CYS C 36 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 167 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO E 168 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO E 168 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 168 " -0.016 5.00e-02 4.00e+02 ... (remaining 2897 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 138 2.43 - 3.05: 9726 3.05 - 3.66: 24069 3.66 - 4.28: 36448 4.28 - 4.90: 62114 Nonbonded interactions: 132495 Sorted by model distance: nonbonded pdb=" CD GLU H 147 " pdb="CA CA H 301 " model vdw 1.812 2.740 nonbonded pdb=" OE1 GLU H 147 " pdb="CA CA H 301 " model vdw 2.018 2.510 nonbonded pdb=" OG1 THR I 98 " pdb=" O GLU I 108 " model vdw 2.207 3.040 nonbonded pdb=" CG GLU I 147 " pdb="CA CA I 301 " model vdw 2.221 2.910 nonbonded pdb=" OG1 THR J 98 " pdb=" O GLU J 108 " model vdw 2.231 3.040 ... (remaining 132490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 45.390 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 0.002 0.027 16780 Z= 0.117 Angle : 0.468 5.385 22810 Z= 0.290 Chirality : 0.043 0.129 2470 Planarity : 0.003 0.032 2900 Dihedral : 12.215 88.982 5980 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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: -3.38 (0.15), residues: 2040 helix: 1.67 (0.44), residues: 110 sheet: -2.26 (0.19), residues: 570 loop : -2.74 (0.13), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP J 100 HIS 0.002 0.001 HIS J 38 PHE 0.006 0.001 PHE J 199 TYR 0.006 0.001 TYR F 54 ARG 0.002 0.000 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 482 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 6 ARG cc_start: 0.8396 (mmm160) cc_final: 0.8121 (mmm160) REVERT: E 54 TYR cc_start: 0.9058 (t80) cc_final: 0.8646 (t80) REVERT: E 108 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8058 (mt-10) REVERT: E 130 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8091 (tm-30) REVERT: E 172 ASN cc_start: 0.9367 (t0) cc_final: 0.8967 (t0) REVERT: A 3 ASP cc_start: 0.8999 (t0) cc_final: 0.8797 (t0) REVERT: A 186 ASN cc_start: 0.9316 (t0) cc_final: 0.8949 (t0) REVERT: B 47 ARG cc_start: 0.7970 (ptt90) cc_final: 0.7708 (ptt-90) REVERT: B 195 GLN cc_start: 0.7834 (tp-100) cc_final: 0.7580 (tp40) REVERT: C 19 TYR cc_start: 0.8563 (p90) cc_final: 0.7329 (p90) REVERT: C 114 LYS cc_start: 0.9056 (mmtm) cc_final: 0.8691 (mmmt) REVERT: C 122 LYS cc_start: 0.9066 (mmtt) cc_final: 0.8645 (mmtt) REVERT: C 186 ASN cc_start: 0.9284 (t0) cc_final: 0.8818 (t0) REVERT: D 3 ASP cc_start: 0.8970 (t0) cc_final: 0.8516 (t70) REVERT: D 70 ASP cc_start: 0.8383 (t0) cc_final: 0.8103 (t0) REVERT: D 98 THR cc_start: 0.8083 (t) cc_final: 0.7600 (t) REVERT: D 195 GLN cc_start: 0.8381 (tp-100) cc_final: 0.8077 (mm-40) REVERT: F 23 LYS cc_start: 0.8843 (mptt) cc_final: 0.8070 (mmtt) REVERT: F 82 ILE cc_start: 0.8944 (pt) cc_final: 0.8594 (pt) REVERT: F 122 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8491 (mmtm) REVERT: F 150 GLN cc_start: 0.7896 (mt0) cc_final: 0.7343 (mm-40) REVERT: F 170 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7258 (mp0) REVERT: I 6 ARG cc_start: 0.8720 (mmm160) cc_final: 0.8491 (mmm-85) REVERT: I 28 LYS cc_start: 0.9288 (mtpt) cc_final: 0.9013 (ttpt) REVERT: I 40 TYR cc_start: 0.9041 (t80) cc_final: 0.8644 (t80) REVERT: I 125 TYR cc_start: 0.8743 (t80) cc_final: 0.8512 (t80) REVERT: I 158 ASN cc_start: 0.8130 (m-40) cc_final: 0.7586 (t0) REVERT: J 172 ASN cc_start: 0.9093 (t0) cc_final: 0.8859 (t0) REVERT: H 122 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8272 (mmtp) REVERT: H 195 GLN cc_start: 0.7852 (tp-100) cc_final: 0.7450 (tp-100) outliers start: 0 outliers final: 0 residues processed: 482 average time/residue: 0.3456 time to fit residues: 230.2545 