Starting phenix.real_space_refine on Thu Feb 22 17:54:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmj_22259/02_2024/6xmj_22259.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmj_22259/02_2024/6xmj_22259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmj_22259/02_2024/6xmj_22259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmj_22259/02_2024/6xmj_22259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmj_22259/02_2024/6xmj_22259.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmj_22259/02_2024/6xmj_22259.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 182 5.16 5 C 22036 2.51 5 N 6025 2.21 5 O 6674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 149": "OD1" <-> "OD2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ASP 227": "OD1" <-> "OD2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C ASP 82": "OD1" <-> "OD2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "D TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E ASP 147": "OD1" <-> "OD2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 240": "OD1" <-> "OD2" Residue "F TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 139": "OD1" <-> "OD2" Residue "F TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "F TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 227": "OD1" <-> "OD2" Residue "F ARG 239": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ASP 83": "OD1" <-> "OD2" Residue "G GLU 177": "OE1" <-> "OE2" Residue "G ASP 202": "OD1" <-> "OD2" Residue "G GLU 233": "OE1" <-> "OE2" Residue "G TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 39": "OD1" <-> "OD2" Residue "H ARG 45": "NH1" <-> "NH2" Residue "H ASP 57": "OD1" <-> "OD2" Residue "H TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "I ASP 53": "OD1" <-> "OD2" Residue "I TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 120": "OD1" <-> "OD2" Residue "J PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 113": "OD1" <-> "OD2" Residue "J PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 134": "OD1" <-> "OD2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 193": "OD1" <-> "OD2" Residue "K ASP 11": "OD1" <-> "OD2" Residue "K PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 51": "OD1" <-> "OD2" Residue "L TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 67": "OE1" <-> "OE2" Residue "L TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 140": "OD1" <-> "OD2" Residue "L TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 190": "OD1" <-> "OD2" Residue "M ASP 19": "OD1" <-> "OD2" Residue "M TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 117": "OD1" <-> "OD2" Residue "N GLU 119": "OE1" <-> "OE2" Residue "N ASP 126": "OD1" <-> "OD2" Residue "N TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 164": "OE1" <-> "OE2" Residue "N GLU 170": "OE1" <-> "OE2" Residue "O TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 65": "OE1" <-> "OE2" Residue "O TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 98": "OE1" <-> "OE2" Residue "O ASP 118": "OD1" <-> "OD2" Residue "O PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "P GLU 65": "OE1" <-> "OE2" Residue "P TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 119": "OE1" <-> "OE2" Residue "P PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 86": "OE1" <-> "OE2" Residue "Q GLU 98": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q ASP 189": "OD1" <-> "OD2" Residue "R GLU 86": "OE1" <-> "OE2" Residue "R GLU 119": "OE1" <-> "OE2" Residue "R ASP 189": "OD1" <-> "OD2" Residue "S GLU 27": "OE1" <-> "OE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S GLU 147": "OE1" <-> "OE2" Residue "S GLU 156": "OE1" <-> "OE2" Residue "S ASP 157": "OD1" <-> "OD2" Residue "S PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 14": "OD1" <-> "OD2" Residue "T TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 45": "OE1" <-> "OE2" Residue "U ASP 14": "OD1" <-> "OD2" Residue "U GLU 26": "OE1" <-> "OE2" Residue "U GLU 35": "OE1" <-> "OE2" Residue "U TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 147": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34917 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1810 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 8, 'TRANS': 228} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1666 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 216} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1854 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 238} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1724 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 6, 'TRANS': 235} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "E" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1707 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1854 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1509 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1643 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1585 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1570 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1548 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1637 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1676 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 209} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1615 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1618 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 2 Chain: "Q" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1579 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 198} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1618 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 2 Chain: "S" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1618 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 2 Chain: "T" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1618 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 2 Chain: "U" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1618 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 2 Time building chain proxies: 18.03, per 1000 atoms: 0.52 Number of scatterers: 34917 At special positions: 0 Unit cell: (134.93, 182.31, 144.2, 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 182 16.00 O 6674 8.00 N 6025 7.00 C 22036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.27 Conformation dependent library (CDL) restraints added in 6.9 seconds 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8458 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 38 sheets defined 52.3% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 83 through 106 removed outlier: 3.624A pdb=" N ARG A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.809A pdb=" N LYS A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 184 removed outlier: 4.001A pdb=" N PHE A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 207 Processing helix chain 'A' and resid 231 through 245 removed outlier: 4.435A pdb=" N ALA A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 242 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 removed outlier: 3.543A pdb=" N ALA B 27 " --> pdb=" O TYR B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 101 removed outlier: 3.726A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 removed outlier: 3.657A pdb=" N TYR B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 176 removed outlier: 3.672A pdb=" N LEU B 173 " --> pdb=" O GLY B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.619A pdb=" N ILE B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 79 through 102 removed outlier: 3.544A pdb=" N ASN C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.569A pdb=" N ILE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.565A pdb=" N ALA C 171 " --> pdb=" O ASN C 167 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 197 removed outlier: 3.501A pdb=" N LYS C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 229 through 250 removed outlier: 3.761A pdb=" N GLN C 235 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU C 250 " --> pdb=" O LYS C 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 27 removed outlier: 3.684A pdb=" N ALA D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA D 25 " --> pdb=" O TYR D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 59 removed outlier: 3.535A pdb=" N VAL D 59 " --> pdb=" O GLU D 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 59' Processing helix chain 'D' and resid 76 through 98 removed outlier: 3.650A pdb=" N ALA D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG D 81 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN D 92 " --> pdb=" O ARG D 88 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG D 95 " --> pdb=" O CYS D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 117 Processing helix chain 'D' and resid 164 through 176 removed outlier: 4.248A pdb=" N GLU D 170 " --> pdb=" O LYS D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.769A pdb=" N VAL D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 240 removed outlier: 3.805A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 30 Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 82 through 104 Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 173 through 185 removed outlier: 4.757A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 204 removed outlier: 3.629A pdb=" N GLN E 204 " --> pdb=" O ILE E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 239 removed outlier: 3.676A pdb=" N VAL E 237 " --> pdb=" O GLU E 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 26 removed outlier: 3.526A pdb=" N GLU F 23 " --> pdb=" O ILE F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 77 through 100 Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.698A pdb=" N LEU F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 174 removed outlier: 4.477A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG F 174 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 180 removed outlier: 3.720A pdb=" N PHE F 179 " --> pdb=" O HIS F 175 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N MET F 180 " --> pdb=" O MET F 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 175 through 180' Processing helix chain 