Starting phenix.real_space_refine on Fri Aug 9 13:19:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8heg_34690/08_2024/8heg_34690.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8heg_34690/08_2024/8heg_34690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8heg_34690/08_2024/8heg_34690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8heg_34690/08_2024/8heg_34690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8heg_34690/08_2024/8heg_34690.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8heg_34690/08_2024/8heg_34690.cif" } resolution = 3.2 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= 0.004 sd= 0.131 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 16940 2.51 5 N 4615 2.21 5 O 4935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 37": "OD1" <-> "OD2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 171": "OD1" <-> "OD2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 106": "OD1" <-> "OD2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ASP 59": "OD1" <-> "OD2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C ASP 135": "OD1" <-> "OD2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C ASP 174": "OD1" <-> "OD2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C ASP 217": "OD1" <-> "OD2" Residue "D PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "E ASP 37": "OD1" <-> "OD2" Residue "E PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "E GLU 174": "OE1" <-> "OE2" Residue "E TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 106": "OD1" <-> "OD2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 49": "OE1" <-> "OE2" Residue "G ASP 59": "OD1" <-> "OD2" Residue "G ASP 78": "OD1" <-> "OD2" Residue "G ASP 135": "OD1" <-> "OD2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G ASP 174": "OD1" <-> "OD2" Residue "G GLU 177": "OE1" <-> "OE2" Residue "G ASP 198": "OD1" <-> "OD2" Residue "G ASP 217": "OD1" <-> "OD2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 55": "OD1" <-> "OD2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 62": "OD1" <-> "OD2" Residue "H ASP 99": "OD1" <-> "OD2" Residue "I ASP 37": "OD1" <-> "OD2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 171": "OD1" <-> "OD2" Residue "I GLU 174": "OE1" <-> "OE2" Residue "I TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 106": "OD1" <-> "OD2" Residue "J PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K ASP 59": "OD1" <-> "OD2" Residue "K ASP 78": "OD1" <-> "OD2" Residue "K ASP 135": "OD1" <-> "OD2" Residue "K GLU 147": "OE1" <-> "OE2" Residue "K ASP 174": "OD1" <-> "OD2" Residue "K GLU 177": "OE1" <-> "OE2" Residue "K ASP 198": "OD1" <-> "OD2" Residue "K ASP 217": "OD1" <-> "OD2" Residue "L PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 55": "OD1" <-> "OD2" Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 62": "OD1" <-> "OD2" Residue "L ASP 99": "OD1" <-> "OD2" Residue "M ASP 37": "OD1" <-> "OD2" Residue "M PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 77": "OE1" <-> "OE2" Residue "M GLU 95": "OE1" <-> "OE2" Residue "M TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 171": "OD1" <-> "OD2" Residue "M GLU 174": "OE1" <-> "OE2" Residue "M TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 49": "OE1" <-> "OE2" Residue "O ASP 59": "OD1" <-> "OD2" Residue "O ASP 78": "OD1" <-> "OD2" Residue "O ASP 135": "OD1" <-> "OD2" Residue "O GLU 147": "OE1" <-> "OE2" Residue "O ASP 174": "OD1" <-> "OD2" Residue "O GLU 177": "OE1" <-> "OE2" Residue "O ASP 198": "OD1" <-> "OD2" Residue "O ASP 217": "OD1" <-> "OD2" Residue "P PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 55": "OD1" <-> "OD2" Residue "P TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 62": "OD1" <-> "OD2" Residue "P ASP 99": "OD1" <-> "OD2" Residue "Q ASP 37": "OD1" <-> "OD2" Residue "Q PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 77": "OE1" <-> "OE2" Residue "Q GLU 95": "OE1" <-> "OE2" Residue "Q TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 171": "OD1" <-> "OD2" Residue "Q GLU 174": "OE1" <-> "OE2" Residue "Q TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 106": "OD1" <-> "OD2" Residue "R PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "S ASP 59": "OD1" <-> "OD2" Residue "S ASP 78": "OD1" <-> "OD2" Residue "S ASP 135": "OD1" <-> "OD2" Residue "S GLU 147": "OE1" <-> "OE2" Residue "S ASP 174": "OD1" <-> "OD2" Residue "S GLU 177": "OE1" <-> "OE2" Residue "S ASP 198": "OD1" <-> "OD2" Residue "S ASP 217": "OD1" <-> "OD2" Residue "T PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 55": "OD1" <-> "OD2" Residue "T TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 62": "OD1" <-> "OD2" Residue "T ASP 99": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 26595 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1318 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "B" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 155} Chain: "C" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "E" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1318 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "F" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 155} Chain: "G" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "I" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1318 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "J" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 155} Chain: "K" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "M" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1318 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "N" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 155} Chain: "O" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "Q" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1318 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "R" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 155} Chain: "S" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Time building chain proxies: 14.26, per 1000 atoms: 0.54 Number of scatterers: 26595 At special positions: 0 Unit cell: (180.83, 181.9, 93.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4935 8.00 N 4615 7.00 C 16940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.67 Conformation dependent library (CDL) restraints added in 5.0 seconds 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6300 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 65 sheets defined 13.1% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.616A pdb=" N MET A 36 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.645A pdb=" N THR A 56 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.596A pdb=" N SER A 99 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 59 removed outlier: 3.802A pdb=" N GLU B 59 " --> pdb=" O THR B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 59' Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.548A pdb=" N HIS B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 143 removed outlier: 3.596A pdb=" N TYR B 138 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 140 " --> pdb=" O LYS B 137 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR B 141 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 142 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE B 143 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 51 removed outlier: 3.644A pdb=" N VAL C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 4.546A pdb=" N ASN C 88 " --> pdb=" O HIS C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.503A