Starting phenix.real_space_refine on Tue Mar 19 16:02:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfo_8662/03_2024/5vfo_8662.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfo_8662/03_2024/5vfo_8662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfo_8662/03_2024/5vfo_8662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfo_8662/03_2024/5vfo_8662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfo_8662/03_2024/5vfo_8662.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vfo_8662/03_2024/5vfo_8662.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 47288 atoms to isotropic. 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 292 5.16 5 C 29827 2.51 5 N 8099 2.21 5 O 9070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "K ARG 10": "NH1" <-> "NH2" Residue "K ARG 20": "NH1" <-> "NH2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "L ARG 157": "NH1" <-> "NH2" Residue "L ARG 239": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 187": "NH1" <-> "NH2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "Q ARG 93": "NH1" <-> "NH2" Residue "Q PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 173": "NH1" <-> "NH2" Residue "T PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 182": "NH1" <-> "NH2" Residue "g ARG 21": "NH1" <-> "NH2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g ARG 132": "NH1" <-> "NH2" Residue "g PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 4": "NH1" <-> "NH2" Residue "h PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 249": "NH1" <-> "NH2" Residue "j PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 20": "NH1" <-> "NH2" Residue "l ARG 96": "NH1" <-> "NH2" Residue "l ARG 157": "NH1" <-> "NH2" Residue "l ARG 239": "NH1" <-> "NH2" Residue "m ARG 19": "NH1" <-> "NH2" Residue "m TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 187": "NH1" <-> "NH2" Residue "m ARG 232": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "o ARG 201": "NH1" <-> "NH2" Residue "p ARG 66": "NH1" <-> "NH2" Residue "q TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47288 Number of models: 1 Model: "" Number of chains: 28 Chain: "G" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1820 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 228} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1688 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'CIS': 3, '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: "I" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1895 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 3, 'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1704 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'CIS': 5, 'PTRANS': 6, 'TRANS': 227} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "K" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 218} 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: "L" 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: "M" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1430 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "O" 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: {'PTRANS': 9, '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: "P" 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: "Q" 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: "R" 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: "S" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1667 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1826 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "h" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1708 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 221} 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: "i" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1912 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "j" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1704 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "k" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1722 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "l" 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: "m" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "n" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1430 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "o" 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: {'CIS': 1, 'PTRANS': 9, 'TRANS': 209} 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: "p" 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: "q" 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: "r" 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: "s" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1667 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 19.34, per 1000 atoms: 0.41 Number of scatterers: 47288 At special positions: 0 Unit cell: (191.25, 138.75, 165.75, 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 292 16.00 O 9070 8.00 N 8099 7.00 C 29827 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 186 " distance=2.03 Simple disulfide: pdb=" SG CYS m 41 " - pdb=" SG CYS m 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.16 Conformation dependent library (CDL) restraints added in 6.8 seconds 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11454 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 72 sheets defined 38.1% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.11 Creating SS restraints... Processing helix chain 'G' and resid 24 through 29 Processing helix chain 'G' and resid 63 through 67 removed outlier: 3.864A pdb=" N VAL G 66 " --> pdb=" O SER G 63 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR G 67 " --> pdb=" O SER G 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 63 through 67' Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 128 removed outlier: 3.644A pdb=" N LEU G 114 " --> pdb=" O PRO G 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 181 Processing helix chain 'G' and resid 191 through 207 Processing helix chain 'G' and resid 231 through 242 Processing helix chain 'H' and resid 19 through 31 removed outlier: 4.410A pdb=" N ALA H 25 " --> pdb=" O GLN H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 102 Processing helix chain 'H' and resid 106 through 123 Processing helix chain 'H' and resid 166 through 178 Processing helix chain 'H' and resid 183 through 199 removed outlier: 4.056A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 230 Processing helix chain 'I' and resid 19 through 30 removed outlier: 4.103A pdb=" N HIS I 30 " --> pdb=" O GLU I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 102 removed outlier: 4.101A pdb=" N VAL I 85 " --> pdb=" O SER I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 124 removed outlier: 3.612A pdb=" N TYR I 121 " --> pdb=" O ILE I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 178 Processing helix chain 'I' and resid 185 through 201 Processing helix chain 'I' and resid 207 through 209 No H-bonds generated for 'chain 'I' and resid 207 through 209' Processing helix chain 'I' and resid 229 through 248 removed outlier: 4.073A pdb=" N VAL I 233 " --> pdb=" O LYS I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 251 No H-bonds generated for 'chain 'I' and resid 249 through 251' Processing helix chain 'J' and resid 16 through 28 removed outlier: 4.201A pdb=" N GLU J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 97 removed outlier: 3.867A pdb=" N ALA J 80 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL J 89 " --> pdb=" O ASN J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 120 Processing helix chain 'J' and resid 138 through 140 No H-bonds generated for 'chain 'J' and resid 138 through 140' Processing helix chain 'J' and resid 164 through 174 removed outlier: 4.190A pdb=" N LEU J 172 " --> pdb=" O VAL J 168 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU J 173 " --> pdb=" O ARG J 169 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS J 174 " --> pdb=" O GLU J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 197 Processing helix chain 'J' and resid 223 through 240 removed outlier: 3.658A pdb=" N GLU J 240 " --> pdb=" O LYS J 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 32 removed outlier: 4.269A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 83 through 104 removed outlier: 4.305A pdb=" N ILE K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL K 94 " --> pdb=" O ASP K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 118 Processing helix chain 'K' and resid 173 through 185 removed outlier: 3.509A pdb=" N VAL K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 206 removed outlier: 3.654A pdb=" N ALA K 194 " --> pdb=" O THR K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 239 Processing helix chain 'L' and resid 19 through 30 removed outlier: 3.848A pdb=" N GLU L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 99 Processing helix chain 'L' and resid 104 through 118 removed outlier: 3.694A pdb=" N LEU L 108 " --> pdb=" O PRO L 104 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 121 No H-bonds generated for 'chain 'L' and resid 119 through 121' Processing helix chain 'L' and resid 165 through 180 removed outlier: 5.046A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 196 Processing helix chain 'L' and resid 229 through 234 removed outlier: 3.603A pdb=" N GLU L 234 " --> pdb=" O SER L 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 28 Processing helix chain 'M' and resid 29 through 33 removed outlier: 3.599A pdb=" N ASN M 32 " --> pdb=" O ALA M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 103 Processing helix chain 'M' and resid 107 through 125 removed outlier: 4.117A pdb=" N TYR M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 177 removed outlier: 3.751A pdb=" N LYS M 173 " --> pdb=" O ARG M 169 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU M 175 " --> pdb=" O ALA M 171 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU M 177 " --> pdb=" O LYS M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 200 removed outlier: 3.569A pdb=" N ILE M 189 " --> pdb=" O THR M 185 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL M 200 " --> pdb=" O ILE M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 240 Processing helix chain 'N' and resid 49 through 71 Processing helix chain 'N' and resid 75 through 89 removed outlier: 3.826A pdb=" N ALA N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 133 removed outlier: 4.408A pdb=" N SER N 133 " --> pdb=" O SER N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 143 removed outlier: 4.609A pdb=" N ASP N 140 " --> pdb=" O TYR N 136 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ALA N 141 " --> pdb=" O GLY N 137 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR N 143 " --> pdb=" O VAL N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 167 Processing helix chain 'O' and resid 48 through 71 Processing helix chain 'O' and resid 75 through 90 removed outlier: 3.575A pdb=" N ALA O 79 " --> pdb=" O ARG O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 142 removed outlier: 4.127A pdb=" N ALA O 134 " --> pdb=" O GLY O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 165 Processing helix chain 'P' and resid 56 through 78 Processing helix chain 'P' and resid 83 through 98 removed outlier: 4.040A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 154 Processing helix chain 'P' and resid 159 through 178 Processing helix chain 'Q' and resid 51 through 72 removed outlier: 4.074A pdb=" N GLN Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 93 removed outlier: 4.428A pdb=" N ARG Q 93 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 146 removed outlier: 5.220A pdb=" N ILE Q 142 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 168 Processing helix chain 'R' and resid 48 through 71 removed outlier: 4.016A pdb=" N CYS R 52 " --> pdb=" O GLY R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 89 removed outlier: 3.505A pdb=" N ALA R 79 " --> pdb=" O SER R 75 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 143 removed outlier: 3.796A pdb=" N ALA R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 167 Processing helix chain 'R' and resid 191 through 200 Processing helix chain 'S' and resid 57 through 80 Processing helix chain 'S' and resid 84 through 99 removed outlier: 3.687A pdb=" N ILE S 88 " --> pdb=" O THR S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 153 Processing helix chain 'S' and resid 167 through 186 removed outlier: 3.518A pdb=" N ALA S 171 " --> pdb=" O SER S 167 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG S 185 " --> pdb=" O SER S 181 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 78 removed outlier: 3.935A pdb=" N GLY T 78 " --> pdb=" O GLU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 102 removed outlier: 3.605A pdb=" N LYS T 102 " --> pdb=" O SER T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 141 through 146 Processing helix chain 'T' and resid 146 through 157 Processing helix chain 'T' and resid 161 through 180 Processing helix chain 'T' and resid 209 through 214 Processing helix chain 'g' and resid 17 through 21 removed outlier: 3.834A pdb=" N GLY g 20 " --> pdb=" O SER g 17 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG g 21 " --> pdb=" O PRO g 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 17 through 21' Processing helix chain 'g' and resid 24 through 29 Processing helix chain 'g' and resid 63 through 67 removed outlier: 3.784A pdb=" N VAL g 66 " --> pdb=" O SER g 63 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR g 67 " --> pdb=" O SER g 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 63 through 67' Processing helix chain 'g' and resid 83 through 106 Processing helix chain 'g' and resid 110 through 128 removed outlier: 3.966A pdb=" N ASN g 128 " --> pdb=" O VAL g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 183 Processing helix chain 'g' and resid 191 through 207 Processing helix chain 'g' and resid 231 through 242 Processing helix chain 'h' and resid 19 through 31 Processing helix chain 'h' and resid 79 through 102 removed outlier: 3.916A pdb=" N VAL h 85 " --> pdb=" O PRO h 81 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 124 Processing helix chain 'h' and resid 166 through 178 removed outlier: 3.629A pdb=" N LYS h 176 " --> pdb=" O THR h 172 " (cutoff:3.500A) Processing helix chain 'h' and resid 183 through 199 removed outlier: 3.986A pdb=" N SER h 198 " --> pdb=" O THR h 194 " (cutoff:3.500A) Processing helix chain 'h' and resid 222 through 230 Processing helix chain 'i' and resid 18 through 30 removed outlier: 3.964A pdb=" N GLU i 22 " --> pdb=" O LEU i 18 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS i 30 " --> pdb=" O GLU i 26 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 102 removed outlier: 3.786A pdb=" N LEU i 86 " --> pdb=" O ASP i 82 " (cutoff:3.500A) Processing helix chain 'i' and resid 107 through 123 removed outlier: 3.707A pdb=" N TYR i 121 " --> pdb=" O ILE i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 168 through 178 Processing helix chain 'i' and resid 185 through 201 Processing helix chain 'i' and resid 207 through 209 No H-bonds generated for 'chain 'i' and resid 207 through 209' Processing helix chain 'i' and resid 230 through 248 Processing helix chain 'i' and resid 249 through 251 No H-bonds generated for 'chain 'i' and resid 249 through 251' Processing helix chain 'j' and resid 18 through 28 removed outlier: 4.287A pdb=" N GLU j 24 " --> pdb=" O GLU j 20 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA j 25 " --> pdb=" O TYR j 21 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) Processing helix chain 'j' and resid 76 through 97 removed outlier: 3.936A pdb=" N ALA j 80 " --> pdb=" O LEU j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 103 through 121 Processing helix chain 'j' and resid 138 through 140 No H-bonds generated for 'chain 'j' and resid 138 through 140' Processing helix chain 'j' and resid 164 through 175 removed outlier: 3.924A pdb=" N LYS j 174 " --> pdb=" O GLU j 170 " (cutoff:3.500A) Processing helix chain 'j' and resid 183 through 196 Processing helix chain 'j' and resid 223 through 240 removed outlier: 3.785A pdb=" N GLU j 240 " --> pdb=" O LYS j 236 " (cutoff:3.500A) Processing helix chain 'k' and resid 21 through 32 removed outlier: 3.733A pdb=" N GLU k 25 " --> pdb=" O LEU k 21 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 60 through 64 removed outlier: 3.576A pdb=" N SER k 63 " --> pdb=" O GLU k 60 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 104 Processing helix chain 'k' and resid 108 through 118 Processing helix chain 'k' and resid 173 through 185 removed outlier: 3.696A pdb=" N VAL k 184 " --> pdb=" O SER k 180 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 206 removed outlier: 3.520A pdb=" N ILE k 201 " --> pdb=" O SER k 197 " (cutoff:3.500A) Processing helix chain 'k' and resid 233 through 240 removed outlier: 3.531A pdb=" N ASP k 240 " --> pdb=" O GLU k 236 " (cutoff:3.500A) Processing helix chain 'l' and resid 19 through 31 removed outlier: 3.794A pdb=" N GLU l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN l 31 " --> pdb=" O GLU l 27 " (cutoff:3.500A) Processing helix chain 'l' and resid 78 through 99 removed outlier: 3.610A pdb=" N SER l 95 " --> pdb=" O GLU l 91 " (cutoff:3.500A) Processing helix chain 'l' and resid 104 through 118 removed outlier: 3.652A pdb=" N LEU l 108 " --> pdb=" O PRO l 104 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) Processing helix chain 'l' and resid 119 through 121 No H-bonds generated for 'chain 'l' and resid 119 through 121' Processing helix chain 'l' and resid 165 through 176 Processing helix chain 'l' and resid 183 through 196 Processing helix chain 'l' and resid 229 through 234 removed outlier: 3.651A pdb=" N GLU l 234 " --> pdb=" O SER l 230 " (cutoff:3.500A) Processing helix chain 'm' and resid 20 through 28 Processing helix chain 'm' and resid 29 through 33 removed outlier: 3.654A pdb=" N ASN m 32 " --> pdb=" O ALA m 29 " (cutoff:3.500A) Processing helix chain 'm' and resid 80 through 103 Processing helix chain 'm' and resid 107 through 125 removed outlier: 4.340A pdb=" N TYR m 125 " --> pdb=" O ALA m 121 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 177 removed outlier: 3.647A pdb=" N LYS m 173 " --> pdb=" O ARG m 169 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU m 175 " --> pdb=" O ALA m 171 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU m 177 " --> pdb=" O LYS m 173 " (cutoff:3.500A) Processing helix chain 'm' and resid 185 through 200 removed outlier: 3.585A pdb=" N ILE m 189 " --> pdb=" O THR m 185 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (cutoff:3.500A) Processing helix chain 'm' and resid 219 through 221 No H-bonds generated for 'chain 'm' and resid 219 through 221' Processing helix chain 'm' and resid 235 through 240 Processing helix chain 'n' and resid 48 through 71 removed outlier: 4.016A pdb=" N THR n 52 " --> pdb=" O SER n 48 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 90 removed outlier: 3.846A pdb=" N ALA n 79 " --> pdb=" O LEU n 75 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR n 90 " --> pdb=" O MET n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 129 through 133 removed outlier: 4.062A pdb=" N SER n 133 " --> pdb=" O SER n 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 134 through 143 removed outlier: 4.545A pdb=" N