'F' and resid 183 through 197 Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'G' and resid 20 through 32 removed outlier: 3.724A pdb=" N GLU G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 103 Processing helix chain 'G' and resid 107 through 121 Processing helix chain 'G' and resid 122 through 124 No H-bonds generated for 'chain 'G' and resid 122 through 124' Processing helix chain 'G' and resid 168 through 177 removed outlier: 3.531A pdb=" N GLU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 184 Processing helix chain 'G' and resid 185 through 201 removed outlier: 4.236A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU G 192 " --> pdb=" O ASP G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 228 through 242 removed outlier: 3.646A pdb=" N TYR G 238 " --> pdb=" O GLU G 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.737A pdb=" N ALA H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 134 Processing helix chain 'H' and resid 135 through 143 removed outlier: 3.625A pdb=" N ASP H 140 " --> pdb=" O TYR H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 167 Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'I' and resid 48 through 71 removed outlier: 3.814A pdb=" N LEU I 68 " --> pdb=" O GLU I 64 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER I 69 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.752A pdb=" N ALA I 79 " --> pdb=" O ARG I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.752A pdb=" N ASP I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 164 Processing helix chain 'J' and resid 3 through 7 removed outlier: 3.772A pdb=" N ASN J 7 " --> pdb=" O MET J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 78 Processing helix chain 'J' and resid 83 through 97 Processing helix chain 'J' and resid 142 through 154 removed outlier: 3.779A pdb=" N SER J 152 " --> pdb=" O GLY J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 176 removed outlier: 3.810A pdb=" N GLU J 165 " --> pdb=" O ASP J 161 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET J 171 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN J 173 " --> pdb=" O GLN J 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 72 removed outlier: 3.787A pdb=" N THR K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL K 54 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR K 67 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS K 68 " --> pdb=" O VAL K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 91 removed outlier: 3.566A pdb=" N ASN K 82 " --> pdb=" O THR K 78 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS K 91 " --> pdb=" O ASN K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 147 removed outlier: 5.027A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU K 143 " --> pdb=" O THR K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 Processing helix chain 'L' and resid 48 through 71 removed outlier: 3.516A pdb=" N ILE L 65 " --> pdb=" O ARG L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 88 removed outlier: 3.526A pdb=" N LEU L 83 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 91 No H-bonds generated for 'chain 'L' and resid 89 through 91' Processing helix chain 'L' and resid 131 through 142 removed outlier: 3.940A pdb=" N GLY L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 167 removed outlier: 3.695A pdb=" N ARG L 166 " --> pdb=" O GLN L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 192 through 201 removed outlier: 3.785A pdb=" N GLU L 197 " --> pdb=" O ALA L 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 80 removed outlier: 3.589A pdb=" N THR M 65 " --> pdb=" O CYS M 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS M 73 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET M 74 " --> pdb=" O ALA M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 98 Processing helix chain 'M' and resid 141 through 153 removed outlier: 3.567A pdb=" N GLN M 146 " --> pdb=" O SER M 142 " (cutoff:3.500A) Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 167 through 183 Processing helix chain 'N' and resid 57 through 78 removed outlier: 3.865A pdb=" N LEU N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 101 Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 146 through 157 removed outlier: 3.632A pdb=" N LYS N 156 " --> pdb=" O GLU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 180 Processing helix chain 'N' and resid 209 through 214 removed outlier: 3.704A pdb=" N ALA N 212 " --> pdb=" O TRP N 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 14 Processing helix chain 'O' and resid 17 through 31 removed outlier: 3.604A pdb=" N SER O 21 " --> pdb=" O THR O 17 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL O 24 " --> pdb=" O SER O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 52 Processing helix chain 'O' and resid 56 through 62 removed outlier: 3.556A pdb=" N GLN O 59 " --> pdb=" O GLY O 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS O 62 " --> pdb=" O GLN O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 94 removed outlier: 4.013A pdb=" N LEU O 68 " --> pdb=" O PRO O 64 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY O 69 " --> pdb=" O GLU O 65 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL O 70 " --> pdb=" O GLN O 66 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR O 87 " --> pdb=" O CYS O 83 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE O 88 " --> pdb=" O GLN O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 125 removed outlier: 3.771A pdb=" N VAL O 109 " --> pdb=" O LEU O 105 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE O 122 " --> pdb=" O ASP O 118 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS O 123 " --> pdb=" O GLU O 119 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU O 125 " --> pdb=" O GLU O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 161 removed outlier: 3.950A pdb=" N GLU O 147 " --> pdb=" O TYR O 143 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA O 151 " --> pdb=" O GLU O 147 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS O 158 " --> pdb=" O THR O 154 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 214 removed outlier: 3.769A pdb=" N LEU O 180 " --> pdb=" O SER O 176 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG O 184 " --> pdb=" O LEU O 180 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE O 190 " --> pdb=" O ILE O 186 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET O 191 " --> pdb=" O ASP O 187 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR O 199 " --> pdb=" O GLU O 195 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN O 210 " --> pdb=" O ARG O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 215 through 221 removed outlier: 3.515A pdb=" N ILE O 220 " --> pdb=" O TRP O 216 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 16 removed outlier: 3.673A pdb=" N SER P 15 " --> pdb=" O ASN P 11 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR P 16 " --> pdb=" O LEU P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 31 removed outlier: 3.804A pdb=" N VAL P 24 " --> pdb=" O SER P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 52 Processing helix chain 'P' and resid 56 through 61 removed outlier: 3.541A pdb=" N GLU P 61 " --> pdb=" O ALA P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 94 removed outlier: 3.546A pdb=" N LEU P 68 " --> pdb=" O PRO P 64 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL P 70 " --> pdb=" O GLN P 66 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN P 84 " --> pdb=" O ASN P 80 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR P 87 " --> pdb=" O CYS P 83 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE P 88 " --> pdb=" O GLN P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 123 removed outlier: 3.531A pdb=" N ILE P 116 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS P 123 " --> pdb=" O GLU P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 161 removed outlier: 3.690A pdb=" N GLU P 147 " --> pdb=" O TYR P 143 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA P 151 " --> pdb=" O GLU P 147 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS P 158 " --> pdb=" O THR P 154 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 214 removed outlier: 3.807A pdb=" N LEU P 180 " --> pdb=" O SER P 176 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG P 184 " --> pdb=" O LEU P 180 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET P 191 " --> pdb=" O ASP P 187 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR P 199 " --> pdb=" O GLU P 195 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR P 203 " --> pdb=" O THR P 199 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL P 208 " --> pdb=" O MET P 204 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN P 210 " --> pdb=" O ARG P 206 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 14 Processing helix chain 'Q' and resid 17 through 31 removed outlier: 3.629A pdb=" N SER Q 21 " --> pdb=" O THR Q 17 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL Q 24 " --> pdb=" O SER Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 52 removed outlier: 3.564A pdb=" N ASN Q 52 " --> pdb=" O GLY Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 62 Processing helix chain 'Q' and resid 64 through 94 removed outlier: 3.553A pdb=" N LEU Q 68 " --> pdb=" O PRO Q 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL Q 70 " --> pdb=" O GLN Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 126 removed outlier: 3.796A pdb=" N VAL Q 109 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS Q 123 " --> pdb=" O GLU Q 119 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR Q 124 " --> pdb=" O LEU Q 120 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY Q 126 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 161 removed outlier: 3.630A pdb=" N GLU Q 147 " --> pdb=" O TYR Q 143 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL Q 155 " --> pdb=" O ALA Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 221 removed outlier: 4.374A pdb=" N LEU Q 180 " --> pdb=" O SER Q 176 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU Q 181 " --> pdb=" O PRO Q 177 