pdb=" N TYR D 31 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.616A pdb=" N MET E 36 " --> pdb=" O VAL E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 56 removed outlier: 3.645A pdb=" N THR E 56 " --> pdb=" O LEU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'E' and resid 94 through 100 removed outlier: 3.596A pdb=" N SER E 99 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 59 removed outlier: 3.802A pdb=" N GLU F 59 " --> pdb=" O THR F 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 56 through 59' Processing helix chain 'F' and resid 89 through 97 removed outlier: 3.548A pdb=" N HIS F 93 " --> pdb=" O GLY F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 143 removed outlier: 3.596A pdb=" N TYR F 138 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU F 140 " --> pdb=" O LYS F 137 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR F 141 " --> pdb=" O TYR F 138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU F 142 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE F 143 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 51 removed outlier: 3.644A pdb=" N VAL G 47 " --> pdb=" O ASN G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 88 removed outlier: 4.546A pdb=" N ASN G 88 " --> pdb=" O HIS G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 138 through 143 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.504A pdb=" N TYR H 31 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 31 through 36 removed outlier: 3.616A pdb=" N MET I 36 " --> pdb=" O VAL I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 56 removed outlier: 3.645A pdb=" N THR I 56 " --> pdb=" O LEU I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 68 Processing helix chain 'I' and resid 94 through 100 removed outlier: 3.596A pdb=" N SER I 99 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN I 100 " --> pdb=" O ALA I 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 59 removed outlier: 3.802A pdb=" N GLU J 59 " --> pdb=" O THR J 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 59' Processing helix chain 'J' and resid 89 through 97 removed outlier: 3.549A pdb=" N HIS J 93 " --> pdb=" O GLY J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 143 removed outlier: 3.596A pdb=" N TYR J 138 " --> pdb=" O ARG J 135 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU J 140 " --> pdb=" O LYS J 137 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR J 141 " --> pdb=" O TYR J 138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU J 142 " --> pdb=" O GLN J 139 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE J 143 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 51 removed outlier: 3.643A pdb=" N VAL K 47 " --> pdb=" O ASN K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 88 removed outlier: 4.546A pdb=" N ASN K 88 " --> pdb=" O HIS K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 96 Processing helix chain 'K' and resid 138 through 143 Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.503A pdb=" N TYR L 31 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR L 32 " --> pdb=" O PHE L 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 32' Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'M' and resid 31 through 36 removed outlier: 3.616A pdb=" N MET M 36 " --> pdb=" O VAL M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 56 removed outlier: 3.645A pdb=" N THR M 56 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 68 Processing helix chain 'M' and resid 94 through 100 removed outlier: 3.596A pdb=" N SER M 99 " --> pdb=" O ALA M 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN M 100 " --> pdb=" O ALA M 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 59 removed outlier: 3.802A pdb=" N GLU N 59 " --> pdb=" O THR N 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 56 through 59' Processing helix chain 'N' and resid 89 through 97 removed outlier: 3.548A pdb=" N HIS N 93 " --> pdb=" O GLY N 89 " (cutoff:3.500A) Processing helix chain 'N' and resid 133 through 143 removed outlier: 3.596A pdb=" N TYR N 138 " --> pdb=" O ARG N 135 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU N 140 " --> pdb=" O LYS N 137 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR N 141 " --> pdb=" O TYR N 138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU N 142 " --> pdb=" O GLN N 139 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE N 143 " --> pdb=" O LEU N 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 51 removed outlier: 3.644A pdb=" N VAL O 47 " --> pdb=" O ASN O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 88 removed outlier: 4.546A pdb=" N ASN O 88 " --> pdb=" O HIS O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 96 Processing helix chain 'O' and resid 138 through 143 Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.503A pdb=" N TYR P 31 " --> pdb=" O ALA P 28 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR P 32 " --> pdb=" O PHE P 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 28 through 32' Processing helix chain 'P' and resid 87 through 91 Processing helix chain 'Q' and resid 31 through 36 removed outlier: 3.616A pdb=" N MET Q 36 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 56 removed outlier: 3.645A pdb=" N THR Q 56 " --> pdb=" O LEU Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 68 Processing helix chain 'Q' and resid 94 through 100 removed outlier: 3.596A pdb=" N SER Q 99 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN Q 100 " --> pdb=" O ALA Q 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 59 removed outlier: 3.802A pdb=" N GLU R 59 " --> pdb=" O THR R 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 56 through 59' Processing helix chain 'R' and resid 89 through 97 removed outlier: 3.548A pdb=" N HIS R 93 " --> pdb=" O GLY R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 143 removed outlier: 3.596A pdb=" N TYR R 138 " --> pdb=" O ARG R 135 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU R 140 " --> pdb=" O LYS R 137 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR R 141 " --> pdb=" O TYR R 138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU R 142 " --> pdb=" O GLN R 139 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE R 143 " --> pdb=" O LEU R 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 51 removed outlier: 3.643A pdb=" N VAL S 47 " --> pdb=" O ASN S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 88 removed outlier: 4.547A pdb=" N ASN S 88 " --> pdb=" O HIS S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 96 Processing helix chain 'S' and resid 138 through 143 Processing helix chain 'T' and resid 28 through 32 removed outlier: 3.503A pdb=" N TYR T 31 " --> pdb=" O ALA T 28 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR T 32 " --> pdb=" O PHE T 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 28 through 32' Processing helix chain 'T' and resid 87 through 91 Processing sheet with id=1, first strand: chain 'A' and resid 40 through 41 removed outlier: 4.321A pdb=" N ASP A 171 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 83 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG A 81 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU A 175 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 79 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL A 177 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU A 77 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=3, first strand: chain 