ASP n 140 " --> pdb=" O TYR n 136 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ALA n 141 " --> pdb=" O GLY n 137 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR n 143 " --> pdb=" O VAL n 139 " (cutoff:3.500A) Processing helix chain 'n' and resid 148 through 167 Processing helix chain 'o' and resid 48 through 71 Processing helix chain 'o' and resid 75 through 90 removed outlier: 3.596A pdb=" N ALA o 79 " --> pdb=" O ARG o 75 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 142 removed outlier: 4.169A pdb=" N ALA o 134 " --> pdb=" O GLY o 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 165 Processing helix chain 'p' and resid 3 through 7 removed outlier: 4.263A pdb=" N ASN p 7 " --> pdb=" O MET p 4 " (cutoff:3.500A) Processing helix chain 'p' and resid 56 through 78 Processing helix chain 'p' and resid 83 through 98 removed outlier: 4.177A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) Processing helix chain 'p' and resid 143 through 154 Processing helix chain 'p' and resid 159 through 178 Processing helix chain 'q' and resid 49 through 72 removed outlier: 4.237A pdb=" N VAL q 54 " --> pdb=" O ALA q 50 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN q 55 " --> pdb=" O GLY q 51 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS q 62 " --> pdb=" O GLU q 58 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN q 65 " --> pdb=" O GLN q 61 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU q 66 " --> pdb=" O LYS q 62 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 93 removed outlier: 4.374A pdb=" N ARG q 93 " --> pdb=" O ALA q 89 " (cutoff:3.500A) Processing helix chain 'q' and resid 134 through 138 Processing helix chain 'q' and resid 152 through 168 removed outlier: 3.564A pdb=" N GLU q 166 " --> pdb=" O LYS q 162 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 71 Processing helix chain 'r' and resid 75 through 89 removed outlier: 3.546A pdb=" N ALA r 79 " --> pdb=" O SER r 75 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 131 through 143 removed outlier: 3.641A pdb=" N ALA r 135 " --> pdb=" O GLY r 131 " (cutoff:3.500A) Processing helix chain 'r' and resid 148 through 167 Processing helix chain 'r' and resid 191 through 200 Processing helix chain 's' and resid 57 through 80 Processing helix chain 's' and resid 84 through 99 removed outlier: 3.777A pdb=" N ILE s 88 " --> pdb=" O THR s 84 " (cutoff:3.500A) Processing helix chain 's' and resid 145 through 153 Processing helix chain 's' and resid 167 through 186 removed outlier: 3.506A pdb=" N ALA s 171 " --> pdb=" O SER s 167 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG s 185 " --> pdb=" O SER s 181 " (cutoff:3.500A) Processing helix chain 't' and resid 56 through 76 removed outlier: 3.508A pdb=" N PHE t 60 " --> pdb=" O ASP t 56 " (cutoff:3.500A) Processing helix chain 't' and resid 84 through 102 removed outlier: 3.633A pdb=" N LYS t 102 " --> pdb=" O SER t 98 " (cutoff:3.500A) Processing helix chain 't' and resid 141 through 146 Processing helix chain 't' and resid 146 through 157 Processing helix chain 't' and resid 161 through 180 Processing helix chain 't' and resid 209 through 214 removed outlier: 3.770A pdb=" N HIS t 213 " --> pdb=" O ASP t 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.489A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 69 through 73 removed outlier: 6.573A pdb=" N LEU G 69 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N MET G 80 " --> pdb=" O LEU G 69 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS G 71 " --> pdb=" O CYS G 78 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N CYS G 78 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 160 through 163 removed outlier: 3.859A pdb=" N GLU H 209 " --> pdb=" O THR H 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 66 through 69 removed outlier: 6.630A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER H 133 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY H 138 " --> pdb=" O TYR H 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 34 through 36 Processing sheet with id=AA6, first strand: chain 'I' and resid 72 through 73 removed outlier: 3.719A pdb=" N ALA I 73 " --> pdb=" O ILE I 137 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY I 138 " --> pdb=" O GLN I 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'J' and resid 158 through 161 removed outlier: 3.788A pdb=" N ALA J 32 " --> pdb=" O ILE J 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 69 through 70 removed outlier: 3.510A pdb=" N VAL J 134 " --> pdb=" O CYS J 70 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU J 144 " --> pdb=" O TRP J 156 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN J 146 " --> pdb=" O HIS J 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 167 through 170 removed outlier: 4.305A pdb=" N ALA K 37 " --> pdb=" O ILE K 170 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL K 50 " --> pdb=" O GLU K 216 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU K 216 " --> pdb=" O VAL K 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 142 through 147 Processing sheet with id=AB3, first strand: chain 'L' and resid 158 through 161 removed outlier: 3.727A pdb=" N ILE L 212 " --> pdb=" O TYR L 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 51 through 52 removed outlier: 4.232A pdb=" N ARG L 51 " --> pdb=" O GLN L 60 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 64 through 65 removed outlier: 3.689A pdb=" N ILE L 72 " --> pdb=" O LEU L 64 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU L 133 " --> pdb=" O SER L 73 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP L 138 " --> pdb=" O GLY L 141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 162 through 165 removed outlier: 3.644A pdb=" N GLY M 44 " --> pdb=" O CYS M 41 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU M 212 " --> pdb=" O VAL M 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 162 through 165 removed outlier: 3.644A pdb=" N GLY M 44 " --> pdb=" O CYS M 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 74 through 79 removed outlier: 3.886A pdb=" N GLY M 74 " --> pdb=" O GLY M 138 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY M 138 " --> pdb=" O GLY M 74 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE M 135 " --> pdb=" O ILE M 151 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE M 151 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU M 137 " --> pdb=" O TYR M 149 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR M 158 " --> pdb=" O MET M 150 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 125 through 128 removed outlier: 3.714A pdb=" N ALA N 177 " --> pdb=" O LEU N 14 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 20 through 22 removed outlier: 6.974A pdb=" N THR N 20 " --> pdb=" O ALA N 27 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 34 through 36 removed outlier: 3.578A pdb=" N VAL N 121 " --> pdb=" O SER N 113 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 124 through 128 removed outlier: 3.513A pdb=" N GLY O 15 " --> pdb=" O ALA O 4 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL O 177 " --> pdb=" O ASP O 184 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 34 through 36 removed outlier: 3.527A pdb=" N SER O 118 " --> pdb=" O TYR O 114 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 211 through 213 removed outlier: 6.454A pdb=" N THR P 199 " --> pdb=" O LEU O 212 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 211 through 213 removed outlier: 6.454A pdb=" N THR P 199 " --> pdb=" O LEU O 212 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL P 11 " --> pdb=" O SER P 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 28 through 29 removed outlier: 6.875A pdb=" N PHE P 28 " --> pdb=" O VAL P 35 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 42 through 44 Processing sheet with id=AC9, first strand: chain 'Q' and resid 5 through 8 removed outlier: 3.667A pdb=" N VAL Q 13 " --> pdb=" O ILE Q 183 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL Q 15 " --> pdb=" O ARG Q 181 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 42 through 48 removed outlier: 3.631A pdb=" N LEU Q 103 " --> pdb=" O LEU Q 45 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 177 through 178 Processing sheet with id=AD3, first strand: chain 'R' and resid 125 through 129 removed outlier: 3.727A pdb=" N SER R 188 " --> pdb=" O LEU R 176 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N HIS R 178 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG R 186 " --> pdb=" O HIS R 178 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 20 through 22 removed outlier: 7.194A pdb=" N ALA R 20 " --> pdb=" O ALA R 27 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 41 through 43 Processing sheet with id=AD6, first strand: chain 'S' and resid 135 through 139 removed outlier: 3.505A pdb=" N LYS S 136 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY S 202 " --> pdb=" O THR S 199 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 29 through 31 removed outlier: 7.085A pdb=" N LEU S 29 " --> pdb=" O HIS S 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 43 through 45 removed outlier: 3.633A pdb=" N VAL S 121 " --> pdb=" O ASP S 133 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN S 131 " --> pdb=" O SER S 123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 136 through 138 removed outlier: 5.140A pdb=" N PHE T 187 " --> pdb=" O PRO T 202 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE T 189 " --> pdb=" O GLU T 200 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'T' and resid 42 through 43 removed outlier: 3.548A pdb=" N THR T 109 " --> pdb=" O SER T 54 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR T 132 " --> pdb=" O TYR T 124 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'g' and resid 166 through 169 removed outlier: 3.600A pdb=" N SER g 39 " --> pdb=" O ALA g 168 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N THR g 38 " --> pdb=" O GLN g 53 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN g 53 " --> pdb=" O THR g 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'g' and resid 70 through 71 Processing sheet with id=AE4, first strand: chain 'h' and resid 160 through 163 Processing sheet with id=AE5, first strand: chain 'h' and resid 66 through 67 removed outlier: 3.542A pdb=" N VAL h 75 " --> pdb=" O LEU h 135 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY h 138 " --> pdb=" O TYR h 145 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'i' and resid 34 through 36 removed outlier: 3.556A pdb=" N LEU i 35 " --> pdb=" O ALA i 46 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'i' and resid 72 through 73 removed outlier: 3.738A pdb=" N ALA i 73 " --> pdb=" O ILE i 137 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY i 138 " --> pdb=" O GLN i 146 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'j' and resid 158 through 160 removed outlier: 3.863A pdb=" N GLY j 34 " --> pdb=" O ASN j 159 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL j 210 " --> pdb=" O LYS j 218 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS j 218 " --> pdb=" O VAL j 210 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'j' and resid 69 through 70 removed outlier: 4.448A pdb=" N LEU j 144 " --> pdb=" O TRP j 156 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'k' and resid 169 through 170 removed outlier: 4.185A pdb=" N ALA k 37 " --> pdb=" O ILE k 170 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL k 50 " --> pdb=" O GLU k 216 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU k 216 " --> pdb=" O VAL k 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'k' and resid 142 through 147 Processing sheet with id=AF3, first strand: chain 'l' and resid 158 through 161 removed outlier: 3.687A pdb=" N ILE l 212 " --> pdb=" O TYR l 224 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'l' and resid 64 through 65 removed outlier: 3.523A pdb=" N LEU l 133 " --> pdb=" O SER l 73 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP l 138 " --> pdb=" O GLY l 141 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'm' and resid 162 through 165 removed outlier: 3.665A pdb=" N GLY m 44 " --> pdb=" O CYS m 41 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU m 212 " --> pdb=" O VAL m 49 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'm' and resid 162 through 165 removed outlier: 3.665A pdb=" N GLY m 44 " --> pdb=" O CYS m 41 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'm' and resid 74 through 75 removed outlier: 3.996A pdb=" N GLY m 74 " --> pdb=" O GLY m 138 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY m 138 " --> pdb=" O GLY m 74 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'm' and resid 74 through 75 removed outlier: 3.996A pdb=" N GLY m 74 " --> pdb=" O GLY m 138 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY m 138 " --> pdb=" O GLY m 74 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN m 147 " --> pdb=" O SER m 139 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR m 158 " --> pdb=" O MET m 150 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'n' and resid 125 through 128 Processing sheet with id=AG1, first strand: chain 'n' and resid 20 through 22 removed outlier: 7.090A pdb=" N THR n 20 " --> pdb=" O ALA n 27 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'n' and resid 34 through 36 removed outlier: 4.015A pdb=" N VAL n 111 " --> pdb=" O GLN n 123 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL n 121 " --> pdb=" O SER n 113 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'o' and resid 124 through 128 Processing sheet with id=AG4, first strand: chain 'o' and resid 34 through 36 removed outlier: 3.528A pdb=" N GLY o 101 " --> pdb=" O TYR o 42 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'o' and resid 216 through 218 removed outlier: 4.567A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA p 10 " --> pdb=" O ASP p 25 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL p 11 " --> pdb=" O SER p 139 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'p' and resid 28 through 29 removed outlier: 6.993A pdb=" N PHE p 28 " --> pdb=" O VAL p 35 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'p' and resid 42 through 44 Processing sheet with id=AG8, first strand: chain 'q' and resid 129 through 132 removed outlier: 3.794A pdb=" N ALA q 130 " --> pdb=" O GLY q 6 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU q 4 " --> pdb=" O HIS q 132 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL q 13 " --> pdb=" O ILE q 183 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL q 15 " --> pdb=" O ARG q 181 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'q' and resid 43 through 48 Processing sheet with id=AH1, first strand: chain 'q' and resid 177 through 178 Processing sheet with id=AH2, first strand: chain 'r' and resid 125 through 129 removed outlier: 3.766A pdb=" N ALA r 16 " --> pdb=" O ASN r 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER r 188 " --> pdb=" O LEU r 176 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N HIS r 178 " --> pdb=" O ARG r 186 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG r 186 " --> pdb=" O HIS r 178 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'r' and resid 20 through 22 removed outlier: 7.337A pdb=" N ALA r 20 " --> pdb=" O ALA r 27 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA r 27 " --> pdb=" O ALA r 20 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'r' and resid 41 through 43 removed outlier: 3.612A pdb=" N LEU r 42 " --> pdb=" O CYS r 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY r 103 " --> pdb=" O GLY r 110 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 's' and resid 135 through 139 Processing sheet with id=AH6, first strand: chain 's' and resid 29 through 31 removed outlier: 6.917A pdb=" N LEU s 29 " --> pdb=" O HIS s 36 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 's' and resid 43 through 47 removed outlier: 6.598A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL s 51 " --> pdb=" O GLY s 111 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL s 121 " --> pdb=" O ASP s 133 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN s 131 " --> pdb=" O SER s 123 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 't' and resid 136 through 138 removed outlier: 3.614A pdb=" N GLY t 19 " --> pdb=" O PHE t 16 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N PHE t 187 " --> pdb=" O PRO t 202 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE t 189 " --> pdb=" O GLU t 200 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY t 196 " --> pdb=" O THR t 193 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 't' and resid 42 through 43 2399 hydrogen bonds defined for protein. 