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA Q 188 " --> pdb=" O ARG Q 184 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N MET Q 191 " --> pdb=" O ASP Q 187 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR Q 203 " --> pdb=" O THR Q 199 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS Q 217 " --> pdb=" O LEU Q 213 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS Q 218 " --> pdb=" O LEU Q 214 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE Q 220 " --> pdb=" O TRP Q 216 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN Q 221 " --> pdb=" O LYS Q 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 16 removed outlier: 3.589A pdb=" N SER R 15 " --> pdb=" O ASN R 11 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR R 16 " --> pdb=" O LEU R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 52 removed outlier: 3.719A pdb=" N SER R 21 " --> pdb=" O THR R 17 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL R 24 " --> pdb=" O SER R 20 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR R 32 " --> pdb=" O TRP R 28 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU R 33 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY R 48 " --> pdb=" O ALA R 44 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL R 49 " --> pdb=" O GLU R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 60 Processing helix chain 'R' and resid 64 through 94 removed outlier: 3.734A pdb=" N LEU R 68 " --> pdb=" O PRO R 64 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL R 70 " --> pdb=" O GLN R 66 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN R 80 " --> pdb=" O ASP R 76 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR R 87 " --> pdb=" O CYS R 83 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE R 88 " --> pdb=" O GLN R 84 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE R 94 " --> pdb=" O THR R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 122 removed outlier: 3.586A pdb=" N ILE R 117 " --> pdb=" O VAL R 113 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 157 removed outlier: 3.624A pdb=" N GLU R 147 " --> pdb=" O TYR R 143 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU R 149 " --> pdb=" O LEU R 145 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR R 154 " --> pdb=" O SER R 150 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL R 155 " --> pdb=" O ALA R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 214 removed outlier: 3.888A pdb=" N LEU R 180 " --> pdb=" O SER R 176 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE R 190 " --> pdb=" O ILE R 186 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET R 191 " --> pdb=" O ASP R 187 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR R 203 " --> pdb=" O THR R 199 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN R 210 " --> pdb=" O ARG R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 221 Processing helix chain 'R' and resid 227 through 231 Processing helix chain 'S' and resid 5 through 16 removed outlier: 3.540A pdb=" N SER S 15 " --> pdb=" O ASN S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 31 removed outlier: 3.581A pdb=" N VAL S 24 " --> pdb=" O SER S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 52 removed outlier: 3.739A pdb=" N VAL S 49 " --> pdb=" O GLU S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 56 through 62 removed outlier: 3.733A pdb=" N LYS S 62 " --> pdb=" O GLN S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 94 removed outlier: 3.792A pdb=" N LEU S 68 " --> pdb=" O PRO S 64 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL S 70 " --> pdb=" O GLN S 66 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE S 88 " --> pdb=" O GLN S 84 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE S 94 " --> pdb=" O THR S 90 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 126 removed outlier: 4.008A pdb=" N THR S 124 " --> pdb=" O LEU S 120 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY S 126 " --> pdb=" O ILE S 122 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 161 removed outlier: 3.970A pdb=" N VAL S 155 " --> pdb=" O ALA S 151 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP S 157 " --> pdb=" O SER S 153 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU S 160 " --> pdb=" O GLU S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 176 through 221 removed outlier: 3.801A pdb=" N LEU S 180 " --> pdb=" O SER S 176 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE S 190 " --> pdb=" O ILE S 186 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET S 191 " --> pdb=" O ASP S 187 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR S 199 " --> pdb=" O GLU S 195 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR S 203 " --> pdb=" O THR S 199 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN S 210 " --> pdb=" O ARG S 206 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LYS S 217 " --> pdb=" O LEU S 213 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS S 218 " --> pdb=" O LEU S 214 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE S 220 " --> pdb=" O TRP S 216 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN S 221 " --> pdb=" O LYS S 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 14 Processing helix chain 'T' and resid 17 through 31 removed outlier: 3.579A pdb=" N VAL T 24 " --> pdb=" O SER T 20 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 52 removed outlier: 3.552A pdb=" N ASN T 52 " --> pdb=" O GLY T 48 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 61 removed outlier: 3.538A pdb=" N GLN T 59 " --> pdb=" O GLY T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 94 removed outlier: 3.922A pdb=" N LEU T 68 " --> pdb=" O PRO T 64 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE T 88 " --> pdb=" O GLN T 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 122 Processing helix chain 'T' and resid 143 through 160 removed outlier: 3.668A pdb=" N LEU T 149 " --> pdb=" O LEU T 145 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS T 158 " --> pdb=" O THR T 154 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 221 removed outlier: 3.898A pdb=" N LEU T 180 " --> pdb=" O SER T 176 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET T 191 " --> pdb=" O ASP T 187 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET T 204 " --> pdb=" O HIS T 200 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA T 207 " --> pdb=" O THR T 203 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN T 210 " --> pdb=" O ARG T 206 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS T 217 " --> pdb=" O LEU T 213 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS T 218 " --> pdb=" O LEU T 214 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN T 221 " --> pdb=" O LYS T 217 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 16 removed outlier: 3.733A pdb=" N ILE U 9 " --> pdb=" O ARG U 5 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER U 15 " --> pdb=" O ASN U 11 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR U 16 " --> pdb=" O LEU U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 31 removed outlier: 3.660A pdb=" N SER U 21 " --> pdb=" O THR U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 52 removed outlier: 4.358A pdb=" N GLU U 37 " --> pdb=" O LEU U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 60 Processing helix chain 'U' and resid 64 through 94 removed outlier: 3.847A pdb=" N LEU U 68 " --> pdb=" O PRO U 64 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY U 69 " --> pdb=" O GLU U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 104 through 120 removed outlier: 3.543A pdb=" N ALA U 108 " --> pdb=" O ASN U 104 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL U 109 " --> pdb=" O LEU U 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 144 through 161 removed outlier: 3.676A pdb=" N VAL U 155 " --> pdb=" O ALA U 151 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS U 158 " --> pdb=" O THR U 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 176 through 221 removed outlier: 3.732A pdb=" N LEU U 180 " --> pdb=" O SER U 176 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG U 184 " --> pdb=" O LEU U 180 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE U 190 " --> pdb=" O ILE U 186 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET U 191 " --> pdb=" O ASP U 187 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR U 199 " --> pdb=" O GLU U 195 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS U 217 " --> pdb=" O LEU U 213 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS U 218 " --> pdb=" O LEU U 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 169 removed outlier: 6.256A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A 53 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 71 removed outlier: 3.586A pdb=" N MET A 138 " --> pdb=" O CYS A 154 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A 151 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY A 162 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 159 through 162 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AA6, first strand: chain 'C' and resid 65 through 69 removed outlier: 6.524A pdb=" N MET C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 134 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY C 138 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU C 147 " --> pdb=" O TRP C 159 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY C 158 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AA8, first strand: chain 'D' and resid 62 through 64 Processing sheet with id=AA9, first strand: chain 'E' and resid 167 through 170 removed outlier: 3.562A pdb=" N GLU E 216 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.389A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL E 163 " --> pdb=" O HIS E 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.389A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 161 removed outlier: 5.197A pdb=" N GLY F 216 " --> pdb=" O GLU F 220 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU F 220 " --> pdb=" O GLY F 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.479A pdb=" N