'A' and resid 126 through 127 removed outlier: 3.563A pdb=" N TYR A 72 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR A 185 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR A 72 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU A 183 " --> pdb=" O TYR A 72 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.912A pdb=" N TYR B 100 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLU B 213 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE B 98 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'B' and resid 68 through 69 removed outlier: 4.120A pdb=" N LYS B 198 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 78 through 82 removed outlier: 6.489A pdb=" N CYS B 120 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLY B 118 " --> pdb=" O PRO B 186 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 158 through 160 removed outlier: 3.587A pdb=" N ILE B 158 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.543A pdb=" N THR C 53 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 73 through 79 removed outlier: 6.736A pdb=" N LEU C 73 " --> pdb=" O GLN C 189 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN C 189 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA C 75 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY C 183 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG C 120 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE C 144 " --> pdb=" O TYR C 125 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=11, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=12, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.322A pdb=" N GLY D 10 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER D 121 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL D 12 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.322A pdb=" N GLY D 10 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER D 121 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL D 12 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D 111 " --> pdb=" O GLY D 98 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'E' and resid 40 through 41 removed outlier: 4.322A pdb=" N ASP E 171 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU E 83 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG E 81 " --> pdb=" O SER E 173 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU E 175 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL E 79 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL E 177 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU E 77 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'E' and resid 48 through 50 Processing sheet with id=16, first strand: chain 'E' and resid 126 through 127 removed outlier: 3.563A pdb=" N TYR E 72 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR E 185 " --> pdb=" O THR E 70 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR E 72 " --> pdb=" O GLU E 183 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU E 183 " --> pdb=" O TYR E 72 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.911A pdb=" N TYR F 100 " --> pdb=" O ALA F 211 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLU F 213 " --> pdb=" O PHE F 98 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE F 98 " --> pdb=" O GLU F 213 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'F' and resid 68 through 69 removed outlier: 4.121A pdb=" N LYS F 198 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'F' and resid 78 through 82 removed outlier: 6.490A pdb=" N CYS F 120 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLY F 118 " --> pdb=" O PRO F 186 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'F' and resid 158 through 160 removed outlier: 3.587A pdb=" N ILE F 158 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.543A pdb=" N THR G 53 " --> pdb=" O VAL G 204 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'G' and resid 73 through 79 removed outlier: 6.736A pdb=" N LEU G 73 " --> pdb=" O GLN G 189 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN G 189 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA G 75 " --> pdb=" O ILE G 187 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY G 183 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG G 120 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE G 144 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'G' and resid 100 through 101 Processing sheet with id=24, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=25, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.322A pdb=" N GLY H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N SER H 121 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL H 12 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.322A pdb=" N GLY H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N SER H 121 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL H 12 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR H 111 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'I' and resid 40 through 41 removed outlier: 4.321A pdb=" N ASP I 171 " --> pdb=" O GLU I 83 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU I 83 " --> pdb=" O ASP I 171 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG I 81 " --> pdb=" O SER I 173 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU I 175 " --> pdb=" O VAL I 79 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL I 79 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL I 177 " --> pdb=" O GLU I 77 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU I 77 " --> pdb=" O VAL I 177 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'I' and resid 48 through 50 Processing sheet with id=29, first strand: chain 'I' and resid 126 through 127 removed outlier: 3.563A pdb=" N TYR I 72 " --> pdb=" O LEU I 126 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR I 185 " --> pdb=" O THR I 70 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR I 72 " --> pdb=" O GLU I 183 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU I 183 " --> pdb=" O TYR I 72 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.911A pdb=" N TYR J 100 " --> pdb=" O ALA J 211 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLU J 213 " --> pdb=" O PHE J 98 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE J 98 " --> pdb=" O GLU J 213 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'J' and resid 68 through 69 removed outlier: 4.121A pdb=" N LYS J 198 " --> pdb=" O VAL J 112 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'J' and resid 78 through 82 removed outlier: 6.489A pdb=" N CYS J 120 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLY J 118 " --> pdb=" O PRO J 186 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'J' and resid 158 through 160 removed outlier: 3.588A pdb=" N ILE J 158 " --> pdb=" O VAL J 107 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.543A pdb=" N THR K 53 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'K' and resid 73 through 79 removed outlier: 6.736A pdb=" N LEU K 73 " --> pdb=" O GLN K 189 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN K 189 " --> pdb=" O LEU K 73 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA K 75 " --> pdb=" O ILE K 187 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY K 183 " --> pdb=" O VAL K 79 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG K 120 " --> pdb=" O ILE K 190 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE K 144 " --> pdb=" O TYR K 125 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'K' and