6837 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: 17.12 Time building geometry restraints manager: 18.41 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: 13458 1.33 - 1.45: 8747 1.45 - 1.57: 25458 1.57 - 1.69: 0 1.69 - 1.81: 474 Bond restraints: 48137 Sorted by residual: bond pdb=" C ILE O 113 " pdb=" N TYR O 114 " ideal model delta sigma weight residual 1.331 1.228 0.103 2.07e-02 2.33e+03 2.48e+01 bond pdb=" C ILE q 142 " pdb=" N LEU q 143 " ideal model delta sigma weight residual 1.331 1.279 0.052 1.38e-02 5.25e+03 1.41e+01 bond pdb=" C ILE L 118 " pdb=" N PRO L 119 " ideal model delta sigma weight residual 1.337 1.370 -0.034 9.80e-03 1.04e+04 1.19e+01 bond pdb=" CA TYR P 104 " pdb=" CB TYR P 104 " ideal model delta sigma weight residual 1.526 1.472 0.054 1.76e-02 3.23e+03 9.49e+00 bond pdb=" N PHE K 22 " pdb=" CA PHE K 22 " ideal model delta sigma weight residual 1.458 1.512 -0.054 1.90e-02 2.77e+03 7.99e+00 ... (remaining 48132 not shown) Histogram of bond angle deviations from ideal: 94.48 - 103.43: 545 103.43 - 112.38: 24682 112.38 - 121.33: 27721 121.33 - 130.28: 12089 130.28 - 139.23: 182 Bond angle restraints: 65219 Sorted by residual: angle pdb=" C LEU K 21 " pdb=" N PHE K 22 " pdb=" CA PHE K 22 " ideal model delta sigma weight residual 121.70 139.23 -17.53 1.80e+00 3.09e-01 9.48e+01 angle pdb=" N GLU G 223 " pdb=" CA GLU G 223 " pdb=" C GLU G 223 " ideal model delta sigma weight residual 114.62 103.93 10.69 1.14e+00 7.69e-01 8.79e+01 angle pdb=" C GLY M 6 " pdb=" N TYR M 7 " pdb=" CA TYR M 7 " ideal model delta sigma weight residual 121.70 137.91 -16.21 1.80e+00 3.09e-01 8.11e+01 angle pdb=" C GLY K 19 " pdb=" N ARG K 20 " pdb=" CA ARG K 20 " ideal model delta sigma weight residual 121.70 136.01 -14.31 1.80e+00 3.09e-01 6.32e+01 angle pdb=" N GLU I 15 " pdb=" CA GLU I 15 " pdb=" CB GLU I 15 " ideal model delta sigma weight residual 114.10 106.87 7.23 1.00e+00 1.00e+00 5.22e+01 ... (remaining 65214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 27448 17.56 - 35.12: 1141 35.12 - 52.69: 199 52.69 - 70.25: 23 70.25 - 87.81: 34 Dihedral angle restraints: 28845 sinusoidal: 10911 harmonic: 17934 Sorted by residual: dihedral pdb=" CA ALA j 180 " pdb=" C ALA j 180 " pdb=" N ILE j 181 " pdb=" CA ILE j 181 " ideal model delta harmonic sigma weight residual 180.00 -118.00 -62.00 0 5.00e+00 4.00e-02 1.54e+02 dihedral pdb=" CA ASP K 9 " pdb=" C ASP K 9 " pdb=" N ARG K 10 " pdb=" CA ARG K 10 " ideal model delta harmonic sigma weight residual 180.00 126.99 53.01 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA ASN O 172 " pdb=" C ASN O 172 " pdb=" N ILE O 173 " pdb=" CA ILE O 173 " ideal model delta harmonic sigma weight residual 180.00 140.84 39.16 0 5.00e+00 4.00e-02 6.13e+01 ... (remaining 28842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 6395 0.087 - 0.175: 935 0.175 - 0.262: 58 0.262 - 0.349: 7 0.349 - 0.437: 4 Chirality restraints: 7399 Sorted by residual: chirality pdb=" CB ILE I 105 " pdb=" CA ILE I 105 " pdb=" CG1 ILE I 105 " pdb=" CG2 ILE I 105 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CB ILE i 105 " pdb=" CA ILE i 105 " pdb=" CG1 ILE i 105 " pdb=" CG2 ILE i 105 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA ARG N 19 " pdb=" N ARG N 19 " pdb=" C ARG N 19 " pdb=" CB ARG N 19 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 7396 not shown) Planarity restraints: 8467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR J 97 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C THR J 97 " 0.066 2.00e-02 2.50e+03 pdb=" O THR J 97 " -0.025 2.00e-02 2.50e+03 pdb=" N VAL J 98 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE I 105 " -0.061 5.00e-02 4.00e+02 9.27e-02 1.37e+01 pdb=" N PRO I 106 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO I 106 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO I 106 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP L 226 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C ASP L 226 " -0.063 2.00e-02 2.50e+03 pdb=" O ASP L 226 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP L 227 " 0.021 2.00e-02 2.50e+03 ... (remaining 8464 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 3109 2.72 - 3.26: 46243 3.26 - 3.81: 80042 3.81 - 4.35: 91275 4.35 - 4.90: 157149 Nonbonded interactions: 377818 Sorted by model distance: nonbonded pdb=" OG1 THR P 58 " pdb=" O LEU Q 121 " model vdw 2.174 2.440 nonbonded pdb=" OG1 THR p 58 " pdb=" O LEU q 121 " model vdw 2.188 2.440 nonbonded pdb=" OG SER h 9 " pdb=" O GLN h 123 " model vdw 2.208 2.440 nonbonded pdb=" OG1 THR J 177 " pdb=" O GLU J 179 " model vdw 2.213 2.440 nonbonded pdb=" OG1 THR h 222 " pdb=" OE1 GLU h 225 " model vdw 2.222 2.440 ... (remaining 377813 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 'G' selection = (chain 'g' and resid 6 through 244) } ncs_group { reference = chain 'H' selection = (chain 'h' and resid 5 through 234) } ncs_group { reference = chain 'I' selection = (chain 'i' and resid 4 through 251) } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = (chain 'K' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 241)) selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'O' selection = chain 'o' } ncs_group { reference = chain 'P' selection = chain 'p' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'r' } ncs_group { reference = chain 'S' selection = chain 's' } ncs_group { reference = chain 'T' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 25.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.460 Construct map_model_manager: 0.060 Extract box with map and model: 36.840 Check model and map are aligned: 0.560 Set scattering table: 0.360 Process input model: 107.530 Find NCS groups from input model: 3.850 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 178.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 48137 Z= 0.552 Angle : 1.070 17.529 65219 Z= 0.597 Chirality : 0.060 0.437 7399 Planarity : 0.007 0.093 8467 Dihedral : 10.889 87.811 17385 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.42 % Favored : 93.40 % Rotamer: Outliers : 0.55 % Allowed : 2.93 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.09), residues: 6155 helix: -1.38 (0.09), residues: 2181 sheet: -1.90 (0.13), residues: 1336 loop : -3.09 (0.10), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.005 TRP M 215 HIS 0.016 0.003 HIS m 201 PHE 0.033 0.004 PHE G 9 TYR 0.040 0.003 TYR N 136 ARG 0.017 0.001 ARG t 179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1677 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1650 time to evaluate : 4.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 ARG cc_start: 0.6787 (pmm-80) cc_final: 0.6323 (tpt170) REVERT: G 80 MET cc_start: 0.8691 (mmm) cc_final: 0.8103 (mmm) REVERT: G 128 ASN cc_start: 0.7967 (t0) cc_final: 0.7399 (p0) REVERT: G 147 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8211 (mp10) REVERT: G 224 ASN cc_start: 0.8465 (t0) cc_final: 0.8182 (p0) REVERT: H 12 THR cc_start: 0.6016 (t) cc_final: 0.5518 (p) REVERT: H 13 PHE cc_start: 0.7623 (m-10) cc_final: 0.7005 (m-80) REVERT: H 49 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7468 (tm-30) REVERT: H 100 VAL cc_start: 0.8288 (t) cc_final: 0.8006 (t) REVERT: H 112 GLN cc_start: 0.8367 (mm110) cc_final: 0.7966 (mt0) REVERT: H 151 PRO cc_start: 0.8662 (Cg_exo) cc_final: 0.8439 (Cg_endo) REVERT: H 185 GLU cc_start: 0.8618 (mp0) cc_final: 0.8192 (pm20) REVERT: H 186 ASP cc_start: 0.8389 (m-30) cc_final: 0.7825 (m-30) REVERT: H 189 HIS cc_start: 0.8202 (t-90) cc_final: 0.7976 (t-90) REVERT: H 206 ASP cc_start: 0.8804 (m-30) cc_final: 0.8501 (p0) REVERT: H 214 ASN cc_start: 0.9105 (m-40) cc_final: 0.8778 (t0) REVERT: I 8 ARG cc_start: 0.6149 (mtt90) cc_final: 0.5856 (ttm-80) REVERT: I 40 ASN cc_start: 0.7711 (m-40) cc_final: 0.7504 (m-40) REVERT: I 48 GLU cc_start: 0.7537 (tt0) cc_final: 0.6918 (tm-30) REVERT: I 50 ARG cc_start: 0.7530 (mmp-170) cc_final: 0.7288 (mmt90) REVERT: I 57 ASP cc_start: 0.7000 (m-30) cc_final: 0.6287 (m-30) REVERT: I 69 ASN cc_start: 0.8331 (t0) cc_final: 0.7686 (t0) REVERT: I 136 TYR cc_start: 0.8685 (m-80) cc_final: 0.8422 (m-80) REVERT: I 219 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7332 (mp0) REVERT: J 3 TYR cc_start: 0.7475 (m-80) cc_final: 0.7110 (m-80) REVERT: J 13 ASP cc_start: 0.8047 (p0) cc_final: 0.7797 (t0) REVERT: J 20 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7754 (tm-30) REVERT: J 30 SER cc_start: 0.7999 (m) cc_final: 0.7635 (p) REVERT: J 38 ARG cc_start: 0.7417 (tpt170) cc_final: 0.7152 (tmm160) REVERT: J 66 ASP cc_start: 0.8422 (t0) cc_final: 0.7536 (t70) REVERT: J 68 ASN cc_start: 0.8183 (m110) cc_final: 0.7846 (m110) REVERT: J 146 GLN cc_start: 0.8047 (pt0) cc_final: 0.7741 (pt0) REVERT: J 171 PHE cc_start: 0.8476 (t80) cc_final: 0.7421 (t80) REVERT: J 179 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7163 (pm20) REVERT: J 188 ILE cc_start: 0.7963 (mt) cc_final: 0.7749 (tt) REVERT: K 107 MET cc_start: 0.7818 (ttm) cc_final: 0.7509 (ttm) REVERT: K 166 ASP cc_start: 0.8098 (m-30) cc_final: 0.7722 (m-30) REVERT: L 6 TYR cc_start: 0.7156 (m-80) cc_final: 0.6879 (m-80) REVERT: L 12 VAL cc_start: 0.9302 (t) cc_final: 0.8911 (p) REVERT: L 27 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8148 (mm-30) REVERT: L 55 GLU cc_start: 0.7715 (mp0) cc_final: 0.7485 (tm-30) REVERT: L 56 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7366 (pp) REVERT: L 60 GLN cc_start: 0.7422 (tp40) cc_final: 0.7207 (tp-100) REVERT: L 123 TYR cc_start: 0.8172 (t80) cc_final: 0.7963 (t80) REVERT: L 180 MET cc_start: 0.8263 (mmm) cc_final: 0.8062 (mmm) REVERT: M 19 ARG cc_start: 0.7561 (ptt-90) cc_final: 0.7133 (ptp90) REVERT: M 43 ASP cc_start: 0.7943 (p0) cc_final: 0.7606 (m-30) REVERT: M 67 PHE cc_start: 0.8116 (m-10) cc_final: 0.7604 (m-10) REVERT: M 75 MET cc_start: 0.8926 (mtp) cc_final: 0.8518 (mtp) REVERT: M 140 TYR cc_start: 0.8507 (t80) cc_final: 0.8280 (t80) REVERT: M 169 ARG cc_start: 0.8485 (ttp80) cc_final: 0.8058 (ttp80) REVERT: M 184 MET cc_start: 0.7579 (mtt) cc_final: 0.7045 (mtp) REVERT: M 191 LYS cc_start: 0.8477 (pttp) cc_final: 0.7546 (ttpt) REVERT: M 226 ILE cc_start: 0.8383 (tt) cc_final: 0.8175 (pt) REVERT: M 241 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7658 (tm-30) REVERT: N 28 ASN cc_start: 0.8264 (t160) cc_final: 0.7959 (t0) REVERT: N 57 ASP cc_start: 0.8182 (m-30) cc_final: 0.7885 (t0) REVERT: N 95 MET cc_start: 0.8741 (mtp) cc_final: 0.8500 (mtm) REVERT: N 98 ILE cc_start: 0.8531 (mm) cc_final: 0.8316 (mt) REVERT: N 110 GLN cc_start: 0.8175 (mt0) cc_final: 0.7282 (mt0) REVERT: N 140 ASP cc_start: 0.7623 (p0) cc_final: 0.7392 (p0) REVERT: N 147 MET cc_start: 0.7874 (mtt) cc_final: 0.7569 (mtt) REVERT: N 185 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7107 (tt0) REVERT: O 64 GLU cc_start: 0.8364 (tt0) cc_final: 0.7917 (tt0) REVERT: O 201 ARG cc_start: 0.7021 (ttm110) cc_final: 0.6608 (ptp90) REVERT: P 59 ASP cc_start: 0.8361 (m-30) cc_final: 0.7805 (m-30) REVERT: P 88 MET cc_start: 0.8712 (ttp) cc_final: 0.8243 (ttp) REVERT: P 89 SER cc_start: 0.8306 (m) cc_final: 0.7753 (t) REVERT: P 117 PHE cc_start: 0.7919 (p90) cc_final: 0.7483 (p90) REVERT: P 127 ILE cc_start: 0.7717 (pt) cc_final: 0.7466 (mt) REVERT: P 129 CYS cc_start: 0.7361 (t) cc_final: 0.7043 (t) REVERT: P 131 MET cc_start: 0.6980 (ttp) cc_final: 0.6624 (mtp) REVERT: P 135 ASP cc_start: 0.7786 (p0) cc_final: 0.7410 (p0) REVERT: P 161 ASP cc_start: 0.7661 (m-30) cc_final: 0.7047 (t70) REVERT: P 162 HIS cc_start: 0.6759 (m170) cc_final: 0.6232 (m170) REVERT: P 168 SER cc_start: 0.9393 (m) cc_final: 0.9101 (p) REVERT: Q 40 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7991 (mp0) REVERT: Q 58 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6713 (mt-10) REVERT: Q 87 ASN cc_start: 0.7593 (m-40) cc_final: 0.7233 (m-40) REVERT: Q 119 ASP cc_start: 0.8221 (t0) cc_final: 0.7913 (t70) REVERT: Q 162 LYS cc_start: 0.7886 (mttt) cc_final: 0.7443 (ptpt) REVERT: Q 166 GLU cc_start: 0.5917 (mm-30) cc_final: 0.5577 (mm-30) REVERT: R 32 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8254 (mptt) REVERT: R 34 VAL cc_start: 0.8584 (t) cc_final: 0.8283 (t) REVERT: R 52 CYS cc_start: 0.8591 (m) cc_final: 0.8298 (m) REVERT: R 67 GLU cc_start: 0.8796 (tt0) cc_final: 0.8325 (tp30) REVERT: R 72 GLU cc_start: 0.7814 (tt0) cc_final: 0.7180 (pp20) REVERT: R 85 ASN cc_start: 0.8242 (m110) cc_final: 0.7943 (m110) REVERT: R 91 LYS cc_start: 0.8452 (tttp) cc_final: 0.8248 (tttp) REVERT: R 117 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7705 (mp0) REVERT: R 175 ASN cc_start: 0.8665 (m-40) cc_final: 0.8251 (m110) REVERT: R 198 LYS cc_start: 0.8079 (tttt) cc_final: 0.7815 (tppp) REVERT: S 35 ILE cc_start: 0.8736 (mm) cc_final: 0.8526 (mt) REVERT: S 76 LYS cc_start: 0.8556 (tttm) cc_final: 0.8018 (tppt) REVERT: S 129 SER cc_start: 0.7753 (t) cc_final: 0.7548 (m) REVERT: S 136 LYS cc_start: 0.9090 (mmmm) cc_final: 0.8821 (mmtt) REVERT: S 162 GLU cc_start: 0.8044 (pm20) cc_final: 0.7767 (tp30) REVERT: S 172 MET cc_start: 0.8587 (mmm) cc_final: 0.8316 (mtp) REVERT: S 197 ILE cc_start: 0.8378 (mp) cc_final: 0.8081 (pt) REVERT: T 15 LYS cc_start: 0.8546 (mttt) cc_final: 0.8253 (mttp) REVERT: T 17 GLU cc_start: 0.8717 (tp30) cc_final: 0.8119 (pt0) REVERT: T 26 MET cc_start: 0.7454 (mtp) cc_final: 0.7050 (mtp) REVERT: T 43 MET cc_start: 0.8206 (ttp) cc_final: 0.7769 (ttm) REVERT: T 64 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8102 (ttmp) REVERT: T 75 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8329 (mt-10) REVERT: T 106 LEU cc_start: 0.7950 (mt) cc_final: 0.7624 (mt) REVERT: T 126 ASP cc_start: 0.8004 (t0) cc_final: 0.7781 (t0) REVERT: T 133 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8231 (mt-10) REVERT: T 162 GLN cc_start: 0.7922 (tt0) cc_final: 0.7641 (tm-30) REVERT: T 167 ASP cc_start: 0.8601 (t70) cc_final: 0.7829 (t0) REVERT: T 170 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8317 (pt0) REVERT: T 173 MET cc_start: 0.8558 (mmm) cc_final: 0.8025 (tpp) REVERT: T 179 ARG cc_start: 0.6640 (pmt100) cc_final: 0.5978 (pmt100) REVERT: T 180 ASP cc_start: 0.7918 (t0) cc_final: 0.7491 (t0) REVERT: T 199 ILE cc_start: 0.8431 (mt) cc_final: 0.8019 (mp) REVERT: T 210 ASP cc_start: 0.8247 (m-30) cc_final: 0.7661 (t0) REVERT: g 73 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8008 (p) REVERT: g 103 TYR cc_start: 0.8587 (t80) cc_final: 0.8342 (t80) REVERT: g 131 MET cc_start: 0.7537 (mtp) cc_final: 0.7096 (mtt) REVERT: g 138 MET cc_start: 0.8435 (ttm) cc_final: 0.8220 (ttp) REVERT: g 180 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8105 (tp30) REVERT: g 238 HIS cc_start: 0.7523 (m-70) cc_final: 0.7183 (m-70) REVERT: h 7 SER cc_start: 0.8203 (t) cc_final: 0.7927 (p) REVERT: h 39 LYS cc_start: 0.7853 (tmtt) cc_final: 0.7653 (ttpt) REVERT: h 76 TYR cc_start: 0.7492 (p90) cc_final: 0.6259 (p90) REVERT: h 82 ASP cc_start: 0.7735 (m-30) cc_final: 0.7530 (m-30) REVERT: h 93 LEU cc_start: 0.8296 (tt) cc_final: 0.7949 (tt) REVERT: h 102 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7399 (mm-40) REVERT: h 181 ASP cc_start: 0.8005 (p0) cc_final: 0.7760 (p0) REVERT: h 182 LEU cc_start: 0.7654 (mt) cc_final: 0.6822 (pt) REVERT: h 183 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7485 (pt0) REVERT: h 207 ASN cc_start: 0.7388 (m110) cc_final: 0.6321 (m110) REVERT: i 5 TYR cc_start: 0.6714 (m-10) cc_final: 0.6444 (m-10) REVERT: i 50 ARG cc_start: 0.6883 (mmp-170) cc_final: 0.6615 (mmm160) REVERT: i 128 ARG cc_start: 0.7021 (ttp80) cc_final: 0.6770 (tmm160) REVERT: i 151 ASP cc_start: 0.7732 (m-30) cc_final: 0.7438 (m-30) REVERT: i 162 THR cc_start: 0.7501 (t) cc_final: 0.6994 (t) REVERT: i 174 MET cc_start: 0.8569 (ttm) cc_final: 0.8118 (mmm) REVERT: j 30 SER cc_start: 0.6585 (m) cc_final: 0.6327 (t) REVERT: j 39 ASP cc_start: 0.7760 (t0) cc_final: 0.7348 (p0) REVERT: j 62 ILE cc_start: 0.8075 (mp) cc_final: 0.7763 (mt) REVERT: j 66 ASP cc_start: 0.7679 (t0) cc_final: 0.6721 (t70) REVERT: j 70 CYS cc_start: 0.8301 (m) cc_final: 0.7733 (t) REVERT: j 101 PRO cc_start: 0.7728 (Cg_endo) cc_final: 0.6984 (Cg_exo) REVERT: j 102 VAL cc_start: 0.8832 (t) cc_final: 0.8428 (p) REVERT: j 177 THR cc_start: 0.7563 (p) cc_final: 0.7156 (p) REVERT: k 22 PHE cc_start: 0.6879 (m-80) cc_final: 0.6199 (m-10) REVERT: k 81 LEU cc_start: 0.8182 (mp) cc_final: 0.7834 (tp) REVERT: k 127 ASP cc_start: 0.1855 (m-30) cc_final: 0.1332 (m-30) REVERT: k 148 GLU cc_start: 0.6959 (mp0) cc_final: 0.6745 (pm20) REVERT: k 162 PHE cc_start: 0.6308 (t80) cc_final: 0.5626 (t80) REVERT: k 168 ARG cc_start: 0.8247 (tpt170) cc_final: 0.7835 (tpp-160) REVERT: l 6 TYR cc_start: 0.5795 (p90) cc_final: 0.4663 (p90) REVERT: l 14 SER cc_start: 0.8296 (m) cc_final: 0.7957 (t) REVERT: l 20 HIS cc_start: 0.5964 (m90) cc_final: 0.5176 (m90) REVERT: l 27 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8481 (mm-30) REVERT: l 61 LYS cc_start: 0.7994 (pttm) cc_final: 0.7143 (mmmm) REVERT: l 92 CYS cc_start: 0.7889 (m) cc_final: 0.7376 (m) REVERT: l 164 ARG cc_start: 0.7774 (ptp90) cc_final: 0.6811 (mmt180) REVERT: l 179 PHE cc_start: 0.8016 (m-10) cc_final: 0.7641 (m-80) REVERT: l 197 GLU cc_start: 0.8371 (mp0) cc_final: 0.8164 (mp0) REVERT: l 227 ASP cc_start: 0.8413 (m-30) cc_final: 0.7936 (p0) REVERT: m 31 GLU cc_start: 0.7411 (tp30) cc_final: 0.6948 (tp30) REVERT: m 67 PHE cc_start: 0.8338 (m-10) cc_final: 0.7812 (m-10) REVERT: m 114 ARG cc_start: 0.7947 (mmm160) cc_final: 0.7548 (mmt180) REVERT: m 184 MET cc_start: 0.8750 (mtt) cc_final: 0.7379 (mtt) REVERT: m 185 THR cc_start: 0.8435 (p) cc_final: 0.8135 (t) REVERT: m 192 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8813 (mm-30) REVERT: m 209 PHE cc_start: 0.7786 (p90) cc_final: 0.7347 (p90) REVERT: m 213 LEU cc_start: 0.9126 (mt) cc_final: 0.8897 (mm) REVERT: n 44 CYS cc_start: 0.7515 (p) cc_final: 0.6850 (p) REVERT: n 62 GLN cc_start: 0.8716 (mt0) cc_final: 0.8257 (tp40) REVERT: n 86 MET cc_start: 0.8265 (tpt) cc_final: 0.8042 (mmm) REVERT: n 95 MET cc_start: 0.8399 (mtp) cc_final: 0.8120 (mtm) REVERT: n 116 MET cc_start: 0.7141 (mtp) cc_final: 0.6870 (ttm) REVERT: n 139 VAL cc_start: 0.8580 (p) cc_final: 0.8358 (p) REVERT: n 147 MET cc_start: 0.6730 (mtt) cc_final: 0.6294 (mtt) REVERT: n 164 MET cc_start: 0.8252 (mtp) cc_final: 0.7952 (mtp) REVERT: n 167 ASP cc_start: 0.8276 (t70) cc_final: 0.7742 (t0) REVERT: o 36 PHE cc_start: 0.8815 (t80) cc_final: 0.8286 (t80) REVERT: o 72 ARG cc_start: 0.6991 (ptp-170) cc_final: 0.6584 (ptt180) REVERT: o 110 LEU cc_start: 0.7740 (tp) cc_final: 0.7522 (tt) REVERT: o 112 SER cc_start: 0.8551 (p) cc_final: 0.8001 (m) REVERT: o 127 MET cc_start: 0.8075 (mmm) cc_final: 0.7712 (mmm) REVERT: o 135 MET cc_start: 0.7811 (tpp) cc_final: 0.7523 (tpp) REVERT: o 152 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8187 (mtmm) REVERT: o 165 ASN cc_start: 0.8216 (t0) cc_final: 0.7765 (m110) REVERT: o 182 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8228 (mmtm) REVERT: o 202 TYR cc_start: 0.7280 (m-80) cc_final: 0.7069 (m-80) REVERT: p 59 ASP cc_start: 0.8438 (m-30) cc_final: 0.8106 (m-30) REVERT: p 78 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6263 (mt-10) REVERT: p 88 MET cc_start: 0.8938 (ttp) cc_final: 0.8660 (ttp) REVERT: p 131 MET cc_start: 0.8119 (ttp) cc_final: 0.7076 (mpp) REVERT: p 134 ASP cc_start: 0.7807 (m-30) cc_final: 0.6905 (t0) REVERT: p 135 ASP cc_start: 0.8557 (p0) cc_final: 0.7723 (p0) REVERT: p 149 MET cc_start: 0.9135 (mmm) cc_final: 0.8884 (mmm) REVERT: p 161 ASP cc_start: 0.8556 (m-30) cc_final: 0.8284 (m-30) REVERT: p 166 THR cc_start: 0.9029 (m) cc_final: 0.8825 (p) REVERT: p 194 LYS cc_start: 0.8534 (pttt) cc_final: 0.7666 (ptmm) REVERT: q 1 MET cc_start: 0.6881 (ttt) cc_final: 0.6108 (tmm) REVERT: q 18 ASP cc_start: 0.8323 (p0) cc_final: 0.8096 (p0) REVERT: q 20 VAL cc_start: 0.8806 (t) cc_final: 0.8545 (m) REVERT: q 52 ASP cc_start: 0.8367 (m-30) cc_final: 0.7090 (m-30) REVERT: q 120 TYR cc_start: 0.8113 (p90) cc_final: 0.7854 (p90) REVERT: q 148 THR cc_start: 0.7967 (m) cc_final: 0.7675 (p) REVERT: q 181 ARG cc_start: 0.8340 (mmt-90) cc_final: 0.7890 (mmt90) REVERT: q 186 ASN cc_start: 0.8014 (m-40) cc_final: 0.7553 (m110) REVERT: r 26 ILE cc_start: 0.8235 (mt) cc_final: 0.7908 (mt) REVERT: r 38 ASN cc_start: 0.7381 (m110) cc_final: 0.6966 (m-40) REVERT: r 40 TYR cc_start: 0.7748 (p90) cc_final: 0.7502 (p90) REVERT: r 45 MET cc_start: 0.7501 (ttm) cc_final: 0.7298 (mtp) REVERT: r 58 LEU cc_start: 0.8900 (tp) cc_final: 0.8564 (tt) REVERT: r 89 GLN cc_start: 0.8810 (mt0) cc_final: 0.8149 (tm-30) REVERT: r 147 LEU cc_start: 0.8830 (mt) cc_final: 0.8530 (tp) REVERT: r 191 ASN cc_start: 0.7286 (t0) cc_final: 0.6969 (m110) REVERT: s 72 LEU cc_start: 0.8818 (mt) cc_final: 0.8526 (mm) REVERT: s 73 LYS cc_start: 0.8286 (mttt) cc_final: 0.7860 (mmtm) REVERT: s 159 GLN cc_start: 0.6877 (tp-100) cc_final: 0.6525 (mt0) REVERT: s 186 ASP cc_start: 0.6519 (t0) cc_final: 0.5739 (p0) REVERT: s 205 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8135 (mt-10) REVERT: t 5 MET cc_start: 0.8705 (mmt) cc_final: 0.8493 (mmm) REVERT: t 17 GLU cc_start: 0.7880 (tp30) cc_final: 0.7479 (pt0) REVERT: t 157 GLN cc_start: 0.7641 (tt0) cc_final: 0.7408 (tp40) REVERT: t 179 ARG cc_start: 0.6112 (pmt100) cc_final: 0.5419 (pmt100) REVERT: t 180 ASP cc_start: 0.7987 (t0) cc_final: 0.7539 (t0) REVERT: t 203 LEU cc_start: 0.7450 (mt) cc_final: 0.6887 (mt) outliers start: 27 outliers final: 2 residues processed: 1671 average time/residue: 0.5483 time to fit residues: 1468.9668 Evaluate side-chains 821 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 816 time to evaluate : 4.