ILE F 70 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE F 144 " --> pdb=" O CYS F 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AB6, first strand: chain 'G' and resid 66 through 70 removed outlier: 6.501A pdb=" N VAL G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR G 158 " --> pdb=" O MET G 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 125 through 129 removed outlier: 3.524A pdb=" N GLN H 187 " --> pdb=" O LEU H 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.875A pdb=" N THR H 20 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR H 25 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 34 through 36 removed outlier: 3.602A pdb=" N VAL H 121 " --> pdb=" O SER H 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 124 through 128 removed outlier: 7.422A pdb=" N ILE I 173 " --> pdb=" O PRO I 188 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS I 182 " --> pdb=" O SER I 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 20 through 21 removed outlier: 6.870A pdb=" N ALA I 20 " --> pdb=" O ALA I 27 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.139A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 211 through 218 removed outlier: 6.608A pdb=" N THR J 199 " --> pdb=" O LEU I 212 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU I 214 " --> pdb=" O THR J 197 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR J 197 " --> pdb=" O GLU I 214 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE I 216 " --> pdb=" O ILE J 195 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE J 195 " --> pdb=" O ILE I 216 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL J 185 " --> pdb=" O LEU J 200 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL J 20 " --> pdb=" O ILE J 190 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ALA J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.471A pdb=" N ILE J 30 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N MET J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 42 through 44 Processing sheet with id=AC7, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AC8, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AC9, first strand: chain 'K' and resid 21 through 22 removed outlier: 6.686A pdb=" N ALA K 21 " --> pdb=" O MET K 28 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 35 through 37 removed outlier: 3.510A pdb=" N LEU K 102 " --> pdb=" O MET K 118 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 125 through 129 removed outlier: 5.810A pdb=" N VAL L 174 " --> pdb=" O SER L 189 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER L 189 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU L 176 " --> pdb=" O VAL L 187 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY L 183 " --> pdb=" O ARG L 180 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 20 through 22 removed outlier: 3.780A pdb=" N SER L 28 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA L 22 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE L 26 " --> pdb=" O ALA L 22 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 34 through 38 removed outlier: 3.570A pdb=" N ILE L 37 " --> pdb=" O LEU L 41 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR L 44 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 135 through 139 removed outlier: 5.709A pdb=" N THR M 11 " --> pdb=" O ASP M 26 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 135 through 139 removed outlier: 5.709A pdb=" N THR M 11 " --> pdb=" O ASP M 26 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 29 through 31 removed outlier: 6.853A pdb=" N LEU M 29 " --> pdb=" O HIS M 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 43 through 45 removed outlier: 3.698A pdb=" N VAL M 121 " --> pdb=" O ASP M 133 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.693A pdb=" N ALA N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR N 30 " --> pdb=" O ALA N 34 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.693A pdb=" N ALA N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR N 30 " --> pdb=" O ALA N 34 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR N 132 " --> pdb=" O TYR N 124 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 136 through 138 2124 hydrogen bonds defined for protein. 6108 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: 13.60 Time building geometry restraints manager: 14.29 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: 7388 1.33 - 1.45: 7804 1.45 - 1.57: 20007 1.57 - 1.69: 0 1.69 - 1.81: 295 Bond restraints: 35494 Sorted by residual: bond pdb=" N ARG E 10 " pdb=" CA ARG E 10 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.21e-02 6.83e+03 8.93e+00 bond pdb=" N ARG C 17 " pdb=" CA ARG C 17 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.29e-02 6.01e+03 8.17e+00 bond pdb=" N LEU T 227 " pdb=" CA LEU T 227 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.46e+00 bond pdb=" N ASP E 9 " pdb=" CA ASP E 9 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.14e+00 bond pdb=" N ALA J 32 " pdb=" CA ALA J 32 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.19e-02 7.06e+03 6.03e+00 ... (remaining 35489 not shown) Histogram of bond angle deviations from ideal: 98.65 - 105.73: 546 105.73 - 112.81: 18615 112.81 - 119.89: 12648 119.89 - 126.97: 15952 126.97 - 134.05: 304 Bond angle restraints: 48065 Sorted by residual: angle pdb=" N ILE B 67 " pdb=" CA ILE B 67 " pdb=" C ILE B 67 " ideal model delta sigma weight residual 111.81 108.11 3.70 8.60e-01 1.35e+00 1.85e+01 angle pdb=" CA ASP E 9 " pdb=" C ASP E 9 " pdb=" O ASP E 9 " ideal model delta sigma weight residual 120.55 116.03 4.52 1.06e+00 8.90e-01 1.81e+01 angle pdb=" CA PHE J 28 " pdb=" C PHE J 28 " pdb=" O PHE J 28 " ideal model delta sigma weight residual 120.36 115.87 4.49 1.08e+00 8.57e-01 1.73e+01 angle pdb=" N SER I 171 " pdb=" CA SER I 171 " pdb=" CB SER I 171 " ideal model delta sigma weight residual 114.17 109.57 4.60 1.14e+00 7.69e-01 1.63e+01 angle pdb=" N GLY C 125 " pdb=" CA GLY C 125 " pdb=" C GLY C 125 " ideal model delta sigma weight residual 111.34 118.55 -7.21 1.82e+00 3.02e-01 1.57e+01 ... (remaining 48060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 19667 17.96 - 35.92: 1432 35.92 - 53.88: 213 53.88 - 71.84: 55 71.84 - 89.80: 23 Dihedral angle restraints: 21390 sinusoidal: 8206 harmonic: 13184 Sorted by residual: dihedral pdb=" CA GLY M 190 " pdb=" C GLY M 190 " pdb=" N ASP M 191 " pdb=" CA ASP M 191 " ideal model delta harmonic sigma weight residual -180.00 -154.45 -25.55 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLU P 121 " pdb=" C GLU P 121 " pdb=" N ILE P 122 " pdb=" CA ILE P 122 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LEU B 73 " pdb=" C LEU B 73 " pdb=" N VAL B 74 " pdb=" CA VAL B 74 " ideal model delta harmonic sigma weight residual 180.00 155.88 24.12 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 21387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3801 0.040 - 0.080: 1297 0.080 - 0.120: 346 0.120 - 0.160: 84 0.160 - 0.200: 5 Chirality restraints: 5533 Sorted by residual: chirality pdb=" CA ILE J 30 " pdb=" N ILE J 30 " pdb=" C ILE J 30 " pdb=" CB ILE J 30 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB ILE J 30 " pdb=" CA ILE J 30 " pdb=" CG1 ILE J 30 " pdb=" CG2 ILE J 30 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA LEU C 18 " pdb=" N LEU C 18 " pdb=" C LEU C 18 " pdb=" CB LEU C 18 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.03e-01 ... (remaining 5530 not shown) Planarity restraints: 6190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 16 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C GLY C 16 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY C 16 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG C 17 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN N 147 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO N 148 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO N 148 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO N 148 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER O 63 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO O 64 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO O 64 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO O 64 " -0.031 5.00e-02 4.00e+02 ... (remaining 6187 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2408 2.74 - 3.28: 34282 3.28 - 3.82: 54807 3.82 - 4.36: 70466 4.36 - 4.90: 122195 Nonbonded interactions: 284158 Sorted by model distance: nonbonded pdb=" O ALA P 30 " pdb=" NE2 GLN P 34 " model vdw 2.202 2.520 nonbonded pdb=" NH1 ARG Q 152 " pdb=" OE2 GLU Q 156 " model vdw 2.209 2.520 nonbonded pdb=" NH1 ARG P 152 " pdb=" OE2 GLU P 156 " model vdw 2.213 2.520 nonbonded pdb=" NH1 ARG L 61 " pdb=" OE1 GLN L 62 " model vdw 2.218 2.520 nonbonded pdb=" NH1 ARG I 203 " pdb=" OE1 GLU J 155 " model vdw 2.221 2.520 ... (remaining 284153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'O' and (resid 4 through 226 or (resid 227 through 228 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'P' and (resid 4 through 225 or (resid 226 through 228 and (name N or nam \ e CA or name C or name O or name CB )))) selection = chain 'Q' selection = (chain 'R' and (resid 4 through 225 or (resid 226 through 228 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'S' and (resid 4 through 225 or (resid 226 through 228 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'T' and (resid 4 through 225 or (resid 226 through 228 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'U' and (resid 4 through 225 or (resid 226 through 228 and (name N or nam \ e CA or name C or name O or name CB )))) } 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: 0.860 Set stop_for_unknowns flag: 0.010 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: 5.710 Check model and map are aligned: 0.540 Set scattering table: 0.340 Process input model: 91.340 Find NCS groups from input model: 3.240 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 35494 Z= 0.298 Angle : 0.739 7.214 48065 Z= 0.418 Chirality : 0.044 0.200 5533 Planarity : 0.005 0.056 6190 Dihedral : 13.220 89.797 12932 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.26 % Favored : 96.72 % Rotamer: Outliers : 0.03 % Allowed : 0.85 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.11), residues: 4483 helix: -1.32 (0.10), residues: 2198 sheet: -1.55 (0.17), residues: 745 loop : -2.21 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 216 HIS 0.013 0.001 HIS O 47 PHE 0.028 0.002 PHE L 8 TYR 0.025 0.002 TYR M 130 ARG 0.017 0.001 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 920 time to evaluate : 4.