Evaluate side-chains 273 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 181 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN B 195 GLN ** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN D 1 GLN D 195 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 ASN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 16780 Z= 0.459 Angle : 0.677 13.272 22810 Z= 0.359 Chirality : 0.050 0.176 2470 Planarity : 0.005 0.071 2900 Dihedral : 4.630 26.338 2200 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.11 % Allowed : 13.72 % Favored : 84.17 % 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: -2.76 (0.17), residues: 2040 helix: 2.44 (0.44), residues: 110 sheet: -1.95 (0.16), residues: 860 loop : -2.17 (0.17), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 100 HIS 0.009 0.002 HIS B 38 PHE 0.021 0.002 PHE A 39 TYR 0.017 0.002 TYR G 175 ARG 0.005 0.001 ARG E 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 223 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 130 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8164 (tm-30) REVERT: E 172 ASN cc_start: 0.9454 (t0) cc_final: 0.8918 (t0) REVERT: E 176 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.8894 (mm) REVERT: E 203 GLN cc_start: 0.8738 (pt0) cc_final: 0.8057 (pt0) REVERT: A 147 GLU cc_start: 0.6983 (mp0) cc_final: 0.6698 (mp0) REVERT: A 186 ASN cc_start: 0.9286 (t0) cc_final: 0.8986 (t0) REVERT: A 195 GLN cc_start: 0.7463 (mp10) cc_final: 0.6943 (mp10) REVERT: B 91 VAL cc_start: 0.8890 (m) cc_final: 0.8615 (p) REVERT: B 94 VAL cc_start: 0.9213 (OUTLIER) cc_final: 0.8989 (p) REVERT: C 60 ASP cc_start: 0.7299 (p0) cc_final: 0.7071 (p0) REVERT: C 122 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8786 (mmtt) REVERT: C 137 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8508 (mm-40) REVERT: C 145 ASN cc_start: 0.8246 (m110) cc_final: 0.7942 (m110) REVERT: C 186 ASN cc_start: 0.9446 (t0) cc_final: 0.9068 (t0) REVERT: D 49 TYR cc_start: 0.9362 (p90) cc_final: 0.9120 (p90) REVERT: D 172 ASN cc_start: 0.9354 (t0) cc_final: 0.9102 (t0) REVERT: F 23 LYS cc_start: 0.8851 (mptt) cc_final: 0.8482 (mmtt) REVERT: I 6 ARG cc_start: 0.8819 (mmm160) cc_final: 0.8283 (mmm-85) REVERT: I 125 TYR cc_start: 0.8879 (t80) cc_final: 0.8645 (t80) REVERT: J 4 MET cc_start: 0.8920 (mmm) cc_final: 0.8577 (mmm) REVERT: J 172 ASN cc_start: 0.9283 (t0) cc_final: 0.9062 (t0) outliers start: 38 outliers final: 19 residues processed: 257 average time/residue: 0.3039 time to fit residues: 113.2828 Evaluate side-chains 217 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 196 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 ASN B 203 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 HIS J 145 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16780 Z= 0.219 Angle : 0.542 13.848 22810 Z= 0.287 Chirality : 0.047 0.204 2470 Planarity : 0.004 0.047 2900 Dihedral : 4.279 28.394 2200 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.72 % Allowed : 15.06 % Favored : 83.22 % 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: -2.18 (0.18), residues: 2040 helix: 3.23 (0.42), residues: 110 sheet: -1.64 (0.17), residues: 870 loop : -1.74 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 110 HIS 0.006 0.002 HIS C 38 PHE 0.014 0.001 PHE A 39 TYR 0.015 0.001 TYR H 54 ARG 0.005 0.001 ARG E 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 228 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9389 (t0) cc_final: 0.8824 (t0) REVERT: E 176 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8692 (mm) REVERT: E 203 GLN cc_start: 0.8816 (pt0) cc_final: 0.8312 (pt0) REVERT: A 112 ASP cc_start: 0.9156 (m-30) cc_final: 0.8927 (m-30) REVERT: A 186 ASN cc_start: 0.9222 (t0) cc_final: 0.8907 (t0) REVERT: A 195 GLN cc_start: 0.7533 (mp10) cc_final: 0.6850 (mp10) REVERT: B 91 VAL cc_start: 0.8889 (m) cc_final: 0.8595 (p) REVERT: C 60 ASP cc_start: 0.7506 (p0) cc_final: 0.7167 (p0) REVERT: C 122 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8821 (mmtt) REVERT: C 186 ASN cc_start: 0.9432 (t0) cc_final: 0.9073 (t0) REVERT: D 49 TYR cc_start: 0.9358 (p90) cc_final: 0.9017 (p90) REVERT: F 23 LYS cc_start: 0.8860 (mptt) cc_final: 0.8421 (mmtt) REVERT: I 125 TYR cc_start: 0.8823 (t80) cc_final: 0.8600 (t80) REVERT: J 4 MET cc_start: 0.9022 (mmm) cc_final: 0.8683 (mmm) REVERT: J 172 ASN cc_start: 0.9331 (t0) cc_final: 0.9112 (t0) outliers start: 31 outliers final: 21 residues processed: 253 average time/residue: 0.3039 time to fit residues: 111.2448 Evaluate side-chains 217 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 HIS F 95 HIS F 158 ASN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16780 Z= 0.341 Angle : 0.572 12.139 22810 Z= 0.303 Chirality : 0.047 0.193 2470 Planarity : 0.004 0.045 2900 Dihedral : 4.484 33.501 2200 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.39 % Allowed : 16.61 % Favored : 81.00 % 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: -1.92 (0.18), residues: 2040 helix: 3.33 (0.41), residues: 110 sheet: -1.45 (0.17), residues: 870 loop : -1.57 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 100 HIS 0.013 0.002 HIS J 38 PHE 0.016 0.001 PHE C 146 TYR 0.030 0.001 TYR G 125 ARG 0.005 0.001 ARG G 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 200 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9415 (t0) cc_final: 0.8859 (t0) REVERT: E 176 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8853 (mm) REVERT: E 203 GLN cc_start: 0.8815 (pt0) cc_final: 0.8295 (pt0) REVERT: A 186 ASN cc_start: 0.9228 (t0) cc_final: 0.8910 (t0) REVERT: B 91 VAL cc_start: 0.8937 (m) cc_final: 0.8668 (p) REVERT: C 19 TYR cc_start: 0.8442 (p90) cc_final: 0.8217 (p90) REVERT: C 60 ASP cc_start: 0.7753 (p0) cc_final: 0.7430 (p0) REVERT: C 122 LYS cc_start: 0.9070 (mmtt) cc_final: 0.8827 (mmtt) REVERT: C 186 ASN cc_start: 0.9446 (t0) cc_final: 0.9143 (t0) REVERT: C 195 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6695 (pp30) REVERT: D 49 TYR cc_start: 0.9371 (p90) cc_final: 0.9031 (p90) REVERT: D 197 GLU cc_start: 0.8223 (pm20) cc_final: 0.7748 (pm20) REVERT: F 23 LYS cc_start: 0.8872 (mptt) cc_final: 0.8385 (mmtt) REVERT: G 195 GLN cc_start: 0.7682 (tp40) cc_final: 0.7377 (tp40) REVERT: I 6 ARG cc_start: 0.8833 (mmm-85) cc_final: 0.8390 (mmm-85) REVERT: J 49 TYR cc_start: 0.9281 (p90) cc_final: 0.8976 (p90) REVERT: J 163 ASP cc_start: 0.8988 (p0) cc_final: 0.8625 (p0) REVERT: J 172 ASN cc_start: 0.9350 (t0) cc_final: 0.9129 (t0) REVERT: J 175 TYR cc_start: 0.9483 (t80) cc_final: 0.9191 (t80) REVERT: J 195 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7655 (mm-40) outliers start: 43 outliers final: 32 residues processed: 240 average time/residue: 0.3156 time to fit residues: 109.1857 Evaluate side-chains 223 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 189 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 158 ASN ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN C 195 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 ASN J 38 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 16780 Z= 0.446 Angle : 0.621 13.172 22810 Z= 0.328 Chirality : 0.048 0.217 2470 Planarity : 0.004 0.045 2900 Dihedral : 4.856 39.217 2200 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.56 % Allowed : 17.56 % Favored : 79.89 % 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: -1.93 (0.18), residues: 2040 helix: 3.29 (0.42), residues: 110 sheet: -1.41 (0.16), residues: 960 loop : -1.58 