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain T residue 64 LYS Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 73 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 515 optimal weight: 0.9990 chunk 462 optimal weight: 1.9990 chunk 256 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 311 optimal weight: 7.9990 chunk 247 optimal weight: 5.9990 chunk 478 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 290 optimal weight: 9.9990 chunk 355 optimal weight: 10.0000 chunk 553 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 71 HIS I 20 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 120 GLN K 152 GLN ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 ASN O 165 ASN ** Q 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN Q 71 ASN Q 82 ASN Q 132 HIS R 62 GLN T 65 GLN g 92 GLN h 21 GLN h 123 GLN ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 146 GLN i 167 ASN ** j 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN m 110 HIS ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 53 GLN n 66 HIS n 110 GLN o 91 GLN ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 3 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 48137 Z= 0.299 Angle : 0.719 12.180 65219 Z= 0.384 Chirality : 0.047 0.288 7399 Planarity : 0.006 0.069 8467 Dihedral : 6.374 80.119 6817 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.92 % Favored : 93.06 % Rotamer: Outliers : 3.85 % Allowed : 11.58 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.10 (0.10), residues: 6155 helix: -0.02 (0.11), residues: 2215 sheet: -1.36 (0.14), residues: 1325 loop : -2.62 (0.11), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP M 215 HIS 0.010 0.001 HIS N 66 PHE 0.027 0.002 PHE G 163 TYR 0.025 0.002 TYR n 138 ARG 0.012 0.001 ARG G 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 897 time to evaluate : 4.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 19 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7724 (pp20) REVERT: G 21 ARG cc_start: 0.6772 (pmm-80) cc_final: 0.6077 (ttt180) REVERT: G 96 TYR cc_start: 0.8241 (t80) cc_final: 0.7976 (t80) REVERT: G 123 GLN cc_start: 0.8157 (tp40) cc_final: 0.7848 (tp40) REVERT: G 128 ASN cc_start: 0.7712 (t0) cc_final: 0.6881 (p0) REVERT: G 224 ASN cc_start: 0.8341 (t0) cc_final: 0.8108 (p0) REVERT: G 230 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7422 (tp) REVERT: I 6 ASP cc_start: 0.7246 (m-30) cc_final: 0.6860 (m-30) REVERT: I 28 ILE cc_start: 0.8443 (mt) cc_final: 0.8224 (mm) REVERT: I 48 GLU cc_start: 0.7887 (tt0) cc_final: 0.6798 (tm-30) REVERT: J 20 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7660 (tm-30) REVERT: J 30 SER cc_start: 0.7888 (m) cc_final: 0.7506 (p) REVERT: J 38 ARG cc_start: 0.7312 (tpt170) cc_final: 0.6543 (mmp80) REVERT: J 90 GLU cc_start: 0.7582 (tp30) cc_final: 0.7363 (tm-30) REVERT: J 105 GLU cc_start: 0.7684 (tp30) cc_final: 0.7311 (tp30) REVERT: J 127 PHE cc_start: 0.7898 (m-80) cc_final: 0.7286 (m-80) REVERT: J 146 GLN cc_start: 0.7600 (pt0) cc_final: 0.7321 (pt0) REVERT: J 231 GLU cc_start: 0.7585 (pt0) cc_final: 0.7250 (pp20) REVERT: K 166 ASP cc_start: 0.8283 (m-30) cc_final: 0.7811 (m-30) REVERT: K 207 GLU cc_start: 0.5792 (pm20) cc_final: 0.5425 (pp20) REVERT: L 55 GLU cc_start: 0.7878 (mp0) cc_final: 0.7511 (tm-30) REVERT: L 56 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7362 (pp) REVERT: L 60 GLN cc_start: 0.7507 (tp40) cc_final: 0.7262 (tp-100) REVERT: L 123 TYR cc_start: 0.8169 (t80) cc_final: 0.7920 (t80) REVERT: L 137 TYR cc_start: 0.7089 (t80) cc_final: 0.6844 (t80) REVERT: M 67 PHE cc_start: 0.8128 (m-10) cc_final: 0.7810 (m-10) REVERT: M 75 MET cc_start: 0.8844 (mtp) cc_final: 0.8496 (mtp) REVERT: M 169 ARG cc_start: 0.8465 (ttp80) cc_final: 0.7929 (ttp80) REVERT: M 191 LYS cc_start: 0.8667 (pttp) cc_final: 0.7760 (ttpt) REVERT: M 241 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7674 (tm-30) REVERT: N 57 ASP cc_start: 0.8357 (m-30) cc_final: 0.7943 (t0) REVERT: N 189 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8341 (tt) REVERT: O 64 GLU cc_start: 0.8367 (tt0) cc_final: 0.7943 (tt0) REVERT: P 59 ASP cc_start: 0.8324 (m-30) cc_final: 0.7890 (m-30) REVERT: P 75 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7588 (mm-30) REVERT: P 88 MET cc_start: 0.8659 (ttp) cc_final: 0.8236 (ttp) REVERT: P 89 SER cc_start: 0.8433 (m) cc_final: 0.7893 (t) REVERT: P 122 CYS cc_start: 0.7753 (p) cc_final: 0.6864 (p) REVERT: P 131 MET cc_start: 0.6413 (ttp) cc_final: 0.6139 (mtp) REVERT: P 135 ASP cc_start: 0.7926 (p0) cc_final: 0.7463 (p0) REVERT: P 158 MET cc_start: 0.6632 (mtm) cc_final: 0.6380 (mtm) REVERT: P 161 ASP cc_start: 0.7529 (m-30) cc_final: 0.7110 (t70) REVERT: Q 27 GLN cc_start: 0.8212 (mp10) cc_final: 0.7637 (mp10) REVERT: Q 58 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7251 (mt-10) REVERT: Q 69 MET cc_start: 0.8666 (mmm) cc_final: 0.8465 (mmt) REVERT: Q 118 MET cc_start: 0.9130 (mmm) cc_final: 0.8595 (mmm) REVERT: Q 158 GLU cc_start: 0.8633 (tt0) cc_final: 0.8117 (pp20) REVERT: Q 162 LYS cc_start: 0.7949 (mttt) cc_final: 0.7373 (mtpt) REVERT: R 32 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8213 (mptt) REVERT: R 34 VAL cc_start: 0.8423 (t) cc_final: 0.7907 (t) REVERT: R 36 GLU cc_start: 0.8278 (mp0) cc_final: 0.7982 (mp0) REVERT: R 45 MET cc_start: 0.7042 (mtp) cc_final: 0.6591 (mtp) REVERT: R 52 CYS cc_start: 0.8436 (m) cc_final: 0.8181 (m) REVERT: R 67 GLU cc_start: 0.8757 (tt0) cc_final: 0.8462 (tp30) REVERT: R 72 GLU cc_start: 0.7778 (tt0) cc_final: 0.7276 (pp20) REVERT: R 117 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7910 (mp0) REVERT: R 151 GLN cc_start: 0.7652 (mt0) cc_final: 0.7448 (mt0) REVERT: R 175 ASN cc_start: 0.8701 (m-40) cc_final: 0.8408 (m110) REVERT: R 198 LYS cc_start: 0.8113 (tttt) cc_final: 0.7643 (tppp) REVERT: S 76 LYS cc_start: 0.8561 (tttm) cc_final: 0.8043 (tppt) REVERT: S 129 SER cc_start: 0.7617 (t) cc_final: 0.7360 (m) REVERT: S 136 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8377 (mmtt) REVERT: S 162 GLU cc_start: 0.8154 (pm20) cc_final: 0.7786 (tp30) REVERT: T 26 MET cc_start: 0.7639 (mtp) cc_final: 0.7138 (mtp) REVERT: T 59 ASP cc_start: 0.8534 (m-30) cc_final: 0.8114 (m-30) REVERT: T 75 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8299 (mt-10) REVERT: T 112 ILE cc_start: 0.9054 (mp) cc_final: 0.8842 (mp) REVERT: T 119 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7974 (tt0) REVERT: T 126 ASP cc_start: 0.8147 (t0) cc_final: 0.7944 (t0) REVERT: T 127 MET cc_start: 0.8209 (ttp) cc_final: 0.7579 (ttm) REVERT: T 173 MET cc_start: 0.8503 (mmm) cc_final: 0.7989 (tpp) REVERT: T 179 ARG cc_start: 0.6292 (pmt100) cc_final: 0.5870 (pmt100) REVERT: T 180 ASP cc_start: 0.7991 (t0) cc_final: 0.7563 (t0) REVERT: T 210 ASP cc_start: 0.8194 (m-30) cc_final: 0.7809 (t0) REVERT: g 73 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.8186 (p) REVERT: g 90 GLN cc_start: 0.8379 (mt0) cc_final: 0.8133 (tt0) REVERT: g 138 MET cc_start: 0.8532 (ttm) cc_final: 0.8092 (ttp) REVERT: g 180 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8254 (tm-30) REVERT: g 215 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8093 (mt) REVERT: h 39 LYS cc_start: 0.8091 (tmtt) cc_final: 0.7692 (ttpp) REVERT: h 51 LYS cc_start: 0.7525 (mttm) cc_final: 0.6744 (mttm) REVERT: h 76 TYR cc_start: 0.7584 (p90) cc_final: 0.6459 (p90) REVERT: h 181 ASP cc_start: 0.8126 (p0) cc_final: 0.7870 (t70) REVERT: h 182 LEU cc_start: 0.7613 (mt) cc_final: 0.6967 (pt) REVERT: h 183 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7608 (pt0) REVERT: h 207 ASN cc_start: 0.7629 (m110) cc_final: 0.7128 (t0) REVERT: i 71 ASP cc_start: 0.9241 (p0) cc_final: 0.8751 (p0) REVERT: i 84 ASN cc_start: 0.7368 (m-40) cc_final: 0.7152 (t0) REVERT: i 121 TYR cc_start: 0.8212 (m-80) cc_final: 0.7807 (m-80) REVERT: i 174 MET cc_start: 0.8517 (ttm) cc_final: 0.8184 (mmm) REVERT: i 209 GLU cc_start: 0.9010 (mp0) cc_final: 0.8767 (mp0) REVERT: j 17 PHE cc_start: 0.6728 (t80) cc_final: 0.6290 (t80) REVERT: j 30 SER cc_start: 0.6724 (m) cc_final: 0.6224 (t) REVERT: j 66 ASP cc_start: 0.7156 (t0) cc_final: 0.6841 (t70) REVERT: j 70 CYS cc_start: 0.7788 (m) cc_final: 0.6645 (m) REVERT: j 71 MET cc_start: 0.7781 (tpp) cc_final: 0.7129 (ttt) REVERT: j 84 ILE cc_start: 0.8904 (mm) cc_final: 0.8423 (mm) REVERT: j 161 ILE cc_start: 0.6122 (OUTLIER) cc_final: 0.5853 (pp) REVERT: k 22 PHE cc_start: 0.6971 (m-80) cc_final: 0.6666 (m-10) REVERT: k 148 GLU cc_start: 0.7071 (mp0) cc_final: 0.6719 (pm20) REVERT: k 157 ASP cc_start: 0.8512 (t0) cc_final: 0.8270 (t0) REVERT: k 189 MET cc_start: 0.8615 (mmm) cc_final: 0.8349 (mmm) REVERT: l 6 TYR cc_start: 0.5328 (p90) cc_final: 0.4832 (p90) REVERT: l 14 SER cc_start: 0.8185 (m) cc_final: 0.7934 (p) REVERT: l 20 HIS cc_start: 0.6185 (m90) cc_final: 0.5745 (m90) REVERT: l 27 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8457 (mm-30) REVERT: l 61 LYS cc_start: 0.7883 (pttm) cc_final: 0.7164 (mmmm) REVERT: l 179 PHE cc_start: 0.7993 (m-10) cc_final: 0.7765 (m-80) REVERT: l 227 ASP cc_start: 0.8440 (m-30) cc_final: 0.8066 (p0) REVERT: m 31 GLU cc_start: 0.7151 (tp30) cc_final: 0.6812 (tp30) REVERT: m 67 PHE cc_start: 0.8113 (m-10) cc_final: 0.7851 (m-10) REVERT: m 114 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7553 (mmt180) REVERT: m 192 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8859 (mm-30) REVERT: n 62 GLN cc_start: 0.8756 (mt0) cc_final: 0.8382 (tp40) REVERT: n 69 GLU cc_start: 0.8237 (tm-30) cc_final: 0.8031 (tm-30) REVERT: n 95 MET cc_start: 0.8432 (mtp) cc_final: 0.8195 (mtm) REVERT: o 24 MET cc_start: 0.8561 (mmt) cc_final: 0.8230 (mmt) REVERT: o 72 ARG cc_start: 0.6949 (ptp-170) cc_final: 0.6575 (mtm-85) REVERT: o 83 LEU cc_start: 0.9063 (mt) cc_final: 0.8851 (tp) REVERT: o 114 TYR cc_start: 0.7844 (m-80) cc_final: 0.7604 (m-80) REVERT: o 135 MET cc_start: 0.7728 (tpp) cc_final: 0.7402 (tpp) REVERT: o 165 ASN cc_start: 0.8075 (t0) cc_final: 0.7640 (m110) REVERT: o 182 LYS cc_start: 0.8553 (ttpt) cc_final: 0.8205 (mmtm) REVERT: o 202 TYR cc_start: 0.6886 (m-80) cc_final: 0.6510 (m-80) REVERT: p 12 MET cc_start: 0.7817 (ttm) cc_final: 0.7463 (ttm) REVERT: p 34 MET cc_start: 0.7152 (ppp) cc_final: 0.6849 (ppp) REVERT: p 88 MET cc_start: 0.8896 (ttp) cc_final: 0.8606 (ttp) REVERT: p 131 MET cc_start: 0.7912 (ttp) cc_final: 0.7077 (mpp) REVERT: p 134 ASP cc_start: 0.7822 (m-30) cc_final: 0.7107 (t0) REVERT: p 149 MET cc_start: 0.9176 (mmm) cc_final: 0.8863 (mmm) REVERT: p 178 ASP cc_start: 0.7544 (t0) cc_final: 0.7282 (t0) REVERT: q 20 VAL cc_start: 0.8795 (t) cc_final: 0.8369 (m) REVERT: q 27 GLN cc_start: 0.8468 (tt0) cc_final: 0.7812 (pp30) REVERT: q 49 GLU cc_start: 0.6226 (tm-30) cc_final: 0.5661 (tm-30) REVERT: q 82 ASN cc_start: 0.8868 (t0) cc_final: 0.8461 (t0) REVERT: q 148 THR cc_start: 0.7972 (m) cc_final: 0.7659 (p) REVERT: q 165 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7470 (mt-10) REVERT: r 45 MET cc_start: 0.7513 (ttm) cc_final: 0.7223 (mtp) REVERT: r 58 LEU cc_start: 0.8765 (tp) cc_final: 0.8521 (mt) REVERT: r 97 MET cc_start: 0.7867 (tmm) cc_final: 0.7611 (ppp) REVERT: r 147 LEU cc_start: 0.8852 (mt) cc_final: 0.8498 (tp) REVERT: r 151 GLN cc_start: 0.8349 (mt0) cc_final: 0.8084 (mt0) REVERT: r 153 TYR cc_start: 0.8787 (m-10) cc_final: 0.8555 (m-80) REVERT: s 8 ASN cc_start: 0.8801 (m-40) cc_final: 0.8572 (t0) REVERT: s 72 LEU cc_start: 0.8735 (mt) cc_final: 0.8450 (mm) REVERT: s 159 GLN cc_start: 0.6897 (tp-100) cc_final: 0.6582 (mt0) REVERT: s 186 ASP cc_start: 0.6325 (t0) cc_final: 0.5741 (p0) REVERT: s 205 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8004 (mt-10) REVERT: t 17 GLU cc_start: 0.7875 (tp30) cc_final: 0.7325 (pt0) REVERT: t 157 GLN cc_start: 0.7751 (tt0) cc_final: 0.7446 (tp-100) REVERT: t 180 ASP cc_start: 0.7795 (t0) cc_final: 0.7346 (t0) outliers start: 188 outliers final: 112 residues processed: 1035 average time/residue: 0.4443 time to fit residues: 778.9324 Evaluate side-chains 826 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 707 time to evaluate : 5.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 202 ASP Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 226 PHE Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 178 GLU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 231 ILE Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 138 TYR Chi-restraints excluded: chain N residue 179 ILE Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 182 ILE Chi-restraints excluded: chain Q residue 186 ASN Chi-restraints excluded: chain R residue 63 CYS Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 182 ASP Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain T residue 5 MET Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 64 LYS Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 210 PHE Chi-restraints excluded: chain g residue 215 ILE Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain h residue 58 ASP Chi-restraints excluded: chain h residue 212 ILE Chi-restraints excluded: chain i residue 35 LEU Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain j residue 67 ASP Chi-restraints excluded: chain j residue 68 ASN Chi-restraints excluded: chain j residue 93 SER Chi-restraints excluded: chain j residue 161 ILE Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain k residue 47 CYS Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain k residue 165 CYS Chi-restraints excluded: chain k residue 202 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 94 ASP Chi-restraints excluded: chain l residue 195 LEU Chi-restraints excluded: chain l residue 222 THR Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 57 LEU Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain m residue 165 ILE Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain n residue 119 MET Chi-restraints excluded: chain n residue 138 TYR Chi-restraints excluded: chain o residue 25 VAL Chi-restraints excluded: chain o residue 62 ASN Chi-restraints excluded: chain p residue 18 ASN Chi-restraints excluded: chain p residue 144 GLU Chi-restraints excluded: chain p residue 159 ASP Chi-restraints excluded: chain q residue 78 THR Chi-restraints excluded: chain q residue 87 ASN Chi-restraints excluded: chain q residue 88 LEU Chi-restraints excluded: chain q residue 96 THR Chi-restraints excluded: chain q residue 158 GLU Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain r residue 21 THR Chi-restraints excluded: chain r residue 63 CYS Chi-restraints excluded: chain r residue 175 ASN Chi-restraints excluded: chain r residue 190 ASP Chi-restraints excluded: chain s residue 13 LEU Chi-restraints excluded: chain s residue 54 CYS Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 191 ASP Chi-restraints excluded: chain s residue 207 THR Chi-restraints excluded: chain t residue 25 ASP Chi-restraints excluded: chain t residue 65 GLN Chi-restraints excluded: chain t residue 175 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 307 optimal weight: 0.0270 chunk 171 optimal weight: 9.9990 chunk 461 optimal weight: 6.9990 chunk 377 optimal weight: 0.2980 chunk 152 optimal weight: 3.9990 chunk 554 optimal weight: 9.9990 chunk 599 optimal weight: 4.9990 chunk 494 optimal weight: 3.9990 chunk 550 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 445 optimal weight: 5.9990 overall best weight: 2.6644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 102 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN ** J 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 HIS ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 HIS ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 123 GLN i 40 ASN i 109 GLN ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 114 GLN ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN l 143 HIS l 152 ASN m 201 HIS ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 168 GLN ** r 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 69 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 48137 Z= 0.217 Angle : 0.640 12.131 65219 Z= 0.339 Chirality : 0.045 0.294 7399 Planarity : 0.005 0.067 8467 Dihedral : 5.883 83.088 6816 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.88 % Favored : 94.10 % Rotamer: Outliers : 4.18 % Allowed : 14.27 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.44 (0.10), residues: 6155 helix: 0.62 (0.11), residues: 2207 sheet: -0.96 (0.14), residues: 1315 loop : -2.36 (0.11), residues: 2633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 215 HIS 0.008 0.001 HIS N 66 PHE 0.021 0.001 PHE G 163 TYR 0.030 0.001 TYR I 19 ARG 0.010 0.000 ARG G 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 801 time to evaluate : 4.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 19 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7683 (pp20) REVERT: G 21 ARG cc_start: 0.6793 (pmm-80) cc_final: 0.6135 (ttt180) REVERT: G 230 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7513 (tp) REVERT: G 231 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7830 (p) REVERT: I 6 ASP cc_start: 0.7085 (m-30) cc_final: 0.6302 (p0) REVERT: I 28 ILE cc_start: 0.8423 (mt) cc_final: 0.8195 (mm) REVERT: I 48 GLU cc_start: 0.7917 (tt0) cc_final: 0.6809 (tm-30) REVERT: I 72 MET cc_start: 0.8304 (mtp) cc_final: 0.7911 (mtp) REVERT: J 13 ASP cc_start: 0.8218 (t0) cc_final: 0.7944 (t0) REVERT: J 20 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7449 (tm-30) REVERT: J 38 ARG cc_start: 0.7364 (tpt170) cc_final: 0.6583 (mmp80) REVERT: J 105 GLU cc_start: 0.7844 (tp30) cc_final: 0.7313 (tp30) REVERT: J 120 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6792 (tp40) REVERT: J 127 PHE cc_start: 0.7830 (m-80) cc_final: 0.7331 (m-80) REVERT: J 231 GLU cc_start: 0.7590 (pt0) cc_final: 0.7301 (pp20) REVERT: K 166 ASP cc_start: 0.8307 (m-30) cc_final: 0.7853 (m-30) REVERT: L 55 GLU cc_start: 0.7832 (mp0) cc_final: 0.7498 (tm-30) REVERT: L 60 GLN cc_start: 0.7535 (tp40) cc_final: 0.7315 (tp-100) REVERT: L 123 TYR cc_start: 0.8157 (t80) cc_final: 0.7924 (t80) REVERT: L 176 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8447 (ttt) REVERT: L 178 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8365 (pm20) REVERT: M 75 MET cc_start: 0.8802 (mtp) cc_final: 0.8500 (mtp) REVERT: M 81 LEU cc_start: 0.7518 (tp) cc_final: 0.7249 (tp) REVERT: M 85 ARG cc_start: 0.7688 (ttm-80) cc_final: 0.7459 (mtm-85) REVERT: M 169 ARG cc_start: 0.8470 (ttp80) cc_final: 0.7954 (ttp80) REVERT: M 191 LYS cc_start: 0.8635 (pttp) cc_final: 0.7690 (ttpt) REVERT: M 241 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7565 (tm-30) REVERT: N 4 MET cc_start: 0.8012 (tpp) cc_final: 0.7705 (tpp) REVERT: N 57 ASP cc_start: 0.8412 (m-30) cc_final: 0.7967 (t0) REVERT: N 68 ILE cc_start: 0.8521 (tp) cc_final: 0.8266 (tp) REVERT: N 89 ARG cc_start: 0.9134 (ttt-90) cc_final: 0.8864 (ttt-90) REVERT: N 189 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8406 (tt) REVERT: O 86 MET cc_start: 0.8866 (tmm) cc_final: 0.8525 (tmm) REVERT: O 167 LEU cc_start: 0.7333 (mm) cc_final: 0.7046 (mm) REVERT: P 59 ASP cc_start: 0.8301 (m-30) cc_final: 0.7446 (t0) REVERT: P 88 MET cc_start: 0.8675 (ttp) cc_final: 0.8278 (ttp) REVERT: P 89 SER cc_start: 0.8402 (m) cc_final: 0.7961 (t) REVERT: P 109 ILE cc_start: 0.7976 (mp) cc_final: 0.7562 (tt) REVERT: P 122 CYS cc_start: 0.7536 (p) cc_final: 0.6179 (p) REVERT: P 135 ASP cc_start: 0.7889 (p0) cc_final: 0.7409 (p0) REVERT: Q 38 MET cc_start: 0.8644 (mmp) cc_final: 0.8331 (mmp) REVERT: Q 118 MET cc_start: 0.9079 (mmm) cc_final: 0.8473 (mmm) REVERT: Q 162 LYS cc_start: 0.7727 (mttt) cc_final: 0.7449 (ptmt) REVERT: Q 171 PHE cc_start: 0.7899 (t80) cc_final: 0.7422 (t80) REVERT: Q 178 PHE cc_start: 0.8330 (m-10) cc_final: 0.8016 (m-10) REVERT: R 32 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8239 (mmtm) REVERT: R 36 GLU cc_start: 0.8265 (mp0) cc_final: 0.8043 (mp0) REVERT: R 45 MET cc_start: 0.7484 (mtp) cc_final: 0.6604 (mtp) REVERT: R 52 CYS cc_start: 0.8280 (m) cc_final: 0.7918 (t) REVERT: R 72 GLU cc_start: 0.7770 (tt0) cc_final: 0.7331 (pp20) REVERT: R 90 TYR cc_start: 0.8776 (m-80) cc_final: 0.8359 (m-80) REVERT: R 117 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7860 (mp0) REVERT: R 198 LYS cc_start: 0.8089 (tttt) cc_final: 0.7533 (tppp) REVERT: S 76 LYS cc_start: 0.8504 (tttm) cc_final: 0.8143 (tppt) REVERT: S 129 SER cc_start: 0.7387 (t) cc_final: 0.7111 (m) REVERT: S 136 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8219 (mmtt) REVERT: S 162 GLU cc_start: 0.8204 (pm20) cc_final: 0.7854 (tp30) REVERT: T 26 MET cc_start: 0.7560 (mtp) cc_final: 0.7067 (mtp) REVERT: T 59 ASP cc_start: 0.8559 (m-30) cc_final: 0.8186 (m-30) REVERT: T 64 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8095 (ttmp) REVERT: T 75 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8202 (mt-10) REVERT: T 127 MET cc_start: 0.8126 (ttp) cc_final: 0.7519 (ttm) REVERT: T 173 MET cc_start: 0.8471 (mmm) cc_final: 0.7921 (tpp) REVERT: T 179 ARG cc_start: 0.6382 (pmt100) cc_final: 0.5939 (pmt100) REVERT: T 180 ASP cc_start: 0.7893 (t0) cc_final: 0.7444 (t0) REVERT: T 210 ASP cc_start: 0.8165 (m-30) cc_final: 0.7804 (t0) REVERT: g 73 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8151 (p) REVERT: g 80 MET cc_start: 0.7675 (mmm) cc_final: 0.7266 (mmm) REVERT: g 138 MET cc_start: 0.8526 (ttm) cc_final: 0.8157 (ttp) REVERT: g 180 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8222 (tm-30) REVERT: g 215 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8274 (mt) REVERT: h 39 LYS cc_start: 0.8058 (tmtt) cc_final: 0.7663 (ttpp) REVERT: h 51 LYS cc_start: 0.7418 (mttm) cc_final: 0.6878 (mttm) REVERT: h 69 THR cc_start: 0.7884 (m) cc_final: 0.7445 (p) REVERT: h 76 TYR cc_start: 0.7522 (p90) cc_final: 0.6135 (p90) REVERT: h 119 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8316 (tm-30) REVERT: h 181 ASP cc_start: 0.8151 (p0) cc_final: 0.7888 (t70) REVERT: h 182 LEU cc_start: 0.7591 (mt) cc_final: 0.6933 (pt) REVERT: h 183 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7731 (tp30) REVERT: h 203 MET cc_start: 0.4882 (mmm) cc_final: 0.4362 (mmm) REVERT: h 207 ASN cc_start: 0.7804 (m110) cc_final: 0.7406 (m-40) REVERT: i 71 ASP cc_start: 0.9240 (p0) cc_final: 0.8611 (p0) REVERT: i 121 TYR cc_start: 0.8144 (m-80) cc_final: 0.7790 (m-80) REVERT: i 174 MET cc_start: 0.8576 (ttm) cc_final: 0.8085 (mmm) REVERT: i 209 GLU cc_start: 0.8989 (mp0) cc_final: 0.8740 (mp0) REVERT: j 30 SER cc_start: 0.6759 (m) cc_final: 0.6274 (t) REVERT: j 70 CYS cc_start: 0.7786 (m) cc_final: 0.6798 (m) REVERT: j 71 MET cc_start: 0.7735 (tpp) cc_final: 0.7440 (ttt) REVERT: j 84 ILE cc_start: 0.8923 (mm) cc_final: 0.8536 (mm) REVERT: j 161 ILE cc_start: 0.6134 (OUTLIER) cc_final: 0.5878 (pp) REVERT: k 22 PHE cc_start: 0.7081 (m-80) cc_final: 0.6448 (m-80) REVERT: k 148 GLU cc_start: 0.7058 (mp0) cc_final: 0.6723 (pm20) REVERT: k 157 ASP cc_start: 0.8475 (t0) cc_final: 0.8257 (t0) REVERT: k 206 MET cc_start: 0.6828 (ptm) cc_final: 0.6447 (ptt) REVERT: l 6 TYR cc_start: 0.5282 (p90) cc_final: 0.4469 (p90) REVERT: l 14 SER cc_start: 0.8163 (m) cc_final: 0.7448 (p) REVERT: l 20 HIS cc_start: 0.6237 (m90) cc_final: 0.5243 (m-70) REVERT: l 23 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6525 (pt0) REVERT: l 27 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8425 (mm-30) REVERT: l 61 LYS cc_start: 0.7937 (pttm) cc_final: 0.7157 (mmmm) REVERT: l 88 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8224 (mmm) REVERT: l 179 PHE cc_start: 0.8101 (m-10) cc_final: 0.7859 (m-80) REVERT: l 227 ASP cc_start: 0.8403 (m-30) cc_final: 0.8072 (p0) REVERT: m 31 GLU cc_start: 0.7180 (tp30) cc_final: 0.6864 (tp30) REVERT: m 60 GLU cc_start: 0.7323 (tt0) cc_final: 0.6043 (pt0) REVERT: m 114 ARG cc_start: 0.7963 (mmm160) cc_final: 0.7562 (mmt180) REVERT: m 136 MET cc_start: 0.8168 (mtt) cc_final: 0.7795 (mtt) REVERT: m 192 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8784 (mm-30) REVERT: n 62 GLN cc_start: 0.8753 (mt0) cc_final: 0.8351 (tp40) REVERT: n 69 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7941 (tm-30) REVERT: n 90 TYR cc_start: 0.7986 (m-80) cc_final: 0.7638 (m-10) REVERT: n 95 MET cc_start: 0.8400 (mtp) cc_final: 0.7854 (mtp) REVERT: n 164 MET cc_start: 0.8511 (mtm) cc_final: 0.8166 (mtp) REVERT: o 24 MET cc_start: 0.8550 (mmt) cc_final: 0.8208 (mmt) REVERT: o 72 ARG cc_start: 0.6680 (ptp-170) cc_final: 0.6421 (mtm-85) REVERT: o 135 MET cc_start: 0.7684 (tpp) cc_final: 0.7402 (tpp) REVERT: o 165 ASN cc_start: 0.8257 (t0) cc_final: 0.7624 (m110) REVERT: o 167 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6825 (tp) REVERT: o 182 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8291 (pptt) REVERT: o 202 TYR cc_start: 0.6811 (m-80) cc_final: 0.6497 (m-80) REVERT: p 34 MET cc_start: 0.7043 (ppp) cc_final: 0.6719 (ppp) REVERT: p 88 MET cc_start: 0.8889 (ttp) cc_final: 0.8590 (ttp) REVERT: p 131 MET cc_start: 0.7814 (ttp) cc_final: 0.7014 (mpp) REVERT: p 134 ASP cc_start: 0.7866 (m-30) cc_final: 0.7145 (t0) REVERT: p 149 MET cc_start: 0.9173 (mmm) cc_final: 0.8857 (mmm) REVERT: p 166 THR cc_start: 0.9169 (m) cc_final: 0.8934 (p) REVERT: p 178 ASP cc_start: 0.7643 (t0) cc_final: 0.7365 (t0) REVERT: q 1 MET cc_start: 0.6823 (tmm) cc_final: 0.6559 (tmm) REVERT: q 20 VAL cc_start: 0.8804 (t) cc_final: 0.8456 (m) REVERT: q 49 GLU cc_start: 0.6049 (tm-30) cc_final: 0.5627 (tm-30) REVERT: q 82 ASN cc_start: 0.8865 (t0) cc_final: 0.8360 (t0) REVERT: q 148 THR cc_start: 0.7953 (m) cc_final: 0.7634 (p) REVERT: q 154 GLU cc_start: 0.8746 (mp0) cc_final: 0.8456 (mp0) REVERT: r 45 MET cc_start: 0.7508 (ttm) cc_final: 0.7180 (mtp) REVERT: r 97 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7659 (ppp) REVERT: r 147 LEU cc_start: 0.8818 (mt) cc_final: 0.8486 (tp) REVERT: r 148 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6619 (tp30) REVERT: r 151 GLN cc_start: 0.8312 (mt0) cc_final: 0.8074 (mt0) REVERT: r 153 TYR cc_start: 0.8742 (m-10) cc_final: 0.8490 (m-80) REVERT: s 8 ASN cc_start: 0.8757 (m-40) cc_final: 0.7620 (t0) REVERT: s 72 LEU cc_start: 0.8769 (mt) cc_final: 0.8482 (mm) REVERT: s 159 GLN cc_start: 0.6968 (tp-100) cc_final: 0.6742 (mt0) REVERT: s 205 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7984 (mt-10) REVERT: t 17 GLU cc_start: 0.7752 (tp30) cc_final: 0.7240 (pt0) REVERT: t 157 GLN cc_start: 0.7751 (tt0) cc_final: 0.7427 (tp-100) REVERT: t 180 ASP cc_start: 0.7474 (t0) cc_final: 0.7025 (t0) outliers start: 204 outliers final: 128 residues processed: 945 average time/residue: 0.4471 time to fit residues: 715.5124 Evaluate side-chains 828 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 685 time to evaluate : 4.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain I residue 19 TYR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 202 ASP Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 162 PHE Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 178 GLU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 198 TYR Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 231 ILE Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 138 TYR Chi-restraints excluded: chain N residue 179 ILE Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 186 ASN Chi-restraints excluded: chain R residue 63 CYS Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 182 ASP Chi-restraints excluded: chain T residue 5 MET Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 64 LYS Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 78 CYS Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain g residue 125 TYR Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 210 PHE Chi-restraints excluded: chain g residue 215 ILE Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain h residue 42 ASN Chi-restraints excluded: chain h residue 58 ASP Chi-restraints excluded: chain h residue 174 LEU Chi-restraints excluded: chain h residue 212 ILE Chi-restraints excluded: chain i residue 35 LEU Chi-restraints excluded: chain i residue 109 GLN Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 134 LEU Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain j residue 68 ASN Chi-restraints excluded: chain j residue 93 SER Chi-restraints excluded: chain j residue 161 ILE Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain j residue 177 THR Chi-restraints excluded: chain k residue 47 CYS Chi-restraints excluded: chain k residue 202 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 88 MET Chi-restraints excluded: chain l residue 94 ASP Chi-restraints excluded: chain l residue 195 LEU Chi-restraints excluded: chain l residue 202 GLU Chi-restraints excluded: chain l residue 222 THR Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 165 ILE Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain m residue 204 VAL Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 119 MET Chi-restraints excluded: chain n residue 138 TYR Chi-restraints excluded: chain n residue 165 GLU Chi-restraints excluded: chain o residue 25 VAL Chi-restraints excluded: chain o residue 167 LEU Chi-restraints excluded: chain o residue 197 THR Chi-restraints excluded: chain p residue 18 ASN Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain p residue 144 GLU Chi-restraints excluded: chain p residue 176 ASP Chi-restraints excluded: chain q residue 78 THR Chi-restraints excluded: chain q residue 87 ASN Chi-restraints excluded: chain q residue 88 LEU Chi-restraints excluded: chain q residue 160 LEU Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain r residue 21 THR Chi-restraints excluded: chain r residue 63 CYS Chi-restraints excluded: chain r residue 97 MET Chi-restraints excluded: chain r residue 139 MET Chi-restraints excluded: chain r residue 148 GLU Chi-restraints excluded: chain r residue 175 ASN Chi-restraints excluded: chain r residue 190 ASP Chi-restraints excluded: chain s residue 13 LEU Chi-restraints excluded: chain s residue 54 CYS Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain s residue 184 GLU Chi-restraints excluded: chain s residue 191 ASP Chi-restraints excluded: chain s residue 207 THR Chi-restraints excluded: chain t residue 25 ASP Chi-restraints excluded: chain t residue 49 THR Chi-restraints excluded: chain t residue 117 ASP Chi-restraints excluded: chain t residue 175 VAL Chi-restraints excluded: chain t residue 179 ARG Chi-restraints excluded: chain t residue 205 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 548 optimal weight: 9.9990 chunk 417 optimal weight: 7.9990 chunk 288 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 264 optimal weight: 9.9990 chunk 372 optimal weight: 8.9990 chunk 556 optimal weight: 9.9990 chunk 589 optimal weight: 7.9990 chunk 290 optimal weight: 10.0000 chunk 527 optimal weight: 5.9990 chunk 158 optimal weight: 0.0670 overall best weight: 6.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 HIS T 81 HIS g 123 GLN ** g 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN r 38 ASN ** s 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 48137 Z= 0.364 Angle : 0.721 12.140 65219 Z= 0.379 Chirality : 0.047 0.285 7399 Planarity : 0.005 0.071 8467 Dihedral : 5.984 89.857 6816 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.51 % Favored : 92.48 % Rotamer: Outliers : 5.43 % Allowed : 15.62 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.38 (0.10), residues: 6155 helix: 0.71 (0.11), residues: 2216 sheet: -1.02 (0.14), residues: 1374 loop : -2.32 (0.11), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 215 HIS 0.007 0.001 HIS K 99 PHE 0.026 0.002 PHE G 163 TYR 0.026 0.002 TYR I 19 ARG 0.017 0.001 ARG M 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 694 time to evaluate : 5.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 HIS cc_start: 0.7966 (m90) cc_final: 0.7725 (m90) REVERT: G 19 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7839 (pp20) REVERT: G 21 ARG cc_start: 0.6963 (pmm-80) cc_final: 0.6142 (ttt180) REVERT: G 128 ASN cc_start: 0.7592 (t0) cc_final: 0.6632 (p0) REVERT: G 230 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7532 (tp) REVERT: G 231 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7923 (p) REVERT: I 6 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6320 (p0) REVERT: I 48 GLU cc_start: 0.7831 (tt0) cc_final: 0.6683 (tm-30) REVERT: I 72 MET cc_start: 0.8258 (mtp) cc_final: 0.7952 (mtt) REVERT: J 13 ASP cc_start: 0.8136 (t0) cc_final: 0.7837 (t0) REVERT: J 20 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7537 (tm-30) REVERT: J 38 ARG cc_start: 0.7322 (tpt170) cc_final: 0.6535 (mmp80) REVERT: J 105 GLU cc_start: 0.7978 (tp30) cc_final: 0.7719 (tp30) REVERT: J 118 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7067 (t80) REVERT: J 127 PHE cc_start: 0.7949 (m-80) cc_final: 0.7656 (m-80) REVERT: J 231 GLU cc_start: 0.7562 (pt0) cc_final: 0.7117 (pp20) REVERT: K 59 MET cc_start: 0.6369 (mmt) cc_final: 0.5725 (mmm) REVERT: K 78 MET cc_start: 0.7616 (ptp) cc_final: 0.7375 (ttp) REVERT: L 123 TYR cc_start: 0.8208 (t80) cc_final: 0.7886 (t80) REVERT: L 176 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8404 (ttt) REVERT: L 178 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8485 (mp0) REVERT: M 75 MET cc_start: 0.8877 (mtp) cc_final: 0.8587 (mtp) REVERT: M 161 TRP cc_start: 0.8132 (OUTLIER) cc_final: 0.7842 (m100) REVERT: M 169 ARG cc_start: 0.8500 (ttp80) cc_final: 0.7939 (ttp80) REVERT: M 191 LYS cc_start: 0.8674 (pttp) cc_final: 0.8350 (ptpt) REVERT: M 241 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7567 (tm-30) REVERT: N 57 ASP cc_start: 0.8461 (m-30) cc_final: 0.7918 (t0) REVERT: N 136 TYR cc_start: 0.6417 (t80) cc_final: 0.6006 (t80) REVERT: O 86 MET cc_start: 0.8752 (tmm) cc_final: 0.8058 (tmm) REVERT: O 167 LEU cc_start: 0.7643 (mm) cc_final: 0.7294 (mm) REVERT: O 173 ILE cc_start: 0.6732 (OUTLIER) cc_final: 0.6180 (mt) REVERT: P 59 ASP cc_start: 0.8304 (m-30) cc_final: 0.7530 (t0) REVERT: P 88 MET cc_start: 0.8691 (ttp) cc_final: 0.8307 (ttp) REVERT: P 89 SER cc_start: 0.8464 (m) cc_final: 0.7998 (t) REVERT: P 122 CYS cc_start: 0.7762 (p) cc_final: 0.7196 (p) REVERT: P 131 MET cc_start: 0.6028 (mpp) cc_final: 0.5749 (mpp) REVERT: P 135 ASP cc_start: 0.7963 (p0) cc_final: 0.7485 (p0) REVERT: P 200 LEU cc_start: 0.7655 (mp) cc_final: 0.7320 (mp) REVERT: Q 38 MET cc_start: 0.8619 (mmp) cc_final: 0.8316 (mmp) REVERT: Q 104 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7946 (tt) REVERT: Q 118 MET cc_start: 0.9159 (mmm) cc_final: 0.7948 (mmm) REVERT: Q 162 LYS cc_start: 0.7850 (mttt) cc_final: 0.7551 (mtmt) REVERT: Q 178 PHE cc_start: 0.8555 (m-10) cc_final: 0.8218 (m-80) REVERT: R 32 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8243 (mmtm) REVERT: R 36 GLU cc_start: 0.8239 (mp0) cc_final: 0.7958 (mp0) REVERT: R 45 MET cc_start: 0.7628 (mtp) cc_final: 0.6908 (mtp) REVERT: R 52 CYS cc_start: 0.8263 (m) cc_final: 0.8027 (t) REVERT: R 72 GLU cc_start: 0.7835 (tt0) cc_final: 0.7604 (pp20) REVERT: R 90 TYR cc_start: 0.8781 (m-80) cc_final: 0.8333 (m-80) REVERT: R 117 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7832 (mp0) REVERT: S 76 LYS cc_start: 0.8590 (tttm) cc_final: 0.8272 (tttt) REVERT: S 129 SER cc_start: 0.7359 (t) cc_final: 0.7012 (m) REVERT: S 136 LYS cc_start: 0.8873 (mmmm) cc_final: 0.8276 (mmtt) REVERT: S 162 GLU cc_start: 0.8309 (pm20) cc_final: 0.7891 (tp30) REVERT: T 26 MET cc_start: 0.7540 (mtp) cc_final: 0.7115 (mtp) REVERT: T 43 MET cc_start: 0.7806 (ttp) cc_final: 0.7481 (ttp) REVERT: T 75 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8372 (mt-10) REVERT: T 126 ASP cc_start: 0.8301 (t0) cc_final: 0.7318 (p0) REVERT: T 127 MET cc_start: 0.8125 (ttp) cc_final: 0.7483 (ttm) REVERT: T 173 MET cc_start: 0.8484 (mmm) cc_final: 0.8032 (tpp) REVERT: T 179 ARG cc_start: 0.6341 (OUTLIER) cc_final: 0.5864 (pmt100) REVERT: T 180 ASP cc_start: 0.8053 (t0) cc_final: 0.7687 (t0) REVERT: T 210 ASP cc_start: 0.8244 (m-30) cc_final: 0.7847 (t0) REVERT: g 24 GLN cc_start: 0.6135 (mm-40) cc_final: 0.5878 (mm-40) REVERT: g 73 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8016 (p) REVERT: g 80 MET cc_start: 0.7748 (mmm) cc_final: 0.7315 (mmm) REVERT: g 138 MET cc_start: 0.8553 (ttm) cc_final: 0.8204 (ttp) REVERT: g 180 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7870 (tm-30) REVERT: g 215 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8420 (mt) REVERT: h 39 LYS cc_start: 0.8155 (tmtt) cc_final: 0.7745 (ttpp) REVERT: h 51 LYS cc_start: 0.7303 (mttm) cc_final: 0.6894 (mttm) REVERT: h 119 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8219 (tm-30) REVERT: h 182 LEU cc_start: 0.7649 (mt) cc_final: 0.6765 (pt) REVERT: h 183 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7721 (tp30) REVERT: h 203 MET cc_start: 0.4542 (mmm) cc_final: 0.3939 (mmm) REVERT: h 207 ASN cc_start: 0.7676 (m110) cc_final: 0.7220 (m-40) REVERT: i 72 MET cc_start: 0.7870 (mtp) cc_final: 0.7612 (mtp) REVERT: i 121 TYR cc_start: 0.8194 (m-80) cc_final: 0.7804 (m-80) REVERT: i 151 ASP cc_start: 0.7895 (m-30) cc_final: 0.7597 (m-30) REVERT: i 174 MET cc_start: 0.8555 (ttm) cc_final: 0.8117 (mmm) REVERT: i 209 GLU cc_start: 0.8944 (mp0) cc_final: 0.8687 (mp0) REVERT: j 17 PHE cc_start: 0.6764 (t80) cc_final: 0.6116 (t80) REVERT: j 23 GLN cc_start: 0.7728 (mt0) cc_final: 0.7315 (mm-40) REVERT: j 30 SER cc_start: 0.7052 (m) cc_final: 0.6545 (t) REVERT: j 84 ILE cc_start: 0.8958 (mm) cc_final: 0.8632 (mm) REVERT: j 161 ILE cc_start: 0.6089 (OUTLIER) cc_final: 0.5817 (pp) REVERT: k 22 PHE cc_start: 0.7203 (m-80) cc_final: 0.6814 (m-80) REVERT: k 29 GLU cc_start: 0.8281 (tp30) cc_final: 0.7708 (tt0) REVERT: k 69 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7718 (mm-30) REVERT: k 71 ASP cc_start: 0.8697 (t70) cc_final: 0.8267 (t0) REVERT: k 148 GLU cc_start: 0.7053 (mp0) cc_final: 0.6698 (pm20) REVERT: k 157 ASP cc_start: 0.8451 (t0) cc_final: 0.8127 (t70) REVERT: k 206 MET cc_start: 0.6478 (ptm) cc_final: 0.6258 (ptt) REVERT: l 6 TYR cc_start: 0.5403 (p90) cc_final: 0.4830 (p90) REVERT: l 20 HIS cc_start: 0.6645 (m90) cc_final: 0.6278 (m90) REVERT: l 23 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6266 (mm-30) REVERT: l 27 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8450 (mm-30) REVERT: l 61 LYS cc_start: 0.8002 (pttm) cc_final: 0.7245 (mmmm) REVERT: m 31 GLU cc_start: 0.7305 (tp30) cc_final: 0.6972 (tp30) REVERT: m 60 GLU cc_start: 0.7477 (tt0) cc_final: 0.6707 (mp0) REVERT: m 114 ARG cc_start: 0.7974 (mmm160) cc_final: 0.7532 (mmt180) REVERT: m 136 MET cc_start: 0.8342 (mtt) cc_final: 0.7999 (mtt) REVERT: m 192 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8777 (mm-30) REVERT: n 62 GLN cc_start: 0.8816 (mt0) cc_final: 0.8413 (tp40) REVERT: n 69 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7982 (tm-30) REVERT: o 24 MET cc_start: 0.8471 (mmt) cc_final: 0.8129 (mmt) REVERT: o 65 LEU cc_start: 0.9172 (tt) cc_final: 0.8921 (pp) REVERT: o 135 MET cc_start: 0.7393 (tpp) cc_final: 0.6890 (tpp) REVERT: o 165 ASN cc_start: 0.8126 (t0) cc_final: 0.7653 (m110) REVERT: o 167 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6741 (tp) REVERT: o 172 ASN cc_start: 0.4503 (OUTLIER) cc_final: 0.4235 (p0) REVERT: o 182 LYS cc_start: 0.8593 (ttpt) cc_final: 0.8299 (pptt) REVERT: o 202 TYR cc_start: 0.6967 (m-80) cc_final: 0.6678 (m-80) REVERT: p 34 MET cc_start: 0.7208 (ppp) cc_final: 0.6821 (ppp) REVERT: p 134 ASP cc_start: 0.7942 (m-30) cc_final: 0.7218 (t0) REVERT: q 1 MET cc_start: 0.7150 (tmm) cc_final: 0.6821 (tmm) REVERT: q 20 VAL cc_start: 0.8767 (t) cc_final: 0.8356 (m) REVERT: q 27 GLN cc_start: 0.8236 (mt0) cc_final: 0.7707 (pp30) REVERT: q 49 GLU cc_start: 0.6187 (tm-30) cc_final: 0.5889 (tm-30) REVERT: r 35 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8354 (tp) REVERT: r 38 ASN cc_start: 0.6893 (OUTLIER) cc_final: 0.6059 (m-40) REVERT: r 45 MET cc_start: 0.7542 (ttm) cc_final: 0.7189 (mtp) REVERT: r 89 GLN cc_start: 0.8711 (mt0) cc_final: 0.8405 (mp10) REVERT: r 97 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7793 (ppp) REVERT: r 132 SER cc_start: 0.7820 (OUTLIER) cc_final: 0.6637 (t) REVERT: r 147 LEU cc_start: 0.8849 (mt) cc_final: 0.8440 (tp) REVERT: r 151 GLN cc_start: 0.8363 (mt0) cc_final: 0.8135 (mt0) REVERT: r 153 TYR cc_start: 0.8757 (m-10) cc_final: 0.8465 (m-80) REVERT: s 72 LEU cc_start: 0.8801 (mt) cc_final: 0.8485 (mp) REVERT: s 159 GLN cc_start: 0.7303 (tp-100) cc_final: 0.6884 (mt0) REVERT: s 205 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7834 (mt-10) REVERT: t 127 MET cc_start: 0.7710 (ttm) cc_final: 0.7413 (mtp) REVERT: t 157 GLN cc_start: 0.7765 (tt0) cc_final: 0.7489 (tp40) REVERT: t 180 ASP cc_start: 0.7743 (t0) cc_final: 0.7309 (t0) outliers start: 265 outliers final: 183 residues processed: 889 average time/residue: 0.4396 time to fit residues: 661.4804 Evaluate side-chains 845 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 641 time to evaluate : 4.