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LYS cc_start: 0.7880 (ttpp) cc_final: 0.7651 (ttmt) REVERT: C 69 ASN cc_start: 0.7365 (t0) cc_final: 0.7003 (t0) REVERT: C 75 SER cc_start: 0.9208 (t) cc_final: 0.8911 (t) REVERT: D 213 ARG cc_start: 0.4970 (mmp-170) cc_final: 0.3982 (mtm180) REVERT: F 170 THR cc_start: 0.9170 (m) cc_final: 0.8964 (m) REVERT: I 195 LYS cc_start: 0.5885 (mmtt) cc_final: 0.5096 (tttp) REVERT: L 105 ASP cc_start: 0.7861 (p0) cc_final: 0.7658 (p0) REVERT: L 167 ASP cc_start: 0.7850 (t0) cc_final: 0.7650 (t0) REVERT: M 26 ASP cc_start: 0.7699 (p0) cc_final: 0.7370 (p0) REVERT: R 100 LYS cc_start: 0.8557 (mttm) cc_final: 0.8336 (mtmt) outliers start: 1 outliers final: 0 residues processed: 921 average time/residue: 1.7453 time to fit residues: 1860.7789 Evaluate side-chains 590 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 590 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 375 optimal weight: 3.9990 chunk 337 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 348 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 chunk 259 optimal weight: 4.9990 chunk 404 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 95 GLN B 111 GLN C 146 GLN C 198 ASN E 41 GLN E 104 ASN E 152 GLN E 204 GLN E 225 ASN F 60 GLN F 146 GLN F 166 GLN G 68 ASN H 38 HIS H 62 GLN H 106 GLN I 153 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN K 61 GLN K 63 ASN K 71 ASN K 87 ASN L 29 GLN L 38 ASN L 85 ASN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN O 66 GLN O 221 GLN P 11 ASN P 84 GLN ** Q 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 GLN Q 111 HIS R 221 GLN S 10 GLN S 34 GLN S 66 GLN S 72 GLN S 221 GLN T 34 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 185 GLN T 221 GLN U 11 ASN U 66 GLN U 72 GLN U 80 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 35494 Z= 0.343 Angle : 0.627 8.525 48065 Z= 0.336 Chirality : 0.046 0.174 5533 Planarity : 0.005 0.055 6190 Dihedral : 5.191 82.927 4979 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.20 % Allowed : 12.48 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % 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: -0.75 (0.12), residues: 4483 helix: 0.38 (0.11), residues: 2209 sheet: -0.71 (0.17), residues: 781 loop : -1.59 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 103 HIS 0.008 0.001 HIS S 79 PHE 0.018 0.002 PHE P 190 TYR 0.021 0.002 TYR M 130 ARG 0.006 0.001 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 619 time to evaluate : 7.398 Fit side-chains revert: symmetry clash REVERT: B 69 LYS cc_start: 0.8174 (ttpp) cc_final: 0.7913 (ttmt) REVERT: C 155 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8468 (m110) REVERT: C 166 ASN cc_start: 0.8197 (t0) cc_final: 0.7981 (t0) REVERT: C 219 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7125 (mm-30) REVERT: D 213 ARG cc_start: 0.5545 (mmp-170) cc_final: 0.4126 (mtm180) REVERT: E 239 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7565 (ptmt) REVERT: F 185 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.7046 (m110) REVERT: H 92 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: H 107 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6942 (mt-10) REVERT: I 33 LYS cc_start: 0.9053 (mttt) cc_final: 0.8849 (mttt) REVERT: I 143 ARG cc_start: 0.8080 (mtp180) cc_final: 0.7843 (mtp180) REVERT: I 195 LYS cc_start: 0.6127 (mmtt) cc_final: 0.5228 (tttt) REVERT: I 216 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8360 (mm) REVERT: J 27 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8713 (ttt180) REVERT: K 27 GLN cc_start: 0.7932 (mt0) cc_final: 0.7707 (pp30) REVERT: K 168 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8395 (mp10) REVERT: M 74 MET cc_start: 0.9031 (mtp) cc_final: 0.8758 (mtp) REVERT: N 5 MET cc_start: 0.8501 (mmm) cc_final: 0.8233 (tpp) REVERT: N 73 ASP cc_start: 0.7815 (m-30) cc_final: 0.7344 (m-30) REVERT: N 186 ARG cc_start: 0.8013 (mtp180) cc_final: 0.7688 (mtm180) REVERT: O 76 ASP cc_start: 0.8016 (m-30) cc_final: 0.7710 (m-30) REVERT: O 80 ASN cc_start: 0.8901 (m-40) cc_final: 0.8507 (m110) REVERT: R 100 LYS cc_start: 0.8706 (mttm) cc_final: 0.8463 (mtmt) REVERT: R 189 ASP cc_start: 0.8162 (m-30) cc_final: 0.7956 (m-30) REVERT: S 89 ARG cc_start: 0.8472 (ttm-80) cc_final: 0.8139 (ttm-80) REVERT: S 226 ASN cc_start: 0.8473 (t0) cc_final: 0.8267 (t0) REVERT: T 65 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6534 (mm-30) REVERT: U 34 GLN cc_start: 0.6618 (OUTLIER) cc_final: 0.5996 (mm-40) outliers start: 116 outliers final: 41 residues processed: 685 average time/residue: 1.6623 time to fit residues: 1335.4634 Evaluate side-chains 599 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 547 time to evaluate : 4.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain K residue 168 GLN Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 56 ASP Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 152 ARG Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain U residue 34 GLN Chi-restraints excluded: chain U residue 153 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 224 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 336 optimal weight: 0.6980 chunk 275 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 404 optimal weight: 3.9990 chunk 437 optimal weight: 9.9990 chunk 360 optimal weight: 9.9990 chunk 401 optimal weight: 3.9990 chunk 138 optimal weight: 0.0030 chunk 324 optimal weight: 7.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN C 240 HIS D 54 GLN D 146 GLN D 175 ASN E 225 ASN G 101 ASN H 62 GLN H 106 GLN I 57 GLN I 153 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN L 38 ASN P 11 ASN P 210 ASN ** Q 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 210 ASN R 210 ASN S 84 GLN S 221 GLN T 34 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 80 ASN T 221 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35494 Z= 0.165 Angle : 0.495 7.983 48065 Z= 0.267 Chirality : 0.041 0.160 5533 Planarity : 0.004 0.055 6190 Dihedral : 4.606 71.766 4979 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.00 % Allowed : 14.85 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % 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: 0.27 (0.13), residues: 4483 helix: 1.25 (0.11), residues: 2214 sheet: -0.09 (0.18), residues: 776 loop : -1.26 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 100 HIS 0.005 0.001 HIS S 79 PHE 0.013 0.001 PHE J 69 TYR 0.018 0.001 TYR K 117 ARG 0.009 0.000 ARG C 226 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 614 time to evaluate : 4.109 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8355 (mtpp) REVERT: A 100 ASN cc_start: 0.8515 (t0) cc_final: 0.8286 (t0) REVERT: A 120 ASP cc_start: 0.7871 (m-30) cc_final: 0.7500 (m-30) REVERT: B 69 LYS cc_start: 0.8183 (ttpp) cc_final: 0.7937 (ttmt) REVERT: C 219 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: D 179 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6086 (mm-30) REVERT: D 213 ARG cc_start: 0.5329 (mmp-170) cc_final: 0.4133 (mtm180) REVERT: E 239 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7383 (ptmt) REVERT: H 71 ASN cc_start: 0.8349 (t0) cc_final: 0.8083 (t0) REVERT: H 72 GLU cc_start: 0.7585 (pt0) cc_final: 0.7302 (pt0) REVERT: H 92 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: H 196 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7684 (mmtt) REVERT: I 30 ASN cc_start: 0.8001 (t0) cc_final: 0.7781 (t0) REVERT: I 33 LYS cc_start: 0.9064 (mttt) cc_final: 0.8850 (mttt) REVERT: I 143 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7901 (mtp180) REVERT: I 195 LYS cc_start: 0.6123 (mmtt) cc_final: 0.5255 (tttt) REVERT: I 216 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8266 (mm) REVERT: J 159 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7387 (p0) REVERT: K 2 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7645 (mt-10) REVERT: K 27 GLN cc_start: 0.7898 (mt0) cc_final: 0.7641 (pp30) REVERT: L 141 ARG cc_start: 0.8181 (mmp-170) cc_final: 0.7324 (mtt180) REVERT: M 105 TYR cc_start: 0.8682 (t80) cc_final: 0.8454 (t80) REVERT: M 172 MET cc_start: 0.7761 (mtp) cc_final: 0.7548 (mtp) REVERT: N 5 MET cc_start: 0.8334 (mmm) cc_final: 0.8091 (tpp) REVERT: N 73 ASP cc_start: 0.7868 (m-30) cc_final: 0.7427 (m-30) REVERT: N 186 ARG cc_start: 0.7941 (mtp180) cc_final: 0.7627 (mtm180) REVERT: O 41 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.7814 (ttpt) REVERT: O 76 ASP cc_start: 0.7945 (m-30) cc_final: 0.7700 (m-30) REVERT: O 80 ASN cc_start: 0.8924 (m-40) cc_final: 0.8561 (m-40) REVERT: P 147 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7328 (tp30) REVERT: R 100 LYS cc_start: 0.8626 (mttm) cc_final: 0.8416 (mtmt) REVERT: S 226 ASN cc_start: 0.8655 (t0) cc_final: 0.8444 (t0) REVERT: T 41 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8012 (mmmm) REVERT: U 34 GLN cc_start: 0.6526 (OUTLIER) cc_final: 0.5883 (mm-40) REVERT: U 50 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8593 (mm) outliers start: 109 outliers final: 40 residues processed: 665 average time/residue: 1.6511 time to fit residues: 1290.6711 Evaluate side-chains 606 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 552 time to evaluate : 4.