resid 100 through 101 Processing sheet with id=37, first strand: chain 'L' and resid 3 through 7 Processing sheet with id=38, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.323A pdb=" N GLY L 10 " --> pdb=" O THR L 119 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N SER L 121 " --> pdb=" O GLY L 10 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL L 12 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET L 34 " --> pdb=" O ALA L 50 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.323A pdb=" N GLY L 10 " --> pdb=" O THR L 119 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N SER L 121 " --> pdb=" O GLY L 10 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL L 12 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR L 111 " --> pdb=" O GLY L 98 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'M' and resid 40 through 41 removed outlier: 4.322A pdb=" N ASP M 171 " --> pdb=" O GLU M 83 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU M 83 " --> pdb=" O ASP M 171 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG M 81 " --> pdb=" O SER M 173 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU M 175 " --> pdb=" O VAL M 79 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL M 79 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL M 177 " --> pdb=" O GLU M 77 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU M 77 " --> pdb=" O VAL M 177 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'M' and resid 48 through 50 Processing sheet with id=42, first strand: chain 'M' and resid 126 through 127 removed outlier: 3.563A pdb=" N TYR M 72 " --> pdb=" O LEU M 126 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR M 185 " --> pdb=" O THR M 70 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR M 72 " --> pdb=" O GLU M 183 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU M 183 " --> pdb=" O TYR M 72 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'N' and resid 53 through 54 removed outlier: 3.912A pdb=" N TYR N 100 " --> pdb=" O ALA N 211 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLU N 213 " --> pdb=" O PHE N 98 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE N 98 " --> pdb=" O GLU N 213 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'N' and resid 68 through 69 removed outlier: 4.121A pdb=" N LYS N 198 " --> pdb=" O VAL N 112 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'N' and resid 78 through 82 removed outlier: 6.489A pdb=" N CYS N 120 " --> pdb=" O VAL N 184 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLY N 118 " --> pdb=" O PRO N 186 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'N' and resid 158 through 160 removed outlier: 3.587A pdb=" N ILE N 158 " --> pdb=" O VAL N 107 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'O' and resid 53 through 54 removed outlier: 3.543A pdb=" N THR O 53 " --> pdb=" O VAL O 204 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'O' and resid 73 through 79 removed outlier: 6.736A pdb=" N LEU O 73 " --> pdb=" O GLN O 189 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN O 189 " --> pdb=" O LEU O 73 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA O 75 " --> pdb=" O ILE O 187 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY O 183 " --> pdb=" O VAL O 79 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG O 120 " --> pdb=" O ILE O 190 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE O 144 " --> pdb=" O TYR O 125 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'O' and resid 100 through 101 Processing sheet with id=50, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=51, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.322A pdb=" N GLY P 10 " --> pdb=" O THR P 119 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER P 121 " --> pdb=" O GLY P 10 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL P 12 " --> pdb=" O SER P 121 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N MET P 34 " --> pdb=" O ALA P 50 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.322A pdb=" N GLY P 10 " --> pdb=" O THR P 119 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER P 121 " --> pdb=" O GLY P 10 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL P 12 " --> pdb=" O SER P 121 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR P 111 " --> pdb=" O GLY P 98 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'Q' and resid 40 through 41 removed outlier: 4.321A pdb=" N ASP Q 171 " --> pdb=" O GLU Q 83 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU Q 83 " --> pdb=" O ASP Q 171 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG Q 81 " --> pdb=" O SER Q 173 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU Q 175 " --> pdb=" O VAL Q 79 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL Q 79 " --> pdb=" O LEU Q 175 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL Q 177 " --> pdb=" O GLU Q 77 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU Q 77 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'Q' and resid 48 through 50 Processing sheet with id=55, first strand: chain 'Q' and resid 126 through 127 removed outlier: 3.563A pdb=" N TYR Q 72 " --> pdb=" O LEU Q 126 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR Q 185 " --> pdb=" O THR Q 70 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR Q 72 " --> pdb=" O GLU Q 183 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU Q 183 " --> pdb=" O TYR Q 72 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'R' and resid 53 through 54 removed outlier: 3.912A pdb=" N TYR R 100 " --> pdb=" O ALA R 211 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLU R 213 " --> pdb=" O PHE R 98 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE R 98 " --> pdb=" O GLU R 213 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'R' and resid 68 through 69 removed outlier: 4.120A pdb=" N LYS R 198 " --> pdb=" O VAL R 112 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'R' and resid 78 through 82 removed outlier: 6.490A pdb=" N CYS R 120 " --> pdb=" O VAL R 184 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLY R 118 " --> pdb=" O PRO R 186 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'R' and resid 158 through 160 removed outlier: 3.587A pdb=" N ILE R 158 " --> pdb=" O VAL R 107 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'S' and resid 53 through 54 removed outlier: 3.544A pdb=" N THR S 53 " --> pdb=" O VAL S 204 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'S' and resid 73 through 79 removed outlier: 6.736A pdb=" N LEU S 73 " --> pdb=" O GLN S 189 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN S 189 " --> pdb=" O LEU S 73 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA S 75 " --> pdb=" O ILE S 187 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY S 183 " --> pdb=" O VAL S 79 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG S 120 " --> pdb=" O ILE S 190 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE S 144 " --> pdb=" O TYR S 125 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'S' and resid 100 through 101 Processing sheet with id=63, first strand: chain 'T' and resid 3 through 7 Processing sheet with id=64, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.322A pdb=" N GLY T 10 " --> pdb=" O THR T 119 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N SER T 121 " --> pdb=" O GLY T 10 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL T 12 " --> pdb=" O SER T 121 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET T 34 " --> pdb=" O ALA T 50 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA T 50 " --> pdb=" O MET T 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP T 36 " --> pdb=" O VAL T 48 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.322A pdb=" N GLY T 10 " --> pdb=" O THR T 119 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N SER T 121 " --> pdb=" O GLY T 10 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL T 12 " --> pdb=" O SER T 121 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR T 111 " --> pdb=" O GLY T 98 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 1665 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: 8.43 Time building geometry restraints manager: 10.