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 19 TYR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 162 PHE Chi-restraints excluded: chain K residue 214 ASN Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 178 GLU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 161 TRP Chi-restraints excluded: chain M residue 198 TYR Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain M residue 231 ILE Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 138 TYR Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 24 MET Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 172 ASN Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 159 ASP Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 53 THR Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain R residue 63 CYS Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 182 ASP Chi-restraints excluded: chain T residue 5 MET Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 179 ARG Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 78 CYS Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain g residue 125 TYR Chi-restraints excluded: chain g residue 128 ASN Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 210 PHE Chi-restraints excluded: chain g residue 215 ILE Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain h residue 42 ASN Chi-restraints excluded: chain h residue 58 ASP Chi-restraints excluded: chain h residue 85 VAL Chi-restraints excluded: chain h residue 174 LEU Chi-restraints excluded: chain h residue 212 ILE Chi-restraints excluded: chain h residue 229 TYR Chi-restraints excluded: chain i residue 41 ASP Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 134 LEU Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain j residue 82 ILE Chi-restraints excluded: chain j residue 93 SER Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 161 ILE Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain j residue 177 THR Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 47 CYS Chi-restraints excluded: chain k residue 69 GLU Chi-restraints excluded: chain k residue 109 VAL Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain k residue 162 PHE Chi-restraints excluded: chain k residue 163 VAL Chi-restraints excluded: chain k residue 165 CYS Chi-restraints excluded: chain k residue 202 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 94 ASP Chi-restraints excluded: chain l residue 195 LEU Chi-restraints excluded: chain l residue 222 THR Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 57 LEU Chi-restraints excluded: chain m residue 75 MET Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 151 ILE Chi-restraints excluded: chain m residue 165 ILE Chi-restraints excluded: chain m residue 175 GLU Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain m residue 204 VAL Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 51 ASP Chi-restraints excluded: chain n residue 66 HIS Chi-restraints excluded: chain n residue 119 MET Chi-restraints excluded: chain n residue 134 TYR Chi-restraints excluded: chain n residue 138 TYR Chi-restraints excluded: chain n residue 165 GLU Chi-restraints excluded: chain o residue 25 VAL Chi-restraints excluded: chain o residue 40 ASN Chi-restraints excluded: chain o residue 44 CYS Chi-restraints excluded: chain o residue 62 ASN Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 167 LEU Chi-restraints excluded: chain o residue 172 ASN Chi-restraints excluded: chain o residue 197 THR Chi-restraints excluded: chain p residue 18 ASN Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain p residue 116 THR Chi-restraints excluded: chain p residue 144 GLU Chi-restraints excluded: chain p residue 159 ASP Chi-restraints excluded: chain p residue 176 ASP Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 78 THR Chi-restraints excluded: chain q residue 87 ASN Chi-restraints excluded: chain q residue 88 LEU Chi-restraints excluded: chain q residue 96 THR Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 38 ASN Chi-restraints excluded: chain r residue 58 LEU Chi-restraints excluded: chain r residue 63 CYS Chi-restraints excluded: chain r residue 97 MET Chi-restraints excluded: chain r residue 132 SER Chi-restraints excluded: chain r residue 139 MET Chi-restraints excluded: chain r residue 148 GLU Chi-restraints excluded: chain r residue 175 ASN Chi-restraints excluded: chain s residue 13 LEU Chi-restraints excluded: chain s residue 27 THR Chi-restraints excluded: chain s residue 54 CYS Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain s residue 184 GLU Chi-restraints excluded: chain s residue 191 ASP Chi-restraints excluded: chain s residue 207 THR Chi-restraints excluded: chain t residue 25 ASP Chi-restraints excluded: chain t residue 49 THR Chi-restraints excluded: chain t residue 65 GLN Chi-restraints excluded: chain t residue 117 ASP Chi-restraints excluded: chain t residue 175 VAL Chi-restraints excluded: chain t residue 179 ARG Chi-restraints excluded: chain t residue 200 GLU Chi-restraints excluded: chain t residue 205 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 491 optimal weight: 9.9990 chunk 334 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 439 optimal weight: 7.9990 chunk 243 optimal weight: 10.0000 chunk 503 optimal weight: 10.0000 chunk 407 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 301 optimal weight: 7.9990 chunk 529 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 193 GLN ** H 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN ** L 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 HIS Q 8 GLN ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 160 ASN g 100 ASN ** g 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 109 GLN i 109 GLN ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 85 ASN ** j 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 97 GLN ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 HIS ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 169 GLN q 27 GLN ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 58 HIS s 77 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 48137 Z= 0.298 Angle : 0.675 12.185 65219 Z= 0.355 Chirality : 0.046 0.290 7399 Planarity : 0.005 0.070 8467 Dihedral : 5.871 84.938 6812 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.61 % Favored : 93.37 % Rotamer: Outliers : 5.47 % Allowed : 16.69 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.11), residues: 6155 helix: 0.82 (0.11), residues: 2228 sheet: -0.89 (0.14), residues: 1370 loop : -2.26 (0.11), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 215 HIS 0.007 0.001 HIS s 77 PHE 0.023 0.002 PHE G 163 TYR 0.026 0.002 TYR I 19 ARG 0.008 0.001 ARG M 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 691 time to evaluate : 4.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 HIS cc_start: 0.7736 (m90) cc_final: 0.7523 (m90) REVERT: G 19 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7821 (pp20) REVERT: G 21 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6031 (ttt180) REVERT: G 113 MET cc_start: 0.9083 (mmm) cc_final: 0.8866 (mmt) REVERT: G 123 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7287 (tt0) REVERT: G 128 ASN cc_start: 0.7644 (t0) cc_final: 0.6688 (p0) REVERT: G 214 GLU cc_start: 0.7846 (mp0) cc_final: 0.7547 (mp0) REVERT: I 6 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6145 (p0) REVERT: I 48 GLU cc_start: 0.7812 (tt0) cc_final: 0.6719 (tm-30) REVERT: I 72 MET cc_start: 0.8329 (mtp) cc_final: 0.8016 (mtt) REVERT: I 114 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8380 (tp) REVERT: I 199 LYS cc_start: 0.8084 (tttt) cc_final: 0.7345 (tptp) REVERT: J 13 ASP cc_start: 0.8199 (t0) cc_final: 0.7891 (t0) REVERT: J 20 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7694 (tm-30) REVERT: J 38 ARG cc_start: 0.7360 (tpt170) cc_final: 0.6569 (mmp80) REVERT: J 105 GLU cc_start: 0.8002 (tp30) cc_final: 0.7565 (tp30) REVERT: J 118 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7241 (t80) REVERT: J 127 PHE cc_start: 0.7887 (m-80) cc_final: 0.7663 (m-80) REVERT: J 231 GLU cc_start: 0.7551 (pt0) cc_final: 0.7087 (pp20) REVERT: K 59 MET cc_start: 0.6389 (mmt) cc_final: 0.5651 (mmp) REVERT: K 219 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7753 (t) REVERT: L 6 TYR cc_start: 0.7419 (m-80) cc_final: 0.6838 (m-80) REVERT: L 123 TYR cc_start: 0.8198 (t80) cc_final: 0.7882 (t80) REVERT: L 176 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8414 (ttt) REVERT: L 178 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8485 (mp0) REVERT: M 75 MET cc_start: 0.8875 (mtp) cc_final: 0.8671 (mtp) REVERT: M 150 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.6816 (tpt) REVERT: M 169 ARG cc_start: 0.8510 (ttp80) cc_final: 0.7935 (ttp80) REVERT: M 191 LYS cc_start: 0.8680 (pttp) cc_final: 0.8373 (ptpt) REVERT: M 241 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7594 (tm-30) REVERT: N 57 ASP cc_start: 0.8488 (m-30) cc_final: 0.7900 (t0) REVERT: N 89 ARG cc_start: 0.9104 (ttt-90) cc_final: 0.8848 (ttt-90) REVERT: N 90 TYR cc_start: 0.8319 (m-10) cc_final: 0.7840 (m-80) REVERT: O 86 MET cc_start: 0.8771 (tmm) cc_final: 0.8086 (tmm) REVERT: O 90 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.8343 (m-10) REVERT: O 167 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7180 (mm) REVERT: P 59 ASP cc_start: 0.8236 (m-30) cc_final: 0.7495 (t0) REVERT: P 88 MET cc_start: 0.8686 (ttp) cc_final: 0.8305 (ttp) REVERT: P 89 SER cc_start: 0.8472 (m) cc_final: 0.8006 (t) REVERT: P 122 CYS cc_start: 0.7655 (p) cc_final: 0.7121 (p) REVERT: P 135 ASP cc_start: 0.7893 (p0) cc_final: 0.7270 (p0) REVERT: P 200 LEU cc_start: 0.7668 (mp) cc_final: 0.7307 (mp) REVERT: Q 38 MET cc_start: 0.8672 (mmp) cc_final: 0.8396 (mmp) REVERT: Q 104 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7906 (tt) REVERT: Q 162 LYS cc_start: 0.7860 (mttt) cc_final: 0.7598 (mtmt) REVERT: Q 169 LYS cc_start: 0.9313 (tttp) cc_final: 0.8813 (tttp) REVERT: R 32 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8250 (mmtm) REVERT: R 36 GLU cc_start: 0.8127 (mp0) cc_final: 0.7796 (mp0) REVERT: R 45 MET cc_start: 0.7683 (mtp) cc_final: 0.7054 (mtp) REVERT: R 52 CYS cc_start: 0.8284 (m) cc_final: 0.8037 (t) REVERT: R 72 GLU cc_start: 0.7787 (tt0) cc_final: 0.7542 (pp20) REVERT: R 90 TYR cc_start: 0.8781 (m-80) cc_final: 0.8330 (m-80) REVERT: R 117 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7892 (mp0) REVERT: R 148 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7810 (mm-30) REVERT: S 76 LYS cc_start: 0.8506 (tttm) cc_final: 0.8183 (tttt) REVERT: S 136 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8312 (mmtt) REVERT: S 162 GLU cc_start: 0.8297 (pm20) cc_final: 0.7931 (tp30) REVERT: T 26 MET cc_start: 0.7528 (mtp) cc_final: 0.7050 (mtp) REVERT: T 126 ASP cc_start: 0.8361 (t0) cc_final: 0.7420 (p0) REVERT: T 127 MET cc_start: 0.8055 (ttp) cc_final: 0.7406 (ttm) REVERT: T 173 MET cc_start: 0.8476 (mmm) cc_final: 0.8037 (tpp) REVERT: T 179 ARG cc_start: 0.6301 (OUTLIER) cc_final: 0.5797 (pmt100) REVERT: T 180 ASP cc_start: 0.8006 (t0) cc_final: 0.7644 (t0) REVERT: T 210 ASP cc_start: 0.8217 (m-30) cc_final: 0.7856 (t0) REVERT: g 24 GLN cc_start: 0.6182 (mm-40) cc_final: 0.5873 (mm-40) REVERT: g 73 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8037 (p) REVERT: g 80 MET cc_start: 0.7763 (mmm) cc_final: 0.7274 (mmm) REVERT: g 96 TYR cc_start: 0.8591 (t80) cc_final: 0.8380 (t80) REVERT: g 138 MET cc_start: 0.8627 (ttm) cc_final: 0.8222 (ttp) REVERT: g 159 TYR cc_start: 0.8150 (t80) cc_final: 0.7937 (t80) REVERT: g 180 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7937 (tm-30) REVERT: g 215 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8458 (mt) REVERT: h 39 LYS cc_start: 0.8207 (tmtt) cc_final: 0.7791 (ttpp) REVERT: h 51 LYS cc_start: 0.7314 (mttm) cc_final: 0.6897 (mttt) REVERT: h 119 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8174 (tm-30) REVERT: h 181 ASP cc_start: 0.8167 (p0) cc_final: 0.7882 (t70) REVERT: h 182 LEU cc_start: 0.7666 (mt) cc_final: 0.6923 (pt) REVERT: h 183 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7773 (tp30) REVERT: h 203 MET cc_start: 0.4494 (mmm) cc_final: 0.3875 (mmm) REVERT: h 207 ASN cc_start: 0.7744 (m110) cc_final: 0.7358 (m-40) REVERT: i 3 ARG cc_start: 0.4482 (ptt180) cc_final: 0.3836 (ptp-170) REVERT: i 72 MET cc_start: 0.7943 (mtp) cc_final: 0.7249 (mtp) REVERT: i 121 TYR cc_start: 0.8187 (m-80) cc_final: 0.7830 (m-80) REVERT: i 151 ASP cc_start: 0.7953 (m-30) cc_final: 0.7672 (m-30) REVERT: i 174 MET cc_start: 0.8530 (ttm) cc_final: 0.8073 (mmm) REVERT: i 209 GLU cc_start: 0.8899 (mp0) cc_final: 0.8634 (mp0) REVERT: j 17 PHE cc_start: 0.6710 (t80) cc_final: 0.6471 (t80) REVERT: j 23 GLN cc_start: 0.7663 (mt0) cc_final: 0.7270 (mm-40) REVERT: j 30 SER cc_start: 0.7096 (m) cc_final: 0.6607 (t) REVERT: j 161 ILE cc_start: 0.5969 (OUTLIER) cc_final: 0.5685 (pp) REVERT: k 10 ARG cc_start: 0.4787 (ptp90) cc_final: 0.4569 (ptp-110) REVERT: k 22 PHE cc_start: 0.7315 (m-80) cc_final: 0.6658 (m-80) REVERT: k 29 GLU cc_start: 0.8226 (tp30) cc_final: 0.7618 (tt0) REVERT: k 69 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7758 (mm-30) REVERT: k 71 ASP cc_start: 0.8698 (t70) cc_final: 0.8307 (t0) REVERT: k 148 GLU cc_start: 0.6945 (mp0) cc_final: 0.6628 (pm20) REVERT: k 157 ASP cc_start: 0.8416 (t0) cc_final: 0.8148 (t70) REVERT: k 206 MET cc_start: 0.6447 (ptm) cc_final: 0.6238 (ptt) REVERT: l 6 TYR cc_start: 0.5600 (p90) cc_final: 0.4884 (p90) REVERT: l 12 VAL cc_start: 0.8838 (t) cc_final: 0.8586 (p) REVERT: l 23 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6254 (mm-30) REVERT: l 27 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8468 (mm-30) REVERT: l 61 LYS cc_start: 0.7963 (pttm) cc_final: 0.7269 (mmmm) REVERT: l 154 PHE cc_start: 0.7832 (m-10) cc_final: 0.7616 (m-10) REVERT: m 31 GLU cc_start: 0.7392 (tp30) cc_final: 0.7053 (tp30) REVERT: m 60 GLU cc_start: 0.7490 (tt0) cc_final: 0.6647 (mp0) REVERT: m 114 ARG cc_start: 0.7970 (mmm160) cc_final: 0.7535 (mmt180) REVERT: m 136 MET cc_start: 0.8357 (mtt) cc_final: 0.8013 (mtt) REVERT: m 192 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8791 (mm-30) REVERT: n 62 GLN cc_start: 0.8809 (mt0) cc_final: 0.8402 (tp40) REVERT: n 69 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7988 (tm-30) REVERT: o 65 LEU cc_start: 0.9176 (tt) cc_final: 0.8961 (pp) REVERT: o 135 MET cc_start: 0.7358 (tpp) cc_final: 0.6725 (tpp) REVERT: o 165 ASN cc_start: 0.8149 (t0) cc_final: 0.7635 (m110) REVERT: o 167 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6687 (tp) REVERT: o 182 LYS cc_start: 0.8585 (ttpt) cc_final: 0.8291 (pptt) REVERT: o 202 TYR cc_start: 0.6961 (m-80) cc_final: 0.6693 (m-80) REVERT: p 34 MET cc_start: 0.6985 (ppp) cc_final: 0.6639 (ppp) REVERT: p 122 CYS cc_start: 0.8134 (p) cc_final: 0.7653 (p) REVERT: p 134 ASP cc_start: 0.7901 (m-30) cc_final: 0.7188 (t0) REVERT: p 178 ASP cc_start: 0.7740 (t0) cc_final: 0.7465 (t0) REVERT: q 1 MET cc_start: 0.7140 (tmm) cc_final: 0.6591 (tmm) REVERT: q 20 VAL cc_start: 0.8774 (t) cc_final: 0.8380 (m) REVERT: q 27 GLN cc_start: 0.8368 (mt0) cc_final: 0.7796 (pp30) REVERT: q 49 GLU cc_start: 0.6187 (tm-30) cc_final: 0.5923 (tm-30) REVERT: r 35 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8430 (tp) REVERT: r 45 MET cc_start: 0.7492 (ttm) cc_final: 0.7187 (mtp) REVERT: r 97 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7876 (ppp) REVERT: r 132 SER cc_start: 0.7716 (OUTLIER) cc_final: 0.6596 (t) REVERT: r 147 LEU cc_start: 0.8861 (mt) cc_final: 0.8422 (tp) REVERT: r 153 TYR cc_start: 0.8683 (m-10) cc_final: 0.8416 (m-80) REVERT: s 72 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8477 (mp) REVERT: s 131 GLN cc_start: 0.7795 (pm20) cc_final: 0.7350 (pm20) REVERT: s 159 GLN cc_start: 0.7415 (tp-100) cc_final: 0.6977 (mt0) REVERT: s 205 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7579 (mt-10) REVERT: t 157 GLN cc_start: 0.7742 (tt0) cc_final: 0.7441 (tp-100) REVERT: t 180 ASP cc_start: 0.7681 (t0) cc_final: 0.7258 (t0) outliers start: 267 outliers final: 186 residues processed: 893 average time/residue: 0.5036 time to fit residues: 776.1616 Evaluate side-chains 856 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 647 time to evaluate : 4.