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain K residue 2 GLU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 107 ARG Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 152 ARG Chi-restraints excluded: chain T residue 41 LYS Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 185 GLN Chi-restraints excluded: chain U residue 34 GLN Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 153 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 399 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 271 optimal weight: 0.9990 chunk 406 optimal weight: 9.9990 chunk 430 optimal weight: 5.9990 chunk 212 optimal weight: 0.6980 chunk 385 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 122 GLN D 146 GLN D 175 ASN G 101 ASN H 106 GLN I 153 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 GLN M 160 ASN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 ASN Q 11 ASN T 34 GLN T 75 GLN T 221 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 35494 Z= 0.165 Angle : 0.488 7.664 48065 Z= 0.261 Chirality : 0.040 0.153 5533 Planarity : 0.004 0.053 6190 Dihedral : 4.422 70.205 4979 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.03 % Allowed : 16.31 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % 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: 0.74 (0.13), residues: 4483 helix: 1.67 (0.11), residues: 2212 sheet: 0.13 (0.18), residues: 780 loop : -1.08 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 55 HIS 0.005 0.001 HIS S 79 PHE 0.016 0.001 PHE J 69 TYR 0.017 0.001 TYR K 117 ARG 0.007 0.000 ARG C 249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 587 time to evaluate : 4.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7938 (mt0) REVERT: B 69 LYS cc_start: 0.8223 (ttpp) cc_final: 0.7957 (ttmt) REVERT: C 219 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7076 (mm-30) REVERT: D 179 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6163 (mm-30) REVERT: D 213 ARG cc_start: 0.5449 (mmp-170) cc_final: 0.4244 (mtm180) REVERT: E 168 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8423 (tpt170) REVERT: E 221 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7744 (mt0) REVERT: E 239 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7353 (ptmt) REVERT: F 185 ASN cc_start: 0.7440 (OUTLIER) cc_final: 0.7055 (m110) REVERT: F 225 ASP cc_start: 0.6714 (m-30) cc_final: 0.6490 (t0) REVERT: G 230 ASP cc_start: 0.6855 (OUTLIER) cc_final: 0.6631 (p0) REVERT: H 69 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6913 (mm-30) REVERT: H 84 LYS cc_start: 0.9047 (tmmm) cc_final: 0.8550 (ttpt) REVERT: H 92 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: H 196 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7726 (mmtt) REVERT: I 195 LYS cc_start: 0.6138 (mmtt) cc_final: 0.5250 (tttp) REVERT: I 216 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8333 (mm) REVERT: J 159 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7393 (p0) REVERT: K 27 GLN cc_start: 0.7886 (mt0) cc_final: 0.7669 (pp30) REVERT: L 97 MET cc_start: 0.7951 (ttp) cc_final: 0.7711 (ttp) REVERT: L 141 ARG cc_start: 0.8136 (mmp-170) cc_final: 0.7323 (mtt180) REVERT: M 105 TYR cc_start: 0.8711 (t80) cc_final: 0.8420 (t80) REVERT: N 5 MET cc_start: 0.8400 (mmm) cc_final: 0.8185 (tpp) REVERT: N 73 ASP cc_start: 0.7877 (m-30) cc_final: 0.7352 (m-30) REVERT: N 186 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7662 (mtm180) REVERT: O 41 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7882 (ttpt) REVERT: O 76 ASP cc_start: 0.7939 (m-30) cc_final: 0.7705 (m-30) REVERT: O 80 ASN cc_start: 0.8901 (m-40) cc_final: 0.8558 (m-40) REVERT: R 100 LYS cc_start: 0.8626 (mttm) cc_final: 0.8414 (mtmt) REVERT: S 189 ASP cc_start: 0.7157 (m-30) cc_final: 0.6941 (m-30) outliers start: 110 outliers final: 53 residues processed: 648 average time/residue: 1.6482 time to fit residues: 1253.6050 Evaluate side-chains 618 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 551 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain C residue 34 CYS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 107 ARG Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 152 ARG Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 157 ASP Chi-restraints excluded: chain T residue 185 GLN Chi-restraints excluded: chain U residue 9 ILE Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 153 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 358 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 320 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 367 optimal weight: 5.9990 chunk 297 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 386 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 95 GLN B 111 GLN B 122 GLN D 146 GLN G 101 ASN H 71 ASN H 106 GLN H 110 GLN I 30 ASN I 153 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 160 ASN N 89 HIS Q 11 ASN Q 210 ASN S 226 ASN T 34 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 ASN U 210 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 35494 Z= 0.388 Angle : 0.616 10.989 48065 Z= 0.324 Chirality : 0.045 0.166 5533 Planarity : 0.004 0.054 6190 Dihedral : 4.929 81.825 4979 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.86 % Allowed : 16.73 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % 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: 0.52 (0.13), residues: 4483 helix: 1.38 (0.11), residues: 2227 sheet: 0.27 (0.18), residues: 777 loop : -1.19 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 103 HIS 0.006 0.001 HIS P 79 PHE 0.022 0.002 PHE J 69 TYR 0.020 0.002 TYR K 117 ARG 0.006 0.001 ARG C 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 560 time to evaluate : 4.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: A 100 ASN cc_start: 0.8563 (t0) cc_final: 0.8326 (t0) REVERT: B 69 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7970 (ttmt) REVERT: B 112 ARG cc_start: 0.8912 (mtt-85) cc_final: 0.8595 (mtt90) REVERT: C 219 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7107 (mm-30) REVERT: D 179 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6249 (mm-30) REVERT: D 213 ARG cc_start: 0.5613 (mmp-170) cc_final: 0.4223 (mtm180) REVERT: E 168 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8432 (tpt170) REVERT: E 239 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7469 (ptmt) REVERT: F 185 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.7094 (m110) REVERT: G 230 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6702 (p0) REVERT: H 69 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6951 (mm-30) REVERT: H 92 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: H 196 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7873 (mmtt) REVERT: I 195 LYS cc_start: 0.6257 (mmtt) cc_final: 0.5332 (tttt) REVERT: I 216 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8501 (mm) REVERT: K 27 GLN cc_start: 0.7999 (mt0) cc_final: 0.7773 (pp30) REVERT: K 154 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5971 (mp0) REVERT: K 168 GLN cc_start: 0.8704 (mp10) cc_final: 0.8429 (mp10) REVERT: L 141 ARG cc_start: 0.8186 (mmp-170) cc_final: 0.7405 (mtt180) REVERT: M 105 TYR cc_start: 0.8744 (t80) cc_final: 0.8520 (t80) REVERT: M 144 MET cc_start: 0.8877 (mtt) cc_final: 0.8665 (mtm) REVERT: N 73 ASP cc_start: 0.7988 (m-30) cc_final: 0.7478 (m-30) REVERT: N 186 ARG cc_start: 0.8046 (mtp180) cc_final: 0.7788 (mtm180) REVERT: O 41 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8017 (ttpt) REVERT: O 62 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7647 (ptmt) REVERT: O 76 ASP cc_start: 0.8145 (m-30) cc_final: 0.7851 (m-30) REVERT: O 80 ASN cc_start: 0.8948 (m-40) cc_final: 0.8735 (m-40) REVERT: O 189 ASP cc_start: 0.7836 (m-30) cc_final: 0.7612 (m-30) REVERT: P 147 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: S 189 ASP cc_start: 0.7245 (m-30) cc_final: 0.6988 (m-30) REVERT: U 34 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6237 (mm-40) outliers start: 140 outliers final: 73 residues processed: 645 average time/residue: 1.6514 time to fit residues: 1249.3892 Evaluate side-chains 625 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 536 time to evaluate : 4.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain G residue 230 ASP Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 107 ARG Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain O residue 62 LYS Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain Q residue 41 LYS Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 152 ARG Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 157 ASP Chi-restraints excluded: chain T residue 185 GLN Chi-restraints excluded: chain U residue 34 GLN Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 153 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 144 optimal weight: 0.9990 chunk 387 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 252 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 430 optimal weight: 30.0000 chunk 357 optimal weight: 10.0000 chunk 199 optimal weight: 8.9990 chunk 35 optimal weight: 0.1980 chunk 142 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN C 166 ASN D 146 GLN D 175 ASN G 101 ASN H 71 ASN H 106 GLN I 153 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 146 GLN M 160 ASN P 11 ASN Q 11 ASN Q 210 ASN S 34 GLN S 226 ASN T 34 GLN T 75 GLN T 80 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35494 Z= 0.137 Angle : 0.471 8.063 48065 Z= 0.252 Chirality : 0.040 0.155 5533 Planarity : 0.003 0.052 6190 Dihedral : 4.353 71.382 4979 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.81 % Allowed : 18.30 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % 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: 1.07 (0.13), residues: 4483 helix: 1.90 (0.11), residues: 2220 sheet: 0.40 (0.18), residues: 776 loop : -0.94 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 55 HIS 0.004 0.000 HIS S 79 PHE 0.015 0.001 PHE J 69 TYR 0.016 0.001 TYR K 117 ARG 0.007 0.000 ARG L 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 589 time to evaluate : 4.