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6610 1.33 - 1.45: 5771 1.45 - 1.57: 14759 1.57 - 1.69: 5 1.69 - 1.81: 165 Bond restraints: 27310 Sorted by residual: bond pdb=" CA TYR F 200 " pdb=" C TYR F 200 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.34e-02 5.57e+03 1.24e+01 bond pdb=" CA TYR J 200 " pdb=" C TYR J 200 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.34e-02 5.57e+03 1.22e+01 bond pdb=" CA TYR B 200 " pdb=" C TYR B 200 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.34e-02 5.57e+03 1.20e+01 bond pdb=" CA TYR R 200 " pdb=" C TYR R 200 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.34e-02 5.57e+03 1.20e+01 bond pdb=" CA TYR N 200 " pdb=" C TYR N 200 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.34e-02 5.57e+03 1.18e+01 ... (remaining 27305 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.67: 970 106.67 - 113.50: 14663 113.50 - 120.34: 9470 120.34 - 127.17: 11699 127.17 - 134.00: 393 Bond angle restraints: 37195 Sorted by residual: angle pdb=" CA PRO S 62 " pdb=" N PRO S 62 " pdb=" CD PRO S 62 " ideal model delta sigma weight residual 112.00 101.42 10.58 1.40e+00 5.10e-01 5.71e+01 angle pdb=" CA PRO O 62 " pdb=" N PRO O 62 " pdb=" CD PRO O 62 " ideal model delta sigma weight residual 112.00 101.44 10.56 1.40e+00 5.10e-01 5.69e+01 angle pdb=" CA PRO C 62 " pdb=" N PRO C 62 " pdb=" CD PRO C 62 " ideal model delta sigma weight residual 112.00 101.44 10.56 1.40e+00 5.10e-01 5.69e+01 angle pdb=" CA PRO K 62 " pdb=" N PRO K 62 " pdb=" CD PRO K 62 " ideal model delta sigma weight residual 112.00 101.44 10.56 1.40e+00 5.10e-01 5.69e+01 angle pdb=" CA PRO G 62 " pdb=" N PRO G 62 " pdb=" CD PRO G 62 " ideal model delta sigma weight residual 112.00 101.44 10.56 1.40e+00 5.10e-01 5.69e+01 ... (remaining 37190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 13996 17.81 - 35.63: 1675 35.63 - 53.44: 336 53.44 - 71.26: 58 71.26 - 89.07: 25 Dihedral angle restraints: 16090 sinusoidal: 6245 harmonic: 9845 Sorted by residual: dihedral pdb=" CA LEU K 212 " pdb=" C LEU K 212 " pdb=" N ARG K 213 " pdb=" CA ARG K 213 " ideal model delta harmonic sigma weight residual -180.00 -159.25 -20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU C 212 " pdb=" C LEU C 212 " pdb=" N ARG C 213 " pdb=" CA ARG C 213 " ideal model delta harmonic sigma weight residual -180.00 -159.25 -20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU G 212 " pdb=" C LEU G 212 " pdb=" N ARG G 213 " pdb=" CA ARG G 213 " ideal model delta harmonic sigma weight residual -180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 16087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2507 0.032 - 0.065: 1033 0.065 - 0.097: 356 0.097 - 0.129: 158 0.129 - 0.161: 26 Chirality restraints: 4080 Sorted by residual: chirality pdb=" CA TYR J 200 " pdb=" N TYR J 200 " pdb=" C TYR J 200 " pdb=" CB TYR J 200 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA TYR R 200 " pdb=" N TYR R 200 " pdb=" C TYR R 200 " pdb=" CB TYR R 200 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA TYR N 200 " pdb=" N TYR N 200 " pdb=" C TYR N 200 " pdb=" CB TYR N 200 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 4077 not shown) Planarity restraints: 4795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS G 61 " 0.059 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO G 62 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO G 62 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 62 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS K 61 " 0.059 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO K 62 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO K 62 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO K 62 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 61 " -0.059 5.00e-02 4.00e+02 8.35e-02 1.11e+01 pdb=" N PRO C 62 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 62 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 62 " -0.046 5.00e-02 4.00e+02 ... (remaining 4792 not shown) Histogram of nonbonded interaction distances: 0.40 - 1.30: 170 1.30 - 2.20: 355 2.20 - 3.10: 18517 3.10 - 4.00: 63829 4.00 - 4.90: 125237 Warning: very small nonbonded interaction distances. Nonbonded interactions: 208108 Sorted by model distance: nonbonded pdb=" C LEU G 81 " pdb=" NH2 ARG I 200 " model vdw 0.403 3.350 nonbonded pdb=" C LEU O 81 " pdb=" NH2 ARG Q 200 " model vdw 0.403 3.350 nonbonded pdb=" NH2 ARG A 200 " pdb=" C LEU S 81 " model vdw 0.403 3.350 nonbonded pdb=" C LEU C 81 " pdb=" NH2 ARG E 200 " model vdw 0.403 3.350 nonbonded pdb=" C LEU K 81 " pdb=" NH2 ARG M 200 " model vdw 0.404 3.350 ... (remaining 208103 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 'E' selection = chain 'I' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 68.970 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 : 0.004 0.120 27310 Z= 0.272 Angle : 0.703 10.578 37195 Z= 0.419 Chirality : 0.044 0.161 4080 Planarity : 0.006 0.084 4795 Dihedral : 15.873 89.073 9775 Min Nonbonded Distance : 0.403 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.08 % Favored : 92.62 % Rotamer: Outliers : 1.09 % Allowed : 22.19 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.33 (0.14), residues: 3335 helix: -0.42 (0.39), residues: 160 sheet: -0.49 (0.17), residues: 1010 loop : -1.13 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 148 HIS 0.002 0.001 HIS M 49 PHE 0.014 0.002 PHE H 47 TYR 0.019 0.002 TYR L 60 ARG 0.006 0.001 ARG L 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 357 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.6974 (p90) REVERT: D 60 TYR cc_start: 0.7958 (m-80) cc_final: 0.7736 (m-80) REVERT: F 62 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.6732 (p90) REVERT: J 59 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6775 (mt-10) REVERT: J 62 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6083 (p90) REVERT: K 184 TRP cc_start: 0.3501 (m-10) cc_final: 0.3226 (m-10) REVERT: N 59 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6889 (mt-10) REVERT: O 84 LYS cc_start: 0.8153 (tttm) cc_final: 0.7572 (ttpp) REVERT: O 86 MET cc_start: 0.9111 (mmm) cc_final: 0.8767 (mmm) REVERT: Q 119 TYR cc_start: 0.8200 (t80) cc_final: 0.7919 (t80) REVERT: R 59 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6965 (mt-10) REVERT: R 62 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.7125 (p90) REVERT: R 101 MET cc_start: 0.7800 (mtm) cc_final: 0.7411 (mtp) REVERT: R 196 GLU cc_start: 0.6689 (tt0) cc_final: 0.6437 (tt0) outliers start: 31 outliers final: 19 residues processed: 373 average time/residue: 0.4202 time to fit residues: 236.5835 Evaluate side-chains 348 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 325 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 