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 100 HIS 0.006 0.002 HIS C 38 PHE 0.016 0.002 PHE C 52 TYR 0.028 0.002 TYR G 125 ARG 0.006 0.001 ARG D 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 190 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9382 (t0) cc_final: 0.8874 (t0) REVERT: E 176 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.8915 (mm) REVERT: E 203 GLN cc_start: 0.8777 (pt0) cc_final: 0.8269 (pt0) REVERT: A 186 ASN cc_start: 0.9258 (t0) cc_final: 0.8913 (t0) REVERT: B 91 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8621 (p) REVERT: B 195 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7519 (mm-40) REVERT: C 60 ASP cc_start: 0.7711 (p0) cc_final: 0.7382 (p0) REVERT: C 122 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8828 (mmtt) REVERT: C 186 ASN cc_start: 0.9471 (t0) cc_final: 0.9142 (t0) REVERT: D 49 TYR cc_start: 0.9365 (p90) cc_final: 0.9040 (p90) REVERT: D 197 GLU cc_start: 0.8294 (pm20) cc_final: 0.7908 (pm20) REVERT: D 203 GLN cc_start: 0.8980 (pt0) cc_final: 0.8703 (pt0) REVERT: F 23 LYS cc_start: 0.8843 (mptt) cc_final: 0.8434 (mmtt) REVERT: I 6 ARG cc_start: 0.8862 (mmm-85) cc_final: 0.8572 (mmm-85) REVERT: I 125 TYR cc_start: 0.8698 (t80) cc_final: 0.8049 (t80) REVERT: J 108 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.6933 (mm-30) REVERT: J 172 ASN cc_start: 0.9391 (t0) cc_final: 0.9184 (t0) REVERT: J 191 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8923 (ttpp) REVERT: J 195 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7816 (mm-40) outliers start: 46 outliers final: 34 residues processed: 230 average time/residue: 0.3123 time to fit residues: 103.8295 Evaluate side-chains 215 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 177 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain J residue 108 GLU Chi-restraints excluded: chain J residue 191 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN C 195 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 16780 Z= 0.225 Angle : 0.546 11.631 22810 Z= 0.288 Chirality : 0.047 0.174 2470 Planarity : 0.004 0.044 2900 Dihedral : 4.583 36.158 2200 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.50 % Allowed : 18.33 % Favored : 79.17 % 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: -1.64 (0.18), residues: 2040 helix: 3.58 (0.41), residues: 110 sheet: -1.23 (0.16), residues: 960 loop : -1.39 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 100 HIS 0.010 0.002 HIS J 38 PHE 0.011 0.001 PHE C 52 TYR 0.022 0.001 TYR G 125 ARG 0.007 0.001 ARG D 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 204 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9362 (t0) cc_final: 0.8789 (t0) REVERT: E 176 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8834 (mm) REVERT: E 203 GLN cc_start: 0.8740 (pt0) cc_final: 0.8207 (pt0) REVERT: A 186 ASN cc_start: 0.9251 (t0) cc_final: 0.8903 (t0) REVERT: B 91 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8610 (p) REVERT: B 195 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7545 (mm-40) REVERT: C 60 ASP cc_start: 0.7671 (p0) cc_final: 0.7382 (p0) REVERT: C 122 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8777 (mmtt) REVERT: C 186 ASN cc_start: 0.9475 (t0) cc_final: 0.9111 (t0) REVERT: D 49 TYR cc_start: 0.9372 (p90) cc_final: 0.9015 (p90) REVERT: D 197 GLU cc_start: 0.8231 (pm20) cc_final: 0.7801 (pm20) REVERT: F 23 LYS cc_start: 0.8851 (mptt) cc_final: 0.8291 (mmtt) REVERT: G 195 GLN cc_start: 0.7628 (tp40) cc_final: 0.7311 (tp40) REVERT: I 6 ARG cc_start: 0.8844 (mmm-85) cc_final: 0.8541 (mmm-85) REVERT: I 125 TYR cc_start: 0.8732 (t80) cc_final: 0.8016 (t80) REVERT: J 172 ASN cc_start: 0.9386 (t0) cc_final: 0.9174 (t0) REVERT: J 195 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7835 (mm-40) outliers start: 45 outliers final: 33 residues processed: 239 average time/residue: 0.3059 time to fit residues: 106.2804 Evaluate side-chains 225 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 190 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 108 optimal weight: 0.0980 chunk 192 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 88 optimal weight: 0.1980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN C 195 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16780 Z= 0.188 Angle : 0.537 10.954 22810 Z= 0.284 Chirality : 0.047 0.166 2470 Planarity : 0.004 0.044 2900 Dihedral : 4.400 31.902 2200 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.11 % Allowed : 18.83 % Favored : 79.06 % 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: -1.48 (0.18), residues: 2040 helix: 3.82 (0.41), residues: 110 sheet: -1.04 (0.17), residues: 910 loop : -1.42 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 100 HIS 0.012 0.002 HIS J 38 PHE 0.019 0.001 PHE D 180 TYR 0.018 0.001 TYR G 125 ARG 0.007 0.001 ARG D 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 212 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9371 (t0) cc_final: 0.8801 (t0) REVERT: E 176 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8753 (mm) REVERT: E 203 GLN cc_start: 0.8706 (pt0) cc_final: 0.8236 (pt0) REVERT: A 186 ASN cc_start: 0.9287 (t0) cc_final: 0.8910 (t0) REVERT: B 91 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8620 (p) REVERT: B 195 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7530 (mp10) REVERT: C 60 ASP cc_start: 0.7678 (p0) cc_final: 0.7396 (p0) REVERT: C 122 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8745 (mmtt) REVERT: C 125 TYR cc_start: 0.8954 (t80) cc_final: 0.8628 (t80) REVERT: C 186 ASN cc_start: 0.9452 (t0) cc_final: 0.9088 (t0) REVERT: D 14 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: D 49 TYR cc_start: 0.9380 (p90) cc_final: 0.9017 (p90) REVERT: F 23 LYS cc_start: 0.8870 (mptt) cc_final: 0.8316 (mmtt) REVERT: F 73 TYR cc_start: 0.9076 (m-80) cc_final: 0.8738 (m-80) REVERT: F 195 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8275 (mm-40) REVERT: G 195 GLN cc_start: 0.7635 (tp40) cc_final: 0.7290 (tp40) REVERT: I 125 TYR cc_start: 0.8688 (t80) cc_final: 0.7968 (t80) REVERT: J 49 TYR cc_start: 0.9303 (p90) cc_final: 0.9031 (p90) REVERT: J 172 ASN cc_start: 0.9368 (t0) cc_final: 0.9161 (t0) REVERT: J 195 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7875 (mm-40) outliers start: 38 outliers final: 28 residues processed: 243 average time/residue: 0.3079 time to fit residues: 108.2875 Evaluate side-chains 228 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 197 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16780 Z= 0.233 Angle : 0.552 10.979 22810 Z= 0.290 Chirality : 0.047 0.174 2470 Planarity : 0.004 0.044 2900 Dihedral : 4.391 31.011 2200 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.06 % Allowed : 19.22 % Favored : 78.72 % 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: -1.35 (0.18), residues: 2040 helix: 3.77 (0.41), residues: 110 sheet: -1.09 (0.16), residues: 980 loop : -1.12 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 100 HIS 0.005 0.001 HIS C 38 PHE 0.011 0.001 PHE J 66 TYR 0.016 0.001 TYR G 125 ARG 0.008 0.001 ARG D 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 205 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9385 (t0) cc_final: 0.8859 (t0) REVERT: E 176 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8767 (mm) REVERT: E 203 GLN cc_start: 0.8706 (pt0) cc_final: 0.8175 (pt0) REVERT: A 186 ASN cc_start: 0.9291 (t0) cc_final: 0.8924 (t0) REVERT: B 91 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8635 (p) REVERT: B 195 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7569 (mp10) REVERT: C 60 ASP cc_start: 0.7783 (p0) cc_final: 0.7484 (p0) REVERT: C 122 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8761 (mmtt) REVERT: C 186 ASN cc_start: 0.9454 (t0) cc_final: 0.9078 (t0) REVERT: D 14 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7513 (tt0) REVERT: D 49 TYR cc_start: 0.9402 (p90) cc_final: 0.9066 (p90) REVERT: F 23 LYS cc_start: 0.8873 (mptt) cc_final: 0.8305 (mmtt) REVERT: F 73 TYR cc_start: 0.9080 (m-80) cc_final: 0.8726 (m-80) REVERT: F 195 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8371 (mm-40) REVERT: I 125 TYR cc_start: 0.8704 (t80) cc_final: 0.8054 (t80) REVERT: J 49 TYR cc_start: 0.9301 (p90) cc_final: 0.9015 (p90) REVERT: J 172 ASN cc_start: 0.9387 (t0) cc_final: 0.9171 (t0) REVERT: J 195 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7938 (mm-40) REVERT: H 38 HIS cc_start: 0.9005 (OUTLIER) cc_final: 0.8772 (m-70) outliers start: 37 outliers final: 31 residues processed: 236 average time/residue: 0.2980 time to fit residues: 102.8353 Evaluate side-chains 231 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 196 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 38 HIS Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 6.9990 chunk 168 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 chunk 108 optimal weight: 0.0870 chunk 78 optimal weight: 0.0370 chunk 141 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 189 optimal weight: 0.9980 overall best weight: 1.1438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN A 195 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16780 Z= 0.182 Angle : 0.544 10.558 22810 Z= 0.286 Chirality : 0.047 0.164 2470 Planarity : 0.004 0.044 2900 Dihedral : 4.296 29.071 2200 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.11 % Allowed : 19.50 % Favored : 78.39 % 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: -1.21 (0.19), residues: 2040 helix: 3.89 (0.41), residues: 110 sheet: -0.99 (0.17), residues: 980 loop : -1.03 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 100 HIS 0.008 0.002 HIS J 38 PHE 0.017 0.001 PHE J 39 TYR 0.017 0.001 TYR G 125 ARG 0.009 0.001 ARG D 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 212 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9375 (t0) cc_final: 0.8864 (t0) REVERT: E 176 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8761 (mm) REVERT: E 203 GLN cc_start: 0.8637 (pt0) cc_final: 0.8118 (pt0) REVERT: A 186 ASN cc_start: 0.9240 (t0) cc_final: 0.8880 (t0) REVERT: B 91 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8614 (p) REVERT: B 195 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7601 (mp10) REVERT: C 60 ASP cc_start: 0.7761 (p0) cc_final: 0.7455 (p0) REVERT: C 122 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8664 (mmtt) REVERT: C 125 TYR cc_start: 0.8929 (t80) cc_final: 0.8598 (t80) REVERT: C 186 ASN cc_start: 0.9432 (t0) cc_final: 0.8983 (t0) REVERT: D 14 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: D 49 TYR cc_start: 0.9401 (p90) cc_final: 0.9056 (p90) REVERT: D 195 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8419 (mm-40) REVERT: F 23 LYS cc_start: 0.8857 (mptt) cc_final: 0.8343 (mmtt) REVERT: F 73 TYR cc_start: 0.9038 (m-80) cc_final: 0.8676 (m-80) REVERT: F 195 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8412 (mm-40) REVERT: I 98 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7784 (t) REVERT: I 125 TYR cc_start: 0.8700 (t80) cc_final: 0.8074 (t80) REVERT: J 137 GLN cc_start: 0.8671 (mp10) cc_final: 0.8160 (mp10) REVERT: J 172 ASN cc_start: 0.9380 (t0) cc_final: 0.9162 (t0) REVERT: J 195 GLN cc_start: 0.8384 (mm-40) cc_final: 0.7831 (mm-40) REVERT: H 38 HIS