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8317 (mtpp) REVERT: A 92 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: A 147 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7278 (mt0) REVERT: B 69 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7968 (ttmt) REVERT: C 219 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7067 (mm-30) REVERT: D 179 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6274 (mm-30) REVERT: D 211 MET cc_start: 0.8513 (ttp) cc_final: 0.8300 (ttt) REVERT: D 213 ARG cc_start: 0.5354 (mmp-170) cc_final: 0.4170 (mtm180) REVERT: E 221 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: E 239 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7316 (ptmt) REVERT: F 140 MET cc_start: 0.8117 (mmm) cc_final: 0.7902 (mmm) REVERT: H 9 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7112 (m-30) REVERT: H 69 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6957 (mm-30) REVERT: H 84 LYS cc_start: 0.9116 (tmmm) cc_final: 0.8888 (tmmm) REVERT: H 92 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: H 196 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7757 (mmtt) REVERT: I 195 LYS cc_start: 0.6250 (mmtt) cc_final: 0.5320 (tttt) REVERT: J 159 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7408 (p0) REVERT: K 27 GLN cc_start: 0.7911 (mt0) cc_final: 0.7691 (pp30) REVERT: L 56 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8050 (mt-10) REVERT: L 97 MET cc_start: 0.7966 (ttp) cc_final: 0.7648 (ttp) REVERT: L 141 ARG cc_start: 0.8133 (mmp-170) cc_final: 0.7409 (mtt180) REVERT: M 105 TYR cc_start: 0.8678 (t80) cc_final: 0.8446 (t80) REVERT: M 144 MET cc_start: 0.8812 (mtt) cc_final: 0.8594 (mtm) REVERT: N 73 ASP cc_start: 0.7898 (m-30) cc_final: 0.7412 (m-30) REVERT: O 41 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7954 (ttpt) REVERT: O 80 ASN cc_start: 0.8884 (m-40) cc_final: 0.8678 (m-40) REVERT: R 11 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7936 (t0) REVERT: S 101 GLU cc_start: 0.5774 (mp0) cc_final: 0.5523 (mp0) outliers start: 102 outliers final: 40 residues processed: 645 average time/residue: 1.6506 time to fit residues: 1246.8900 Evaluate side-chains 606 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 552 time to evaluate : 3.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain C residue 34 CYS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain R residue 11 ASN Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 152 ARG Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain U residue 9 ILE Chi-restraints excluded: chain U residue 124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 415 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 314 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 362 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 428 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 198 optimal weight: 0.1980 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN C 30 HIS D 146 GLN E 41 GLN G 101 ASN H 71 ASN H 106 GLN I 153 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 160 ASN P 11 ASN Q 11 ASN Q 210 ASN R 84 GLN S 34 GLN S 226 ASN T 34 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 80 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 35494 Z= 0.453 Angle : 0.650 11.605 48065 Z= 0.340 Chirality : 0.047 0.178 5533 Planarity : 0.005 0.054 6190 Dihedral : 4.988 82.411 4979 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.53 % Allowed : 18.24 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % 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: 0.64 (0.13), residues: 4483 helix: 1.43 (0.11), residues: 2226 sheet: 0.41 (0.18), residues: 767 loop : -1.08 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 103 HIS 0.007 0.001 HIS P 79 PHE 0.023 0.002 PHE J 69 TYR 0.022 0.002 TYR K 117 ARG 0.008 0.001 ARG L 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 551 time to evaluate : 4.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: A 100 ASN cc_start: 0.8569 (t0) cc_final: 0.8312 (t0) REVERT: B 184 GLU cc_start: 0.7304 (mp0) cc_final: 0.6874 (mp0) REVERT: C 219 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7148 (mm-30) REVERT: C 226 ARG cc_start: 0.7615 (mtp85) cc_final: 0.7185 (ttp80) REVERT: D 179 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6300 (mm-30) REVERT: D 211 MET cc_start: 0.8565 (ttp) cc_final: 0.8351 (ttt) REVERT: D 213 ARG cc_start: 0.5721 (mmp-170) cc_final: 0.4320 (mtm180) REVERT: E 91 LYS cc_start: 0.9008 (tptm) cc_final: 0.8167 (tttp) REVERT: E 168 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8477 (tpt170) REVERT: E 239 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7384 (ptmt) REVERT: H 92 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: H 196 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7896 (mmtt) REVERT: I 195 LYS cc_start: 0.6014 (mmtt) cc_final: 0.5062 (tttp) REVERT: I 216 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8490 (mm) REVERT: K 27 GLN cc_start: 0.8043 (mt0) cc_final: 0.7784 (pp30) REVERT: K 168 GLN cc_start: 0.8716 (mp10) cc_final: 0.8428 (mp10) REVERT: L 89 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7538 (mp10) REVERT: L 141 ARG cc_start: 0.8218 (mmp-170) cc_final: 0.7409 (mtt180) REVERT: M 105 TYR cc_start: 0.8732 (t80) cc_final: 0.8509 (t80) REVERT: M 144 MET cc_start: 0.8877 (mtt) cc_final: 0.8672 (mtm) REVERT: N 73 ASP cc_start: 0.8014 (m-30) cc_final: 0.7502 (m-30) REVERT: O 62 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7607 (ptmt) REVERT: O 80 ASN cc_start: 0.8979 (m-40) cc_final: 0.8765 (m-40) REVERT: Q 75 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: Q 76 ASP cc_start: 0.8185 (m-30) cc_final: 0.7921 (m-30) REVERT: R 11 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7970 (t0) REVERT: S 191 MET cc_start: 0.8884 (mmp) cc_final: 0.8485 (mmt) REVERT: U 57 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7361 (ttp-170) outliers start: 128 outliers final: 68 residues processed: 627 average time/residue: 1.6548 time to fit residues: 1220.4086 Evaluate side-chains 613 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 532 time to evaluate : 4.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 107 ARG Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 62 LYS Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 224 THR Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 75 GLN Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain R residue 11 ASN Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 152 ARG Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 157 ASP Chi-restraints excluded: chain U residue 9 ILE Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 57 ARG Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 153 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 265 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 337 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN D 146 GLN F 152 ASN G 101 ASN H 71 ASN H 106 GLN I 153 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN L 38 ASN M 160 ASN P 11 ASN ** Q 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 84 GLN R 226 ASN S 34 GLN S 226 ASN T 75 GLN T 80 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 35494 Z= 0.303 Angle : 0.574 10.619 48065 Z= 0.304 Chirality : 0.044 0.168 5533 Planarity : 0.004 0.053 6190 Dihedral : 4.837 80.442 4979 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.39 % Allowed : 18.57 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % 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: 0.74 (0.13), residues: 4483 helix: 1.49 (0.11), residues: 2226 sheet: 0.45 (0.18), residues: 773 loop : -1.00 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 189 HIS 0.005 0.001 HIS P 79 PHE 0.019 0.002 PHE J 69 TYR 0.019 0.002 TYR K 117 ARG 0.009 0.000 ARG L 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 534 time to evaluate : 4.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: A 100 ASN cc_start: 0.8549 (t0) cc_final: 0.8297 (t0) REVERT: B 184 GLU cc_start: 0.7292 (mp0) cc_final: 0.6887 (mp0) REVERT: C 219 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: D 85 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7919 (m-40) REVERT: D 179 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6319 (mm-30) REVERT: D 213 ARG cc_start: 0.5577 (mmp-170) cc_final: 0.4169 (mtm180) REVERT: E 168 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8468 (tpt170) REVERT: E 239 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7399 (ptmt) REVERT: F 185 ASN cc_start: 0.7465 (OUTLIER) cc_final: 0.7040 (m110) REVERT: H 69 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6969 (mm-30) REVERT: H 92 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: H 196 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7856 (mmtt) REVERT: I 195 LYS cc_start: 0.6000 (mmtt) cc_final: 0.4795 (tttt) REVERT: I 216 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8455 (mm) REVERT: K 27 GLN cc_start: 0.8041 (mt0) cc_final: 0.7767 (pp30) REVERT: K 168 GLN cc_start: 0.8686 (mp10) cc_final: 0.8433 (mp10) REVERT: L 97 MET cc_start: 0.8136 (ttp) cc_final: 0.7901 (ttp) REVERT: L 141 ARG cc_start: 0.8201 (mmp-170) cc_final: 0.7454 (mtt180) REVERT: M 105 TYR cc_start: 0.8704 (t80) cc_final: 0.8425 (t80) REVERT: N 73 ASP cc_start: 0.8007 (m-30) cc_final: 0.7500 (m-30) REVERT: N 206 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.6227 (pm20) REVERT: O 41 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8045 (ttpt) REVERT: O 62 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7661 (ptmt) REVERT: O 76 ASP cc_start: 0.8312 (m-30) cc_final: 0.8072 (m-30) REVERT: O 80 ASN cc_start: 0.8928 (m-40) cc_final: 0.8594 (m-40) REVERT: O 158 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.7467 (ttpt) REVERT: P 147 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7408 (tt0) REVERT: P 189 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7332 (t0) REVERT: R 11 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7962 (t0) REVERT: S 189 ASP cc_start: 0.7218 (m-30) cc_final: 0.6995 (m-30) REVERT: S 191 MET cc_start: 0.8845 (mmp) cc_final: 0.8477 (mmt) REVERT: T 158 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.7885 (mtpt) REVERT: U 57 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7349 (ttp-170) outliers start: 123 outliers final: 77 residues processed: 608 average time/residue: 1.6584 time to fit residues: 1186.5399 Evaluate side-chains 634 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 537 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 107 ARG Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 206 GLU Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain O residue 62 LYS Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 189 ASP Chi-restraints excluded: chain P residue 224 THR Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain R residue 11 ASN Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 152 ARG Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain U residue 9 ILE Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 57 ARG Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 147 GLU Chi-restraints excluded: chain U residue 153 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 390 optimal weight: 4.9990 chunk 410 optimal weight: 9.9990 chunk 374 optimal weight: 0.9990 chunk 399 optimal weight: 9.9990 chunk 240 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 313 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 361 optimal weight: 0.9990 chunk 378 optimal weight: 8.9990 chunk 398 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN D 146 GLN G 101 ASN H 71 ASN H 106 GLN I 153 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN M 160 ASN P 11 ASN Q 11 ASN R 84 GLN R 226 ASN S 34 GLN S 226 ASN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 80 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35494 Z= 0.210 Angle : 0.526 9.977 48065 Z= 0.280 Chirality : 0.042 0.160 5533 Planarity : 0.004 0.053 6190 Dihedral : 4.611 75.968 4979 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.95 % Allowed : 19.10 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % 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: 0.97 (0.13), residues: 4483 helix: 1.72 (0.11), residues: 2223 sheet: 0.57 (0.18), residues: 765 loop : -0.96 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 55 HIS 0.004 0.001 HIS S 79 PHE 0.017 0.001 PHE J 69 TYR 0.017 0.001 TYR K 117 ARG 0.011 0.000 ARG L 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 552 time to evaluate : 4.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: B 184 GLU cc_start: 0.7227 (mp0) cc_final: 0.6817 (mp0) REVERT: C 219 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7095 (mm-30) REVERT: D 179 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6323 (mm-30) REVERT: D 213 ARG cc_start: 0.5538 (mmp-170) cc_final: 0.4112 (mtm180) REVERT: E 168 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8454 (tpt170) REVERT: E 239 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7324 (ptmt) REVERT: F 185 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.7033 (m110) REVERT: H 9 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7206 (m-30) REVERT: H 69 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6941 (mm-30) REVERT: H 92 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: H 196 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7815 (mmtt) REVERT: I 195 LYS cc_start: 0.5945 (mmtt) cc_final: 0.5091 (tttt) REVERT: K 27 GLN cc_start: 0.7985 (mt0) cc_final: 0.7735 (pp30) REVERT: L 56 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8123 (mt-10) REVERT: L 97 MET cc_start: 0.8101 (ttp) cc_final: 0.7825 (ttp) REVERT: L 139 MET cc_start: 0.8774 (ttp) cc_final: 0.8537 (ttp) REVERT: L 141 ARG cc_start: 0.8173 (mmp-170) cc_final: 0.7406 (mtt180) REVERT: M 105 TYR cc_start: 0.8700 (t80) cc_final: 0.8459 (t80) REVERT: N 73 ASP cc_start: 0.7951 (m-30) cc_final: 0.7427 (m-30) REVERT: N 186 ARG cc_start: 0.8187 (mtp180) cc_final: 0.7964 (mtm180) REVERT: N 206 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6194 (pm20) REVERT: O 41 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8016 (ttpt) REVERT: O 80 ASN cc_start: 0.8910 (m-40) cc_final: 0.8604 (m-40) REVERT: P 147 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7413 (tt0) REVERT: P 189 ASP cc_start: 0.7705 (m-30) cc_final: 0.7303 (t0) REVERT: R 11 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7963 (t0) REVERT: S 101 GLU cc_start: 0.6118 (mp0) cc_final: 0.5710 (mp0) REVERT: S 189 ASP cc_start: 0.7134 (m-30) cc_final: 0.6904 (m-30) REVERT: S 191 MET cc_start: 0.8814 (mmp) cc_final: 0.8371 (mmt) REVERT: T 158 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.7874 (mtpt) REVERT: U 57 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7332 (ttp-170) outliers start: 107 outliers final: 67 residues processed: 614 average time/residue: 1.6417 time to fit residues: 1180.3703 Evaluate side-chains 617 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 534 time to evaluate : 4.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 143 ARG Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 107 ARG Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 206 GLU Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 115 LYS Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain R residue 11 ASN Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 152 ARG Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain U residue 9 ILE Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 57 ARG Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 147 GLU Chi-restraints excluded: chain U residue 153 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 262 optimal weight: 0.2980 chunk 422 optimal weight: 0.9990 chunk 257 optimal weight: 3.9990 chunk 200 optimal weight: 0.1980 chunk 293 optimal weight: 0.8980 chunk 443 optimal weight: 0.9980 chunk 408 optimal weight: 8.9990 chunk 353 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 216 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN C 146 GLN D 146 GLN D 175 ASN F 20 HIS F 59 HIS G 101 ASN H 71 ASN H 106 GLN I 153 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 160 ASN Q 11 ASN R 84 GLN S 34 GLN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 GLN T 75 GLN T 80 ASN T 99 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35494 Z= 0.130 Angle : 0.469 8.946 48065 Z= 0.251 Chirality : 0.040 0.169 5533 Planarity : 0.004 0.053 6190 Dihedral : 4.200 66.437 4979 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.87 % Allowed : 20.12 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % 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: 1.37 (0.13), residues: 4483 helix: 2.09 (0.11), residues: 2224 sheet: 0.64 (0.18), residues: 778 loop : -0.79 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 55 HIS 0.004 0.000 HIS S 79 PHE 0.016 0.001 PHE J 69 TYR 0.015 0.001 TYR K 117 ARG 0.007 0.000 ARG H 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8966 Ramachandran restraints generated. 4483 Oldfield, 0 Emsley, 4483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 583 time to evaluate : 4.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: D 56 GLU cc_start: 0.7832 (pm20) cc_final: 0.7619 (mp0) REVERT: D 179 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6412 (mm-30) REVERT: D 213 ARG cc_start: 0.5295 (mmp-170) cc_final: 0.3999 (mtp180) REVERT: E 168 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8422 (tpt170) REVERT: F 152 ASN cc_start: 0.8462 (t0) cc_final: 0.7951 (m-40) REVERT: H 92 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: H 196 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7775 (mmtt) REVERT: I 195 LYS cc_start: 0.5980 (mmtt) cc_final: 0.5101 (tttt) REVERT: K 27 GLN cc_start: 0.7881 (mt0) cc_final: 0.7679 (pp30) REVERT: L 97 MET cc_start: 0.7987 (ttp) cc_final: 0.7708 (ttp) REVERT: L 141 ARG cc_start: 0.8139 (mmp-170) cc_final: 0.7391 (mtt180) REVERT: M 105 TYR cc_start: 0.8681 (t80) cc_final: 0.8428 (t80) REVERT: N 73 ASP cc_start: 0.7884 (m-30) cc_final: 0.7516 (m-30) REVERT: N 214 MET cc_start: 0.6900 (mtt) cc_final: 0.6570 (mtt) REVERT: O 80 ASN cc_start: 0.8859 (m-40) cc_final: 0.8529 (m-40) REVERT: P 189 ASP cc_start: 0.7597 (m-30) cc_final: 0.7185 (t0) REVERT: R 11 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7958 (t0) REVERT: S 41 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7789 (pttm) REVERT: S 101 GLU cc_start: 0.5902 (mp0) cc_final: 0.5518 (mp0) REVERT: U 34 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6167 (mm-40) REVERT: U 57 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7212 (ttp-170) outliers start: 68 outliers final: 36 residues processed: 620 average time/residue: 1.6377 time to fit residues: 1192.2544 Evaluate side-chains 591 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 546 time to evaluate : 4.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 107 ARG Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 115 LYS Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain R residue 11 ASN Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain S residue 152 ARG Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain U residue 9 ILE Chi-restraints excluded: chain U residue 34 GLN Chi-restraints excluded: chain U residue 57 ARG Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain U residue 147 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 280 optimal weight: 4.9990 chunk 376 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 325 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 353 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 363 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN C 146 GLN C 166 ASN D 146 GLN G 101 ASN H 71 ASN H 106 GLN I 153 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN M 160 ASN O 200 HIS ** Q 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 210 ASN R 84 GLN S 34 GLN T 34 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 80 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.115776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.097012 restraints weight = 44259.661| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.14 r_work: 0.2837 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 35494 Z= 0.306 Angle : 0.572 10.376 48065 Z= 0.301 Chirality : 0.044 0.189 5533 Planarity : 0.004 0.060 6190 Dihedral : 4.623 77.376 4979 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.29 % Allowed : 20.53 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % 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: 1.14 (0.13), residues: 4483 helix: 1.85 (0.11), residues: 2229 sheet: 0.63 (0.18), residues: 776 loop : -0.87 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 103 HIS 0.005 0.001 HIS I 66 PHE 0.020 0.002 PHE J 69 TYR 0.019 0.002 TYR K 117 ARG 0.012 0.001 ARG L 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16898.97 seconds wall clock time: 298 minutes 30.95 seconds (17910.95 seconds total)