62 PHE Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain R residue 62 PHE Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain T residue 58 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 0.7980 chunk 250 optimal weight: 10.0000 chunk 138 optimal weight: 0.0470 chunk 85 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 258 optimal weight: 9.9990 chunk 100 optimal weight: 0.3980 chunk 157 optimal weight: 0.6980 chunk 192 optimal weight: 7.9990 chunk 299 optimal weight: 0.0970 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS C 221 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 HIS G 31 ASN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 HIS K 31 ASN ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 209 HIS O 31 ASN ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 209 HIS S 31 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27310 Z= 0.233 Angle : 0.716 14.924 37195 Z= 0.372 Chirality : 0.044 0.165 4080 Planarity : 0.008 0.167 4795 Dihedral : 5.871 48.079 3759 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.91 % Favored : 93.94 % Rotamer: Outliers : 3.25 % Allowed : 19.75 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.19 (0.14), residues: 3335 helix: -0.16 (0.42), residues: 160 sheet: -0.21 (0.16), residues: 1040 loop : -1.17 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 148 HIS 0.028 0.002 HIS A 29 PHE 0.015 0.002 PHE E 73 TYR 0.018 0.001 TYR H 60 ARG 0.026 0.001 ARG Q 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 330 time to evaluate : 3.000 Fit side-chains REVERT: A 125 VAL cc_start: 0.7423 (OUTLIER) cc_final: 0.7000 (m) REVERT: D 60 TYR cc_start: 0.7802 (m-80) cc_final: 0.7477 (m-80) REVERT: E 54 MET cc_start: 0.8722 (tpp) cc_final: 0.8478 (mmm) REVERT: E 65 LEU cc_start: 0.8920 (mt) cc_final: 0.8558 (mt) REVERT: E 125 VAL cc_start: 0.7248 (OUTLIER) cc_final: 0.6744 (m) REVERT: G 145 HIS cc_start: 0.6792 (p-80) cc_final: 0.6562 (p90) REVERT: I 54 MET cc_start: 0.8576 (tpp) cc_final: 0.8262 (mmm) REVERT: I 125 VAL cc_start: 0.7308 (OUTLIER) cc_final: 0.6799 (m) REVERT: J 59 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6852 (mt-10) REVERT: M 125 VAL cc_start: 0.7527 (OUTLIER) cc_final: 0.6979 (m) REVERT: N 101 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7463 (mtp) REVERT: Q 54 MET cc_start: 0.8535 (tpp) cc_final: 0.8248 (mmm) REVERT: Q 125 VAL cc_start: 0.7515 (OUTLIER) cc_final: 0.6924 (m) REVERT: R 59 GLU cc_start: 0.7262 (mt-10) cc_final: 0.7022 (mt-10) REVERT: R 101 MET cc_start: 0.7490 (mtm) cc_final: 0.6977 (mtp) REVERT: S 122 MET cc_start: 0.6573 (OUTLIER) cc_final: 0.6254 (ptt) outliers start: 92 outliers final: 38 residues processed: 393 average time/residue: 0.4206 time to fit residues: 249.9674 Evaluate side-chains 337 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 292 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 101 MET Chi-restraints excluded: chain N residue 146 GLN Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain S residue 37 TYR Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 122 MET Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain T residue 31 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 249 optimal weight: 20.0000 chunk 204 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 300 optimal weight: 0.9980 chunk 324 optimal weight: 5.9990 chunk 267 optimal weight: 0.0670 chunk 297 optimal weight: 0.0270 chunk 102 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 221 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27310 Z= 0.183 Angle : 0.566 6.938 37195 Z= 0.300 Chirality : 0.043 0.141 4080 Planarity : 0.006 0.129 4795 Dihedral : 5.039 33.733 3739 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.27 % Favored : 93.58 % Rotamer: Outliers : 3.17 % Allowed : 19.51 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.00 (0.14), residues: 3335 helix: -0.01 (0.44), residues: 160 sheet: -0.02 (0.16), residues: 1065 loop : -1.08 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 148 HIS 0.012 0.001 HIS E 29 PHE 0.010 0.001 PHE P 47 TYR 0.019 0.001 TYR H 60 ARG 0.008 0.000 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 302 time to evaluate : 2.890 Fit side-chains REVERT: B 101 MET cc_start: 0.7587 (mtm) cc_final: 0.7380 (mtp) REVERT: B 171 TYR cc_start: 0.8649 (m-10) cc_final: 0.7803 (m-10) REVERT: E 54 MET cc_start: 0.8721 (tpp) cc_final: 0.8504 (mmm) REVERT: G 145 HIS cc_start: 0.7177 (p-80) cc_final: 0.6865 (p90) REVERT: I 54 MET cc_start: 0.8566 (tpp) cc_final: 0.8294 (mmm) REVERT: J 59 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6817 (mt-10) REVERT: Q 54 MET cc_start: 0.8533 (tpp) cc_final: 0.8308 (mmm) outliers start: 90 outliers final: 61 residues processed: 368 average time/residue: 0.3873 time to fit residues: 221.4389 Evaluate side-chains 350 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 289 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 143 CYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 143 CYS Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 143 CYS Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 161 SER Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain S residue 37 TYR Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 80 SER Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 143 CYS Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain T residue 31 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 5.9990 chunk 225 optimal weight: 0.0000 chunk 155 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 201 optimal weight: 0.9990 chunk 301 optimal weight: 4.9990 chunk 318 optimal weight: 20.0000 chunk 157 optimal weight: 0.9990 chunk 285 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27310 Z= 0.167 Angle : 0.531 9.572 37195 Z= 0.282 Chirality : 0.042 0.175 4080 Planarity : 0.005 0.108 4795 Dihedral : 4.616 20.258 3732 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.85 % Favored : 94.00 % Rotamer: Outliers : 3.03 % Allowed : 20.21 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3335 helix: -0.02 (0.44), residues: 160 sheet: 0.04 (0.16), residues: 1070 loop : -1.03 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 148 HIS 0.010 0.001 HIS E 29 PHE 0.012 0.001 PHE D 68 TYR 0.010 0.001 TYR T 60 ARG 0.007 0.000 ARG M 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 311 time to evaluate : 3.453 Fit side-chains REVERT: B 171 TYR cc_start: 0.8669 (m-10) cc_final: 0.7888 (m-10) REVERT: C 76 LYS cc_start: 0.7358 (mttm) cc_final: 0.7073 (mtpt) REVERT: E 54 MET cc_start: 0.8714 (tpp) cc_final: 0.8355 (mmm) REVERT: E 65 LEU cc_start: 0.8886 (mt) cc_final: 0.8684 (mt) REVERT: G 43 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8619 (t0) REVERT: G 145 HIS cc_start: 0.7390 (p-80) cc_final: 0.7044 (p90) REVERT: I 54 MET cc_start: 0.8629 (tpp) cc_final: 0.8344 (mmm) REVERT: K 110 MET cc_start: 0.6754 (tmm) cc_final: 0.6552 (tmm) REVERT: O 86 MET cc_start: 0.9117 (mmm) cc_final: 0.8691 (mmm) REVERT: Q 54 MET cc_start: 0.8556 (tpp) cc_final: 0.8313 (mmm) REVERT: R 196 GLU cc_start: 0.6847 (tt0) cc_final: 0.6355 (tp30) REVERT: S 43 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8585 (t0) outliers start: 86 outliers final: 60 residues processed: 362 average time/residue: 0.4036 time to fit residues: 224.4200 Evaluate side-chains 362 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 300 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 143 CYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 