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 19 TYR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 162 PHE Chi-restraints excluded: chain K residue 214 ASN Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 178 GLU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 14 PHE Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 198 TYR Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain M residue 229 LYS Chi-restraints excluded: chain M residue 231 ILE Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 38 HIS Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 138 TYR Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 24 MET Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 90 TYR Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain O residue 172 ASN Chi-restraints excluded: chain O residue 176 CYS Chi-restraints excluded: chain P residue 159 ASP Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 53 THR Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain R residue 63 CYS Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 182 ASP Chi-restraints excluded: chain T residue 5 MET Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 179 ARG Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 78 CYS Chi-restraints excluded: chain g residue 100 ASN Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain g residue 125 TYR Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 210 PHE Chi-restraints excluded: chain g residue 215 ILE Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain h residue 42 ASN Chi-restraints excluded: chain h residue 58 ASP Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 85 VAL Chi-restraints excluded: chain h residue 110 LEU Chi-restraints excluded: chain h residue 174 LEU Chi-restraints excluded: chain h residue 212 ILE Chi-restraints excluded: chain i residue 41 ASP Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain j residue 93 SER Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 161 ILE Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain j residue 177 THR Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 47 CYS Chi-restraints excluded: chain k residue 68 VAL Chi-restraints excluded: chain k residue 69 GLU Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain k residue 162 PHE Chi-restraints excluded: chain k residue 165 CYS Chi-restraints excluded: chain k residue 202 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 88 MET Chi-restraints excluded: chain l residue 94 ASP Chi-restraints excluded: chain l residue 202 GLU Chi-restraints excluded: chain l residue 222 THR Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 151 ILE Chi-restraints excluded: chain m residue 165 ILE Chi-restraints excluded: chain m residue 175 GLU Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain m residue 204 VAL Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 24 SER Chi-restraints excluded: chain n residue 51 ASP Chi-restraints excluded: chain n residue 66 HIS Chi-restraints excluded: chain n residue 119 MET Chi-restraints excluded: chain n residue 134 TYR Chi-restraints excluded: chain n residue 138 TYR Chi-restraints excluded: chain n residue 165 GLU Chi-restraints excluded: chain o residue 25 VAL Chi-restraints excluded: chain o residue 44 CYS Chi-restraints excluded: chain o residue 62 ASN Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 167 LEU Chi-restraints excluded: chain o residue 197 THR Chi-restraints excluded: chain p residue 18 ASN Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain p residue 127 ILE Chi-restraints excluded: chain p residue 144 GLU Chi-restraints excluded: chain p residue 159 ASP Chi-restraints excluded: chain p residue 176 ASP Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 78 THR Chi-restraints excluded: chain q residue 87 ASN Chi-restraints excluded: chain q residue 88 LEU Chi-restraints excluded: chain q residue 96 THR Chi-restraints excluded: chain q residue 160 LEU Chi-restraints excluded: chain q residue 164 LEU Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 58 LEU Chi-restraints excluded: chain r residue 63 CYS Chi-restraints excluded: chain r residue 97 MET Chi-restraints excluded: chain r residue 132 SER Chi-restraints excluded: chain r residue 139 MET Chi-restraints excluded: chain r residue 148 GLU Chi-restraints excluded: chain r residue 175 ASN Chi-restraints excluded: chain r residue 194 ASP Chi-restraints excluded: chain s residue 13 LEU Chi-restraints excluded: chain s residue 27 THR Chi-restraints excluded: chain s residue 54 CYS Chi-restraints excluded: chain s residue 72 LEU Chi-restraints excluded: chain s residue 84 THR Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 127 VAL Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain s residue 184 GLU Chi-restraints excluded: chain s residue 191 ASP Chi-restraints excluded: chain s residue 207 THR Chi-restraints excluded: chain t residue 25 ASP Chi-restraints excluded: chain t residue 49 THR Chi-restraints excluded: chain t residue 65 GLN Chi-restraints excluded: chain t residue 117 ASP Chi-restraints excluded: chain t residue 175 VAL Chi-restraints excluded: chain t residue 179 ARG Chi-restraints excluded: chain t residue 200 GLU Chi-restraints excluded: chain t residue 205 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 198 optimal weight: 10.0000 chunk 530 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 346 optimal weight: 0.9980 chunk 145 optimal weight: 9.9990 chunk 590 optimal weight: 9.9990 chunk 489 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 chunk 195 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 HIS T 89 HIS g 100 ASN ** g 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 77 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 48137 Z= 0.388 Angle : 0.742 12.375 65219 Z= 0.390 Chirality : 0.048 0.311 7399 Planarity : 0.005 0.070 8467 Dihedral : 6.071 81.147 6812 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.35 % Favored : 91.63 % Rotamer: Outliers : 5.97 % Allowed : 17.73 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.38 (0.11), residues: 6155 helix: 0.62 (0.11), residues: 2240 sheet: -0.88 (0.14), residues: 1348 loop : -2.34 (0.11), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP m 215 HIS 0.013 0.002 HIS l 65 PHE 0.028 0.002 PHE G 163 TYR 0.026 0.002 TYR i 19 ARG 0.007 0.001 ARG T 179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 650 time to evaluate : 4.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 19 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7921 (pp20) REVERT: G 21 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6231 (ttt180) REVERT: G 96 TYR cc_start: 0.8291 (t80) cc_final: 0.8067 (t80) REVERT: G 123 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: G 128 ASN cc_start: 0.7703 (t0) cc_final: 0.6726 (p0) REVERT: G 214 GLU cc_start: 0.7942 (mp0) cc_final: 0.7576 (mp0) REVERT: I 6 ASP cc_start: 0.6754 (OUTLIER) cc_final: 0.6133 (p0) REVERT: I 48 GLU cc_start: 0.7662 (tt0) cc_final: 0.6608 (tm-30) REVERT: I 72 MET cc_start: 0.8392 (mtp) cc_final: 0.8065 (mtt) REVERT: I 114 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8447 (tp) REVERT: I 228 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8270 (pp) REVERT: J 20 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7799 (tm-30) REVERT: J 38 ARG cc_start: 0.7407 (tpt170) cc_final: 0.6583 (mmp80) REVERT: J 105 GLU cc_start: 0.8074 (tp30) cc_final: 0.7676 (tp30) REVERT: K 71 ASP cc_start: 0.8074 (m-30) cc_final: 0.7711 (m-30) REVERT: K 78 MET cc_start: 0.7390 (ttp) cc_final: 0.7160 (ttp) REVERT: K 79 SER cc_start: 0.7198 (OUTLIER) cc_final: 0.6830 (p) REVERT: L 6 TYR cc_start: 0.7610 (m-80) cc_final: 0.7005 (m-80) REVERT: L 123 TYR cc_start: 0.8220 (t80) cc_final: 0.7903 (t80) REVERT: L 176 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8506 (ttt) REVERT: L 178 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8478 (mp0) REVERT: M 75 MET cc_start: 0.8928 (mtp) cc_final: 0.8718 (mtp) REVERT: M 150 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.6633 (tpt) REVERT: M 161 TRP cc_start: 0.8047 (OUTLIER) cc_final: 0.5695 (m-90) REVERT: M 169 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8013 (ttp80) REVERT: M 188 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8154 (p0) REVERT: M 191 LYS cc_start: 0.8688 (pttp) cc_final: 0.8153 (mtpt) REVERT: M 241 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7617 (tm-30) REVERT: N 57 ASP cc_start: 0.8489 (m-30) cc_final: 0.7826 (t0) REVERT: O 86 MET cc_start: 0.8795 (tmm) cc_final: 0.8091 (tmm) REVERT: O 90 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.8331 (m-10) REVERT: O 167 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7489 (tp) REVERT: P 59 ASP cc_start: 0.8303 (m-30) cc_final: 0.7582 (t0) REVERT: P 88 MET cc_start: 0.8722 (ttp) cc_final: 0.8353 (ttp) REVERT: P 89 SER cc_start: 0.8516 (m) cc_final: 0.8061 (t) REVERT: P 122 CYS cc_start: 0.7767 (p) cc_final: 0.7308 (p) REVERT: P 135 ASP cc_start: 0.7907 (p0) cc_final: 0.7432 (p0) REVERT: P 162 HIS cc_start: 0.6741 (m90) cc_final: 0.6398 (m-70) REVERT: P 200 LEU cc_start: 0.7822 (mp) cc_final: 0.7419 (mp) REVERT: Q 38 MET cc_start: 0.8682 (mmp) cc_final: 0.8433 (mmp) REVERT: Q 69 MET cc_start: 0.8638 (mmm) cc_final: 0.8309 (mmp) REVERT: Q 104 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7933 (tt) REVERT: Q 162 LYS cc_start: 0.7928 (mttt) cc_final: 0.7668 (mtmt) REVERT: Q 174 ASN cc_start: 0.8312 (t0) cc_final: 0.8018 (t0) REVERT: R 32 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8285 (mmtm) REVERT: R 36 GLU cc_start: 0.8015 (mp0) cc_final: 0.7631 (mp0) REVERT: R 45 MET cc_start: 0.7774 (mtp) cc_final: 0.7528 (mtp) REVERT: R 72 GLU cc_start: 0.7781 (tt0) cc_final: 0.7487 (pp20) REVERT: R 117 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7889 (mp0) REVERT: S 31 GLU cc_start: 0.8144 (tp30) cc_final: 0.7853 (tp30) REVERT: S 76 LYS cc_start: 0.8573 (tttm) cc_final: 0.8235 (tttt) REVERT: S 136 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8275 (mmtt) REVERT: S 162 GLU cc_start: 0.8345 (pm20) cc_final: 0.7947 (tp30) REVERT: T 26 MET cc_start: 0.7445 (mtp) cc_final: 0.6992 (mtp) REVERT: T 108 ASN cc_start: 0.8379 (t0) cc_final: 0.7999 (t0) REVERT: T 110 MET cc_start: 0.8292 (mtp) cc_final: 0.7951 (mmm) REVERT: T 126 ASP cc_start: 0.8420 (t0) cc_final: 0.7541 (p0) REVERT: T 127 MET cc_start: 0.8029 (ttp) cc_final: 0.7432 (ttm) REVERT: T 173 MET cc_start: 0.8472 (mmm) cc_final: 0.8095 (tpp) REVERT: T 179 ARG cc_start: 0.6407 (OUTLIER) cc_final: 0.5914 (pmt100) REVERT: T 180 ASP cc_start: 0.8042 (t0) cc_final: 0.7779 (t0) REVERT: T 210 ASP cc_start: 0.8322 (m-30) cc_final: 0.7949 (t0) REVERT: g 24 GLN cc_start: 0.6021 (mm-40) cc_final: 0.5674 (mm110) REVERT: g 73 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7914 (p) REVERT: g 80 MET cc_start: 0.7693 (mmm) cc_final: 0.7319 (mmm) REVERT: g 83 MET cc_start: 0.8180 (mtm) cc_final: 0.7680 (mpp) REVERT: g 131 MET cc_start: 0.6996 (mtp) cc_final: 0.6513 (mtt) REVERT: g 138 MET cc_start: 0.8658 (ttm) cc_final: 0.8237 (ttp) REVERT: g 202 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6644 (mt) REVERT: g 206 LEU cc_start: 0.7850 (mp) cc_final: 0.7308 (tp) REVERT: g 215 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8450 (mt) REVERT: h 39 LYS cc_start: 0.8190 (tmtt) cc_final: 0.7728 (ttpp) REVERT: h 51 LYS cc_start: 0.7425 (mttm) cc_final: 0.6991 (mttt) REVERT: h 79 MET cc_start: 0.1069 (OUTLIER) cc_final: 0.0528 (mmt) REVERT: h 119 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8100 (tm-30) REVERT: h 123 GLN cc_start: 0.7914 (tt0) cc_final: 0.7711 (tt0) REVERT: h 182 LEU cc_start: 0.7596 (mt) cc_final: 0.6660 (pt) REVERT: h 183 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7687 (tp30) REVERT: h 214 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7817 (p0) REVERT: i 72 MET cc_start: 0.7912 (mtp) cc_final: 0.7256 (mtp) REVERT: i 137 ILE cc_start: 0.8664 (pt) cc_final: 0.8008 (pt) REVERT: i 151 ASP cc_start: 0.7991 (m-30) cc_final: 0.7763 (m-30) REVERT: i 209 GLU cc_start: 0.8873 (mp0) cc_final: 0.8611 (mp0) REVERT: j 17 PHE cc_start: 0.6679 (t80) cc_final: 0.6040 (t80) REVERT: j 23 GLN cc_start: 0.7703 (mt0) cc_final: 0.7292 (mm-40) REVERT: j 30 SER cc_start: 0.7263 (m) cc_final: 0.6844 (t) REVERT: j 31 THR cc_start: 0.7114 (OUTLIER) cc_final: 0.6576 (m) REVERT: j 118 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.5486 (t80) REVERT: j 161 ILE cc_start: 0.6038 (OUTLIER) cc_final: 0.5226 (pp) REVERT: k 22 PHE cc_start: 0.7308 (m-80) cc_final: 0.7047 (m-80) REVERT: k 29 GLU cc_start: 0.8273 (tp30) cc_final: 0.7619 (tt0) REVERT: k 59 MET cc_start: 0.7667 (mtt) cc_final: 0.7240 (mtm) REVERT: k 69 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7576 (mm-30) REVERT: k 148 GLU cc_start: 0.6866 (mp0) cc_final: 0.6541 (pm20) REVERT: k 157 ASP cc_start: 0.8453 (t0) cc_final: 0.8195 (t70) REVERT: l 6 TYR cc_start: 0.5420 (p90) cc_final: 0.4836 (p90) REVERT: l 61 LYS cc_start: 0.8028 (pttm) cc_final: 0.7343 (mmmm) REVERT: l 180 MET cc_start: 0.8311 (tpp) cc_final: 0.8101 (tpp) REVERT: m 114 ARG cc_start: 0.7978 (mmm160) cc_final: 0.7556 (mmt180) REVERT: m 136 MET cc_start: 0.8418 (mtt) cc_final: 0.8099 (mtt) REVERT: n 62 GLN cc_start: 0.8804 (mt0) cc_final: 0.8393 (tp40) REVERT: n 69 GLU cc_start: 0.8239 (tm-30) cc_final: 0.8027 (tm-30) REVERT: n 106 GLN cc_start: 0.7962 (tp40) cc_final: 0.7285 (tp40) REVERT: o 24 MET cc_start: 0.8630 (tpp) cc_final: 0.8036 (mmt) REVERT: o 127 MET cc_start: 0.7299 (mtp) cc_final: 0.6935 (mtm) REVERT: o 135 MET cc_start: 0.7296 (tpp) cc_final: 0.6856 (tpp) REVERT: o 150 GLU cc_start: 0.8992 (tt0) cc_final: 0.8782 (tt0) REVERT: o 165 ASN cc_start: 0.7908 (t0) cc_final: 0.7581 (m110) REVERT: o 167 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6725 (tp) REVERT: o 182 LYS cc_start: 0.8604 (ttpt) cc_final: 0.8310 (pptt) REVERT: o 202 TYR cc_start: 0.7056 (m-80) cc_final: 0.6766 (m-80) REVERT: p 122 CYS cc_start: 0.8012 (p) cc_final: 0.7621 (p) REVERT: p 178 ASP cc_start: 0.7871 (t0) cc_final: 0.7605 (t0) REVERT: p 203 ARG cc_start: 0.8021 (mtp85) cc_final: 0.7342 (ttt180) REVERT: q 1 MET cc_start: 0.7288 (tmm) cc_final: 0.6791 (tmm) REVERT: q 20 VAL cc_start: 0.8761 (t) cc_final: 0.8403 (m) REVERT: r 45 MET cc_start: 0.7502 (ttm) cc_final: 0.7209 (mtp) REVERT: r 97 MET cc_start: 0.8507 (tmm) cc_final: 0.8092 (ppp) REVERT: r 132 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.6897 (t) REVERT: r 153 TYR cc_start: 0.8580 (m-10) cc_final: 0.8276 (m-80) REVERT: s 72 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8447 (mp) REVERT: s 115 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7748 (pp20) REVERT: s 131 GLN cc_start: 0.7839 (pm20) cc_final: 0.7422 (pm20) REVERT: s 159 GLN cc_start: 0.7703 (tp-100) cc_final: 0.6801 (pt0) REVERT: s 205 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7551 (mt-10) REVERT: t 157 GLN cc_start: 0.7749 (tt0) cc_final: 0.7492 (tp40) REVERT: t 173 MET cc_start: 0.8608 (mmm) cc_final: 0.8179 (mmm) REVERT: t 180 ASP cc_start: 0.7787 (t0) cc_final: 0.7379 (t0) outliers start: 291 outliers final: 203 residues processed: 877 average time/residue: 0.4369 time to fit residues: 653.4144 Evaluate side-chains 846 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 615 time to evaluate : 4.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 19 TYR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 202 ASP Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 118 TYR Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 162 PHE Chi-restraints excluded: chain K residue 214 ASN Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 178 GLU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 14 PHE Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 161 TRP Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 198 TYR Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 229 LYS Chi-restraints excluded: chain M residue 231 ILE Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 134 TYR Chi-restraints excluded: chain N residue 138 TYR Chi-restraints excluded: chain N residue 148 THR Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 24 MET Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 90 TYR Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain O residue 172 ASN Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 181 ASN Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 76 LEU Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 186 ASN Chi-restraints excluded: chain R residue 63 CYS Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 182 ASP Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain T residue 5 MET Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 179 ARG Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 78 CYS Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 197 THR Chi-restraints excluded: chain g residue 202 LEU Chi-restraints excluded: chain g residue 210 PHE Chi-restraints excluded: chain g residue 215 ILE Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain h residue 42 ASN Chi-restraints excluded: chain h residue 58 ASP Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 79 MET Chi-restraints excluded: chain h residue 85 VAL Chi-restraints excluded: chain h residue 174 LEU Chi-restraints excluded: chain h residue 212 ILE Chi-restraints excluded: chain h residue 214 ASN Chi-restraints excluded: chain i residue 41 ASP Chi-restraints excluded: chain i residue 59 VAL Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 70 CYS Chi-restraints excluded: chain j residue 93 SER Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 118 TYR Chi-restraints excluded: chain j residue 161 ILE Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain j residue 177 THR Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 47 CYS Chi-restraints excluded: chain k residue 68 VAL Chi-restraints excluded: chain k residue 69 GLU Chi-restraints excluded: chain k residue 109 VAL Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain k residue 162 PHE Chi-restraints excluded: chain k residue 163 VAL Chi-restraints excluded: chain k residue 165 CYS Chi-restraints excluded: chain k residue 202 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 88 MET Chi-restraints excluded: chain l residue 94 ASP Chi-restraints excluded: chain l residue 222 THR Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 75 MET Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 151 ILE Chi-restraints excluded: chain m residue 165 ILE Chi-restraints excluded: chain m residue 175 GLU Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain m residue 204 VAL Chi-restraints excluded: chain m residue 213 LEU Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 24 SER Chi-restraints excluded: chain n residue 51 ASP Chi-restraints excluded: chain n residue 66 HIS Chi-restraints excluded: chain n residue 134 TYR Chi-restraints excluded: chain n residue 138 TYR Chi-restraints excluded: chain n residue 165 GLU Chi-restraints excluded: chain o residue 25 VAL Chi-restraints excluded: chain o residue 40 ASN Chi-restraints excluded: chain o residue 44 CYS Chi-restraints excluded: chain o residue 62 ASN Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 167 LEU Chi-restraints excluded: chain o residue 197 THR Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain p residue 116 THR Chi-restraints excluded: chain p residue 127 ILE Chi-restraints excluded: chain p residue 144 GLU Chi-restraints excluded: chain p residue 159 ASP Chi-restraints excluded: chain p residue 176 ASP Chi-restraints excluded: chain p residue 189 ILE Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 78 THR Chi-restraints excluded: chain q residue 87 ASN Chi-restraints excluded: chain q residue 88 LEU Chi-restraints excluded: chain q residue 96 THR Chi-restraints excluded: chain q residue 164 LEU Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain r residue 21 THR Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 63 CYS Chi-restraints excluded: chain r residue 132 SER Chi-restraints excluded: chain r residue 139 MET Chi-restraints excluded: chain r residue 148 GLU Chi-restraints excluded: chain r residue 175 ASN Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 194 ASP Chi-restraints excluded: chain s residue 13 LEU Chi-restraints excluded: chain s residue 27 THR Chi-restraints excluded: chain s residue 54 CYS Chi-restraints excluded: chain s residue 72 LEU Chi-restraints excluded: chain s residue 84 THR Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 127 VAL Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain s residue 191 ASP Chi-restraints excluded: chain s residue 207 THR Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain t residue 25 ASP Chi-restraints excluded: chain t residue 49 THR Chi-restraints excluded: chain t residue 63 LEU Chi-restraints excluded: chain t residue 65 GLN Chi-restraints excluded: chain t residue 117 ASP Chi-restraints excluded: chain t residue 175 VAL Chi-restraints excluded: chain t residue 179 ARG Chi-restraints excluded: chain t residue 200 GLU Chi-restraints excluded: chain t residue 205 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 569 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 336 optimal weight: 0.9980 chunk 431 optimal weight: 1.9990 chunk 333 optimal weight: 0.8980 chunk 496 optimal weight: 1.9990 chunk 329 optimal weight: 10.0000 chunk 587 optimal weight: 10.0000 chunk 367 optimal weight: 20.0000 chunk 358 optimal weight: 4.9990 chunk 271 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 166 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 ASN Q 132 HIS S 151 ASN S 152 GLN ** g 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN h 102 GLN ** i 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 48137 Z= 0.193 Angle : 0.627 15.190 65219 Z= 0.329 Chirality : 0.045 0.279 7399 Planarity : 0.004 0.066 8467 Dihedral : 5.587 75.567 6812 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.67 % Allowed : 19.50 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.91 (0.11), residues: 6155 helix: 1.08 (0.11), residues: 2233 sheet: -0.63 (0.14), residues: 1333 loop : -2.15 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP m 215 HIS 0.008 0.001 HIS l 65 PHE 0.026 0.001 PHE K 123 TYR 0.028 0.001 TYR I 19 ARG 0.006 0.000 ARG N 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 700 time to evaluate : 4.