cc_start: 0.8952 (OUTLIER) cc_final: 0.8721 (m-70) outliers start: 38 outliers final: 30 residues processed: 242 average time/residue: 0.3084 time to fit residues: 108.3894 Evaluate side-chains 236 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 201 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 38 HIS Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 97 optimal weight: 0.3980 chunk 126 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16780 Z= 0.315 Angle : 0.592 11.415 22810 Z= 0.312 Chirality : 0.047 0.181 2470 Planarity : 0.004 0.044 2900 Dihedral : 4.547 33.347 2200 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.06 % Allowed : 19.83 % Favored : 78.11 % 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: -1.29 (0.18), residues: 2040 helix: 3.65 (0.41), residues: 110 sheet: -0.98 (0.17), residues: 960 loop : -1.15 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 100 HIS 0.005 0.002 HIS C 38 PHE 0.013 0.001 PHE C 52 TYR 0.021 0.001 TYR I 175 ARG 0.008 0.001 ARG B 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 196 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 172 ASN cc_start: 0.9379 (t0) cc_final: 0.8847 (t0) REVERT: E 176 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8670 (mm) REVERT: E 203 GLN cc_start: 0.8615 (pt0) cc_final: 0.8001 (pt0) REVERT: A 186 ASN cc_start: 0.9242 (t0) cc_final: 0.8907 (t0) REVERT: B 91 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8612 (p) REVERT: B 195 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7550 (mp10) REVERT: C 60 ASP cc_start: 0.7732 (p0) cc_final: 0.7403 (p0) REVERT: C 186 ASN cc_start: 0.9429 (t0) cc_final: 0.8986 (t0) REVERT: D 14 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: D 49 TYR cc_start: 0.9386 (p90) cc_final: 0.9058 (p90) REVERT: F 23 LYS cc_start: 0.8854 (mptt) cc_final: 0.8291 (mmtt) REVERT: F 73 TYR cc_start: 0.9104 (m-80) cc_final: 0.8752 (m-80) REVERT: I 125 TYR cc_start: 0.8770 (t80) cc_final: 0.8184 (t80) REVERT: J 49 TYR cc_start: 0.9288 (p90) cc_final: 0.9002 (p90) REVERT: J 172 ASN cc_start: 0.9399 (t0) cc_final: 0.9188 (t0) REVERT: J 195 GLN cc_start: 0.8460 (mm-40) cc_final: 0.7897 (mm-40) REVERT: H 38 HIS cc_start: 0.9020 (OUTLIER) cc_final: 0.8749 (m-70) outliers start: 37 outliers final: 30 residues processed: 226 average time/residue: 0.3028 time to fit residues: 100.3954 Evaluate side-chains 225 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 38 HIS Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 158 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN C 195 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 GLN J 38 HIS ** H 38 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 = 0.2963 r_free = 0.2963 target = 0.063877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.051940 restraints weight = 47822.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.054023 restraints weight = 21599.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.055434 restraints weight = 12955.381| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 16780 Z= 0.274 Angle : 0.586 11.078 22810 Z= 0.310 Chirality : 0.047 0.174 2470 Planarity : 0.004 0.044 2900 Dihedral : 4.558 31.956 2200 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.94 % Allowed : 20.22 % Favored : 77.83 % 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: -1.24 (0.18), residues: 2040 helix: 3.62 (0.41), residues: 110 sheet: -0.95 (0.17), residues: 960 loop : -1.11 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 100 HIS 0.005 0.001 HIS C 38 PHE 0.012 0.001 PHE C 52 TYR 0.019 0.001 TYR I 175 ARG 0.008 0.001 ARG B 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3096.40 seconds wall clock time: 56 minutes 23.42 seconds (3383.42 seconds total)