143 CYS Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain N residue 108 GLU Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 37 TYR Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 143 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain S residue 37 TYR Chi-restraints excluded: chain S residue 43 ASN Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 80 SER Chi-restraints excluded: chain S residue 143 CYS Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain T residue 31 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 272 optimal weight: 3.9990 chunk 220 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 286 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS B 174 HIS C 31 ASN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 HIS F 174 HIS G 31 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 201 HIS J 174 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 201 HIS N 146 GLN N 174 HIS O 31 ASN ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 HIS R 174 HIS S 36 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 27310 Z= 0.388 Angle : 0.692 8.377 37195 Z= 0.361 Chirality : 0.047 0.238 4080 Planarity : 0.005 0.041 4795 Dihedral : 5.323 23.513 3728 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.60 % Favored : 93.10 % Rotamer: Outliers : 3.70 % Allowed : 20.32 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.22 (0.14), residues: 3335 helix: -1.31 (0.39), residues: 190 sheet: -0.03 (0.16), residues: 1060 loop : -1.22 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 148 HIS 0.011 0.002 HIS E 29 PHE 0.018 0.002 PHE C 77 TYR 0.022 0.002 TYR S 11 ARG 0.010 0.001 ARG M 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 330 time to evaluate : 2.975 Fit side-chains revert: symmetry clash REVERT: B 171 TYR cc_start: 0.8860 (m-10) cc_final: 0.8063 (m-10) REVERT: C 76 LYS cc_start: 0.7907 (mttm) cc_final: 0.7605 (mtpt) REVERT: C 122 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6135 (ptt) REVERT: F 62 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6877 (p90) REVERT: G 59 ASP cc_start: 0.7682 (t0) cc_final: 0.7456 (t0) REVERT: J 62 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.5848 (p90) REVERT: N 125 MET cc_start: 0.8511 (mmt) cc_final: 0.7995 (mmm) REVERT: O 37 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: O 76 LYS cc_start: 0.7698 (mttm) cc_final: 0.7132 (mttt) REVERT: O 211 GLU cc_start: 0.7755 (tt0) cc_final: 0.7338 (mm-30) REVERT: P 83 MET cc_start: 0.4766 (tpt) cc_final: 0.4496 (mmt) REVERT: Q 119 TYR cc_start: 0.8296 (t80) cc_final: 0.7816 (t80) REVERT: R 62 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6469 (p90) REVERT: R 196 GLU cc_start: 0.7228 (tt0) cc_final: 0.6815 (tp30) REVERT: S 76 LYS cc_start: 0.7749 (mttm) cc_final: 0.7485 (mtpt) outliers start: 105 outliers final: 81 residues processed: 404 average time/residue: 0.4123 time to fit residues: 257.7921 Evaluate side-chains 393 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 307 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 143 CYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 62 PHE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 143 CYS Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 203 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 101 MET Chi-restraints excluded: chain N residue 108 GLU Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 37 TYR Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain O residue 143 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 161 SER Chi-restraints excluded: chain Q residue 174 GLU Chi-restraints excluded: chain R residue 62 PHE Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 37 TYR Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 80 SER Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 123 VAL Chi-restraints excluded: chain S residue 143 CYS Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain T residue 31 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 0.0470 chunk 287 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 319 optimal weight: 0.0870 chunk 265 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS A 29 HIS ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS G 36 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS I 29 HIS K 36 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 HIS M 29 HIS ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27310 Z= 0.164 Angle : 0.541 6.101 37195 Z= 0.289 Chirality : 0.042 0.136 4080 Planarity : 0.004 0.040 4795 Dihedral : 4.813 20.809 3728 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.97 % Favored : 93.88 % Rotamer: Outliers : 3.21 % Allowed : 20.74 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3335 helix: -0.46 (0.41), residues: 160 sheet: 0.07 (0.16), residues: 1055 loop : -1.08 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 148 HIS 0.006 0.001 HIS O 145 PHE 0.012 0.001 PHE L 47 TYR 0.012 0.001 TYR D 60 ARG 0.004 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 314 time to evaluate : 3.066 Fit side-chains REVERT: A 31 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: B 101 MET cc_start: 0.7645 (mtm) cc_final: 0.7365 (mtp) REVERT: B 171 TYR cc_start: 0.8784 (m-10) cc_final: 0.8029 (m-10) REVERT: C 23 ASP cc_start: 0.7383 (p0) cc_final: 0.6879 (m-30) REVERT: C 76 LYS cc_start: 0.7783 (mttm) cc_final: 0.7490 (mtpt) REVERT: E 54 MET cc_start: 0.8635 (tpp) cc_final: 0.8342 (mmm) REVERT: G 43 ASN cc_start: 0.9146 (OUTLIER) cc_final: 0.8684 (t0) REVERT: G 145 HIS cc_start: 0.7894 (p-80) cc_final: 0.7667 (p-80) REVERT: K 110 MET cc_start: 0.7047 (tmm) cc_final: 0.6839 (tmm) REVERT: K 120 ARG cc_start: 0.6368 (tpp80) cc_final: 0.6021 (tpp-160) REVERT: L 72 ARG cc_start: 0.7923 (ptp-110) cc_final: 0.7711 (ptp-110) REVERT: N 125 MET cc_start: 0.8468 (mmt) cc_final: 0.8004 (mmm) REVERT: O 37 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: O 76 LYS cc_start: 0.7677 (mttm) cc_final: 0.7236 (mttm) REVERT: P 112 TRP cc_start: 0.8017 (m100) cc_final: 0.7743 (m100) REVERT: Q 119 TYR cc_start: 0.8221 (t80) cc_final: 0.7829 (t80) REVERT: R 196 GLU cc_start: 0.7238 (tt0) cc_final: 0.6923 (tp30) outliers start: 91 outliers final: 63 residues processed: 368 average time/residue: 0.3936 time to fit residues: 225.1890 Evaluate side-chains 367 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 301 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 143 CYS Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 143 CYS Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 37 TYR Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 143 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 174 GLU Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain S residue 37 TYR Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 80 SER Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 143 CYS Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain T residue 31 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 181 optimal weight: 0.7980 chunk 233 optimal weight: 0.0170 chunk 180 optimal weight: 3.9990 chunk 268 optimal weight: 0.9980 chunk 178 optimal weight: 9.9990 chunk 318 optimal weight: 10.0000 chunk 199 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 29 HIS ** S 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27310 Z= 0.143 Angle : 0.515 5.547 37195 Z= 0.274 Chirality : 0.042 0.143 4080 Planarity : 0.004 0.040 4795 Dihedral : 4.536 19.082 3728 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.06 % Favored : 93.79 % Rotamer: Outliers : 3.35 % Allowed : 20.49 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3335 helix: -0.33 (0.41), residues: 160 sheet: 0.15 (0.16), residues: 1055 loop : -1.00 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 148 HIS 0.005 0.000 HIS Q 29 PHE 0.016 0.001 PHE P 47 TYR 0.012 0.001 TYR O 30 ARG 0.003 0.000 ARG M 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 316 time to evaluate : 3.008 Fit side-chains REVERT: A 31 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7811 (m-30) REVERT: B 171 TYR cc_start: 0.8796 (m-10) cc_final: 0.8058 (m-10) REVERT: C 23 ASP cc_start: 0.6970 (p0) cc_final: 0.6594 (m-30) REVERT: C 76 LYS cc_start: 0.7656 (mttm) cc_final: 0.7401 (mtpt) REVERT: E 37 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7566 (m-30) REVERT: E 54 MET cc_start: 0.8701 (tpp) cc_final: 0.8312 (mmm) REVERT: G 76 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7281 (mttm) REVERT: J 62 PHE cc_start: 0.6909 (OUTLIER) cc_final: 0.6007 (p90) REVERT: K 23 ASP cc_start: 0.7428 (p0) cc_final: 0.6943 (m-30) REVERT: K 120 ARG cc_start: 0.6276 (tpp80) cc_final: 0.5940 (tpp-160) REVERT: K 184 TRP cc_start: 0.4818 (m100) cc_final: 0.3674 (m-90) REVERT: N 125 MET cc_start: 0.8394 (mmt) cc_final: 0.7907 (mmm) REVERT: N 196 GLU cc_start: 0.7334 (tt0) cc_final: 0.6728 (tp30) REVERT: O 37 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.7370 (m-80) REVERT: O 76 LYS cc_start: 0.7646 (mttm) cc_final: 0.7268 (mttm) REVERT: O 120 ARG cc_start: 0.6383 (tpp80) cc_final: 0.6011 (tpp-160) REVERT: P 112 TRP cc_start: 0.7933 (m100) cc_final: 0.7655 (m100) REVERT: R 62 PHE cc_start: 0.7069 (OUTLIER) cc_final: 0.6526 (p90) REVERT: R 196 GLU cc_start: 0.7219 (tt0) cc_final: 0.6661 (tp30) outliers start: 95 outliers final: 72 residues processed: 370 average time/residue: 0.4040 time to fit residues: 230.5227 Evaluate side-chains 384 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 306 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 143 CYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 62 PHE Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 143 CYS Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 37 TYR Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 143 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain P residue 83 MET Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 37 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 62 PHE Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain S residue 37 TYR Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 80 SER Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 143 CYS Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain T residue 31 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 10.0000 chunk 127 optimal weight: 0.1980 chunk 189 optimal weight: 7.9990 chunk 95 optimal weight: 0.0770 chunk 62 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 202 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 overall best weight: 1.6544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 HIS ** S 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27310 Z= 0.230 Angle : 0.566 9.230 37195 Z= 0.296 Chirality : 0.043 0.170 4080 Planarity : 0.004 0.039 4795 Dihedral : 4.692 20.089 3728 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.06 % Favored : 93.79 % Rotamer: Outliers : 3.21 % Allowed : 20.67 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3335 helix: -0.30 (0.42), residues: 160 sheet: 0.18 (0.16), residues: 1040 loop : -1.05 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 148 HIS 0.003 0.001 HIS K 145 PHE 0.016 0.002 PHE H 47 TYR 0.012 0.001 TYR C 11 ARG 0.004 0.000 ARG S 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 308 time to evaluate : 3.124 Fit side-chains REVERT: A 31 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: B 101 MET cc_start: 0.7700 (mtm) cc_final: 0.7439 (mtp) REVERT: B 171 TYR cc_start: 0.8809 (m-10) cc_final: 0.8046 (m-10) REVERT: C 23 ASP cc_start: 0.7022 (p0) cc_final: 0.6817 (m-30) REVERT: E 37 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: E 54 MET cc_start: 0.8625 (tpp) cc_final: 0.8329 (mmm) REVERT: G 76 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7252 (mttm) REVERT: K 120 ARG cc_start: 0.6308 (tpp80) cc_final: 0.6010 (tpp-160) REVERT: N 125 MET cc_start: 0.8462 (mmt) cc_final: 0.8053 (mmm) REVERT: O 37 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: O 76 LYS cc_start: 0.7721 (mttm) cc_final: 0.7397 (mttm) REVERT: P 112 TRP cc_start: 0.8025 (m100) cc_final: 0.7731 (m100) REVERT: Q 119 TYR cc_start: 0.8284 (t80) cc_final: 0.7882 (t80) REVERT: R 196 GLU cc_start: 0.7297 (tt0) cc_final: 0.6728 (tp30) outliers start: 91 outliers final: 79 residues processed: 364 average time/residue: 0.3876 time to fit residues: 219.9628 Evaluate side-chains 385 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 302 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 143 CYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 143 CYS Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 37 TYR Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 143 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain S residue 37 TYR Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 80 SER Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 143 CYS Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain T residue 31 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.334 > 50: distance: 98 - 156: 35.428 distance: 133 - 136: 33.416 distance: 137 - 138: 57.253 distance: 137 - 140: 57.354 distance: 138 - 145: 57.509 distance: 140 - 141: 38.693 distance: 141 - 142: 57.511 distance: 142 - 143: 55.924 distance: 142 - 144: 56.371 distance: 145 - 146: 56.890 distance: 146 - 147: 41.006 distance: 147 - 148: 56.454 distance: 147 - 153: 55.838 distance: 149 - 150: 40.322 distance: 150 - 151: 56.104 distance: 150 - 152: 56.862 distance: 153 - 154: 56.059 distance: 154 - 155: 40.801 distance: 154 - 157: 56.817 distance: 155 - 156: 39.932 distance: 155 - 165: 38.789 distance: 157 - 158: 40.669 distance: 158 - 159: 40.695 distance: 158 - 160: 55.748 distance: 160 - 162: 39.345 distance: 165 - 166: 57.427 distance: 166 - 167: 39.879 distance: 166 - 169: 56.338 distance: 167 - 168: 40.086 distance: 167 - 171: 56.731 distance: 169 - 170: 39.164 distance: 171 - 172: 69.635 distance: 171 - 177: 68.290 distance: 172 - 173: 57.763 distance: 172 - 175: 56.921 distance: 173 - 174: 56.307 distance: 173 - 178: 55.984 distance: 175 - 176: 55.952 distance: 176 - 177: 57.115 distance: 178 - 179: 57.657 distance: 179 - 180: 55.202 distance: 179 - 182: 69.223 distance: 182 - 183: 38.714 distance: 183 - 184: 70.482 distance: 184 - 185: 55.770 distance: 185 - 186: 70.452 distance: 186 - 187: 55.378 distance: 186 - 188: 57.245 distance: 189 - 190: 41.365 distance: 189 - 195: 39.872 distance: 190 - 191: 39.640 distance: 190 - 193: 68.633 distance: 191 - 192: 39.784 distance: 191 - 196: 56.727 distance: 193 - 194: 39.461 distance: 194 - 195: 56.508 distance: 196 - 197: 39.050 distance: 197 - 198: 39.778 distance: 197 - 200: 39.318 distance: 198 - 199: 56.019 distance: 198 - 204: 40.311 distance: 201 - 202: 38.901 distance: 205 - 206: 56.468 distance: 205 - 208: 69.371 distance: 206 - 212: 68.918 distance: 208 - 209: 57.901 distance: 209 - 210: 57.012 distance: 209 - 211: 41.150 distance: 212 - 213: 40.080 distance: 213 - 214: 39.305 distance: 213 - 216: 38.646 distance: 214 - 217: 33.432