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 19 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7688 (pp20) REVERT: G 21 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6116 (ttt180) REVERT: H 166 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.6749 (t0) REVERT: I 10 THR cc_start: 0.5975 (OUTLIER) cc_final: 0.5454 (p) REVERT: I 48 GLU cc_start: 0.7720 (tt0) cc_final: 0.6686 (tm-30) REVERT: I 114 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8380 (tp) REVERT: I 174 MET cc_start: 0.7521 (mtp) cc_final: 0.7259 (mtp) REVERT: I 228 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8247 (pp) REVERT: J 20 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7714 (tm-30) REVERT: J 38 ARG cc_start: 0.7369 (tpt170) cc_final: 0.6560 (mmp80) REVERT: J 105 GLU cc_start: 0.7952 (tp30) cc_final: 0.7505 (tp30) REVERT: J 231 GLU cc_start: 0.7525 (pt0) cc_final: 0.7003 (pp20) REVERT: K 59 MET cc_start: 0.5792 (mmm) cc_final: 0.5516 (mmp) REVERT: K 71 ASP cc_start: 0.8076 (m-30) cc_final: 0.7720 (m-30) REVERT: L 6 TYR cc_start: 0.7598 (m-80) cc_final: 0.6991 (m-80) REVERT: L 123 TYR cc_start: 0.8189 (t80) cc_final: 0.7897 (t80) REVERT: L 176 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8435 (ttt) REVERT: L 178 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8363 (pm20) REVERT: M 85 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7376 (mtm-85) REVERT: M 150 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.6804 (tpt) REVERT: M 161 TRP cc_start: 0.8018 (OUTLIER) cc_final: 0.5708 (m-90) REVERT: M 169 ARG cc_start: 0.8525 (ttp80) cc_final: 0.8065 (ttp80) REVERT: M 188 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8280 (p0) REVERT: M 191 LYS cc_start: 0.8630 (pttp) cc_final: 0.8320 (ptpt) REVERT: M 241 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7576 (tm-30) REVERT: N 57 ASP cc_start: 0.8493 (m-30) cc_final: 0.7892 (t0) REVERT: N 89 ARG cc_start: 0.9035 (ttt-90) cc_final: 0.8823 (ttm110) REVERT: N 107 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7876 (mm-30) REVERT: O 86 MET cc_start: 0.8792 (tmm) cc_final: 0.8047 (tmm) REVERT: O 90 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.8278 (m-10) REVERT: O 167 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7275 (mm) REVERT: P 14 MET cc_start: 0.8161 (ttm) cc_final: 0.7531 (ttm) REVERT: P 59 ASP cc_start: 0.8187 (m-30) cc_final: 0.7920 (m-30) REVERT: P 74 TYR cc_start: 0.8677 (t80) cc_final: 0.8436 (t80) REVERT: P 88 MET cc_start: 0.8651 (ttp) cc_final: 0.8189 (ttp) REVERT: P 89 SER cc_start: 0.8433 (m) cc_final: 0.7979 (t) REVERT: P 122 CYS cc_start: 0.7462 (p) cc_final: 0.6584 (p) REVERT: P 135 ASP cc_start: 0.7833 (p0) cc_final: 0.7245 (p0) REVERT: Q 38 MET cc_start: 0.8670 (mmp) cc_final: 0.8419 (mmp) REVERT: Q 69 MET cc_start: 0.8614 (mmm) cc_final: 0.8327 (mmp) REVERT: Q 174 ASN cc_start: 0.8342 (t0) cc_final: 0.8051 (t0) REVERT: R 32 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8237 (mmtm) REVERT: R 36 GLU cc_start: 0.7979 (mp0) cc_final: 0.7619 (mp0) REVERT: R 72 GLU cc_start: 0.7782 (tt0) cc_final: 0.7519 (pp20) REVERT: R 90 TYR cc_start: 0.8777 (m-80) cc_final: 0.8299 (m-80) REVERT: R 117 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7875 (mp0) REVERT: S 76 LYS cc_start: 0.8451 (tttm) cc_final: 0.8074 (tttt) REVERT: S 136 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8166 (mmtt) REVERT: S 144 MET cc_start: 0.8356 (mmm) cc_final: 0.7736 (mmm) REVERT: S 162 GLU cc_start: 0.8331 (pm20) cc_final: 0.7996 (tp30) REVERT: T 26 MET cc_start: 0.7389 (mtp) cc_final: 0.6940 (mtp) REVERT: T 126 ASP cc_start: 0.8398 (t0) cc_final: 0.7548 (p0) REVERT: T 127 MET cc_start: 0.7892 (ttp) cc_final: 0.7329 (ttm) REVERT: T 173 MET cc_start: 0.8509 (mmm) cc_final: 0.8003 (tpp) REVERT: T 179 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.5764 (pmt100) REVERT: T 180 ASP cc_start: 0.7935 (t0) cc_final: 0.7617 (t0) REVERT: T 210 ASP cc_start: 0.8177 (m-30) cc_final: 0.7846 (t0) REVERT: g 24 GLN cc_start: 0.6137 (mm-40) cc_final: 0.5803 (mm-40) REVERT: g 69 LEU cc_start: 0.8597 (mm) cc_final: 0.8309 (tp) REVERT: g 73 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.8003 (p) REVERT: g 80 MET cc_start: 0.7667 (mmm) cc_final: 0.7216 (mmm) REVERT: g 83 MET cc_start: 0.8102 (mtm) cc_final: 0.7663 (mpp) REVERT: g 131 MET cc_start: 0.6989 (mtp) cc_final: 0.6506 (mtt) REVERT: g 138 MET cc_start: 0.8648 (ttm) cc_final: 0.8183 (ttp) REVERT: g 180 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7835 (tm-30) REVERT: g 206 LEU cc_start: 0.7638 (mp) cc_final: 0.6915 (tp) REVERT: g 215 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8425 (mt) REVERT: h 39 LYS cc_start: 0.8160 (tmtt) cc_final: 0.7765 (ttpp) REVERT: h 79 MET cc_start: 0.0875 (OUTLIER) cc_final: 0.0360 (mtp) REVERT: h 109 GLN cc_start: 0.8343 (mm110) cc_final: 0.7866 (mt0) REVERT: h 119 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8192 (tm-30) REVERT: h 181 ASP cc_start: 0.8133 (p0) cc_final: 0.7867 (t70) REVERT: h 182 LEU cc_start: 0.7647 (mt) cc_final: 0.6954 (pt) REVERT: h 183 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7732 (tp30) REVERT: h 203 MET cc_start: 0.4343 (mmm) cc_final: 0.3871 (mmm) REVERT: h 207 ASN cc_start: 0.7692 (m-40) cc_final: 0.7036 (t0) REVERT: i 72 MET cc_start: 0.7930 (mtp) cc_final: 0.7255 (mtp) REVERT: i 137 ILE cc_start: 0.8561 (pt) cc_final: 0.7852 (pt) REVERT: i 151 ASP cc_start: 0.7983 (m-30) cc_final: 0.7742 (m-30) REVERT: i 174 MET cc_start: 0.8521 (ttm) cc_final: 0.7934 (mmm) REVERT: i 209 GLU cc_start: 0.8859 (mp0) cc_final: 0.8598 (mp0) REVERT: i 228 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8549 (pt) REVERT: j 17 PHE cc_start: 0.6774 (t80) cc_final: 0.6046 (t80) REVERT: j 23 GLN cc_start: 0.7581 (mt0) cc_final: 0.7180 (mm-40) REVERT: j 30 SER cc_start: 0.7267 (m) cc_final: 0.6832 (t) REVERT: j 31 THR cc_start: 0.7136 (OUTLIER) cc_final: 0.6895 (m) REVERT: j 161 ILE cc_start: 0.5923 (OUTLIER) cc_final: 0.5112 (pp) REVERT: k 10 ARG cc_start: 0.4708 (ptp90) cc_final: 0.4284 (ptm160) REVERT: k 22 PHE cc_start: 0.7274 (m-80) cc_final: 0.5661 (m-80) REVERT: k 59 MET cc_start: 0.7729 (mtt) cc_final: 0.7295 (mtm) REVERT: k 69 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: k 116 VAL cc_start: 0.9212 (t) cc_final: 0.9009 (p) REVERT: k 148 GLU cc_start: 0.6857 (mp0) cc_final: 0.6485 (pm20) REVERT: l 6 TYR cc_start: 0.5207 (p90) cc_final: 0.4825 (p90) REVERT: l 12 VAL cc_start: 0.8835 (t) cc_final: 0.8620 (p) REVERT: l 61 LYS cc_start: 0.8005 (pttm) cc_final: 0.7308 (mmmm) REVERT: l 154 PHE cc_start: 0.7610 (m-10) cc_final: 0.7365 (m-10) REVERT: m 114 ARG cc_start: 0.7966 (mmm160) cc_final: 0.7522 (mmt180) REVERT: m 136 MET cc_start: 0.8276 (mtt) cc_final: 0.7786 (mtt) REVERT: m 150 MET cc_start: 0.7521 (tpt) cc_final: 0.7097 (tpt) REVERT: n 62 GLN cc_start: 0.8787 (mt0) cc_final: 0.8406 (tp40) REVERT: n 69 GLU cc_start: 0.8229 (tm-30) cc_final: 0.8007 (tm-30) REVERT: n 138 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7673 (t80) REVERT: o 24 MET cc_start: 0.8657 (tpp) cc_final: 0.8109 (mmt) REVERT: o 127 MET cc_start: 0.7206 (mtp) cc_final: 0.6844 (mtm) REVERT: o 135 MET cc_start: 0.7345 (tpp) cc_final: 0.6758 (tpp) REVERT: o 150 GLU cc_start: 0.8939 (tt0) cc_final: 0.8690 (tt0) REVERT: o 165 ASN cc_start: 0.8044 (t0) cc_final: 0.7568 (m110) REVERT: o 167 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6686 (tp) REVERT: o 182 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8168 (pptt) REVERT: o 202 TYR cc_start: 0.6916 (m-80) cc_final: 0.6661 (m-80) REVERT: p 122 CYS cc_start: 0.7913 (p) cc_final: 0.7645 (p) REVERT: p 203 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7469 (ttm170) REVERT: q 20 VAL cc_start: 0.8744 (t) cc_final: 0.8419 (m) REVERT: r 38 ASN cc_start: 0.7094 (t0) cc_final: 0.6658 (t0) REVERT: r 45 MET cc_start: 0.7383 (ttm) cc_final: 0.7107 (mtp) REVERT: r 89 GLN cc_start: 0.8752 (mt0) cc_final: 0.8441 (mp10) REVERT: r 97 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8197 (ppp) REVERT: r 148 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7325 (tp30) REVERT: r 153 TYR cc_start: 0.8569 (m-10) cc_final: 0.8329 (m-80) REVERT: s 72 LEU cc_start: 0.8835 (mt) cc_final: 0.8569 (mp) REVERT: s 131 GLN cc_start: 0.7712 (pm20) cc_final: 0.7313 (pm20) REVERT: s 159 GLN cc_start: 0.7620 (tp-100) cc_final: 0.7314 (mt0) REVERT: s 205 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7581 (mt-10) REVERT: t 157 GLN cc_start: 0.7743 (tt0) cc_final: 0.7436 (tp-100) REVERT: t 173 MET cc_start: 0.8609 (mmm) cc_final: 0.8184 (mmm) REVERT: t 180 ASP cc_start: 0.7423 (t0) cc_final: 0.7030 (t0) outliers start: 228 outliers final: 164 residues processed: 871 average time/residue: 0.4758 time to fit residues: 703.3077 Evaluate side-chains 818 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 629 time to evaluate : 4.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 19 TYR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 202 ASP Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 123 PHE Chi-restraints excluded: chain K residue 162 PHE Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 178 GLU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 14 PHE Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 161 TRP Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 198 TYR Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 229 LYS Chi-restraints excluded: chain M residue 231 ILE Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 134 TYR Chi-restraints excluded: chain N residue 138 TYR Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 24 MET Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 90 TYR Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain O residue 172 ASN Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain P residue 76 LEU Chi-restraints excluded: chain P residue 93 ASN Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 182 ILE Chi-restraints excluded: chain R residue 63 CYS Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 182 ASP Chi-restraints excluded: chain T residue 5 MET Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 179 ARG Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 78 CYS Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain g residue 125 TYR Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 210 PHE Chi-restraints excluded: chain g residue 215 ILE Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain h residue 42 ASN Chi-restraints excluded: chain h residue 79 MET Chi-restraints excluded: chain h residue 174 LEU Chi-restraints excluded: chain h residue 212 ILE Chi-restraints excluded: chain i residue 41 ASP Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 134 LEU Chi-restraints excluded: chain i residue 149 GLN Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 93 SER Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 161 ILE Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain j residue 177 THR Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 47 CYS Chi-restraints excluded: chain k residue 69 GLU Chi-restraints excluded: chain k residue 84 ASP Chi-restraints excluded: chain k residue 109 VAL Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain k residue 162 PHE Chi-restraints excluded: chain k residue 163 VAL Chi-restraints excluded: chain k residue 202 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 88 MET Chi-restraints excluded: chain l residue 94 ASP Chi-restraints excluded: chain l residue 202 GLU Chi-restraints excluded: chain l residue 222 THR Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 128 VAL Chi-restraints excluded: chain m residue 165 ILE Chi-restraints excluded: chain m residue 175 GLU Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain m residue 213 LEU Chi-restraints excluded: chain n residue 24 SER Chi-restraints excluded: chain n residue 51 ASP Chi-restraints excluded: chain n residue 134 TYR Chi-restraints excluded: chain n residue 138 TYR Chi-restraints excluded: chain n residue 173 VAL Chi-restraints excluded: chain o residue 25 VAL Chi-restraints excluded: chain o residue 44 CYS Chi-restraints excluded: chain o residue 62 ASN Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 167 LEU Chi-restraints excluded: chain o residue 197 THR Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain p residue 116 THR Chi-restraints excluded: chain p residue 127 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 78 THR Chi-restraints excluded: chain q residue 87 ASN Chi-restraints excluded: chain q residue 88 LEU Chi-restraints excluded: chain q residue 160 LEU Chi-restraints excluded: chain q residue 164 LEU Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain r residue 58 LEU Chi-restraints excluded: chain r residue 63 CYS Chi-restraints excluded: chain r residue 97 MET Chi-restraints excluded: chain r residue 100 MET Chi-restraints excluded: chain r residue 132 SER Chi-restraints excluded: chain r residue 136 TYR Chi-restraints excluded: chain r residue 139 MET Chi-restraints excluded: chain r residue 148 GLU Chi-restraints excluded: chain r residue 175 ASN Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 200 SER Chi-restraints excluded: chain s residue 13 LEU Chi-restraints excluded: chain s residue 27 THR Chi-restraints excluded: chain s residue 54 CYS Chi-restraints excluded: chain s residue 84 THR Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 127 VAL Chi-restraints excluded: chain s residue 191 ASP Chi-restraints excluded: chain s residue 207 THR Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain t residue 25 ASP Chi-restraints excluded: chain t residue 49 THR Chi-restraints excluded: chain t residue 117 ASP Chi-restraints excluded: chain t residue 175 VAL Chi-restraints excluded: chain t residue 179 ARG Chi-restraints excluded: chain t residue 200 GLU Chi-restraints excluded: chain t residue 205 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 363 optimal weight: 7.9990 chunk 234 optimal weight: 5.9990 chunk 351 optimal weight: 20.0000 chunk 177 optimal weight: 7.9990 chunk 115 optimal weight: 0.0070 chunk 113 optimal weight: 10.0000 chunk 373 optimal weight: 20.0000 chunk 400 optimal weight: 7.9990 chunk 290 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 462 optimal weight: 6.9990 overall best weight: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 166 ASN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 HIS ** O 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 HIS ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 40 ASN ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 110 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 48137 Z= 0.303 Angle : 0.683 12.147 65219 Z= 0.357 Chirality : 0.046 0.294 7399 Planarity : 0.005 0.069 8467 Dihedral : 5.714 75.395 6812 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.75 % Favored : 92.23 % Rotamer: Outliers : 5.00 % Allowed : 19.84 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.03 (0.11), residues: 6155 helix: 0.96 (0.11), residues: 2239 sheet: -0.68 (0.14), residues: 1349 loop : -2.21 (0.12), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP m 215 HIS 0.009 0.001 HIS l 65 PHE 0.031 0.002 PHE G 163 TYR 0.028 0.002 TYR I 19 ARG 0.016 0.001 ARG r 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 636 time to evaluate : 4.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 19 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8021 (pp20) REVERT: G 21 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6162 (ttt180) REVERT: G 128 ASN cc_start: 0.7566 (t0) cc_final: 0.6497 (p0) REVERT: I 48 GLU cc_start: 0.7626 (tt0) cc_final: 0.6606 (tm-30) REVERT: I 114 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8429 (tp) REVERT: I 174 MET cc_start: 0.7509 (mtp) cc_final: 0.7234 (mtp) REVERT: J 20 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7811 (tm-30) REVERT: J 38 ARG cc_start: 0.7397 (tpt170) cc_final: 0.6587 (mmp80) REVERT: J 105 GLU cc_start: 0.8024 (tp30) cc_final: 0.7615 (tp30) REVERT: K 71 ASP cc_start: 0.7980 (m-30) cc_final: 0.7568 (m-30) REVERT: K 79 SER cc_start: 0.6984 (OUTLIER) cc_final: 0.6664 (p) REVERT: L 6 TYR cc_start: 0.7709 (m-80) cc_final: 0.7160 (m-80) REVERT: L 123 TYR cc_start: 0.8219 (t80) cc_final: 0.7914 (t80) REVERT: L 176 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8478 (ttt) REVERT: M 85 ARG cc_start: 0.7665 (ttm-80) cc_final: 0.7378 (mtm-85) REVERT: M 136 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.6448 (mpp) REVERT: M 150 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.6647 (tpt) REVERT: M 161 TRP cc_start: 0.8045 (OUTLIER) cc_final: 0.5740 (m-90) REVERT: M 169 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8030 (ttp80) REVERT: M 188 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8253 (p0) REVERT: M 191 LYS cc_start: 0.8610 (pttp) cc_final: 0.8114 (mtpt) REVERT: M 241 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7586 (tm-30) REVERT: N 57 ASP cc_start: 0.8500 (m-30) cc_final: 0.7833 (t0) REVERT: N 89 ARG cc_start: 0.9042 (ttt-90) cc_final: 0.8766 (ttt-90) REVERT: N 107 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7855 (mm-30) REVERT: O 86 MET cc_start: 0.8770 (tmm) cc_final: 0.8040 (tmm) REVERT: O 90 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.8318 (m-10) REVERT: O 167 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7400 (tp) REVERT: O 172 ASN cc_start: 0.6640 (OUTLIER) cc_final: 0.5952 (m-40) REVERT: P 14 MET cc_start: 0.8172 (ttm) cc_final: 0.7586 (ttm) REVERT: P 59 ASP cc_start: 0.8220 (m-30) cc_final: 0.7848 (m-30) REVERT: P 86 THR cc_start: 0.9053 (m) cc_final: 0.8824 (p) REVERT: P 88 MET cc_start: 0.8663 (ttp) cc_final: 0.8277 (ttp) REVERT: P 89 SER cc_start: 0.8502 (m) cc_final: 0.8106 (t) REVERT: P 122 CYS cc_start: 0.7785 (p) cc_final: 0.7310 (p) REVERT: P 135 ASP cc_start: 0.7860 (p0) cc_final: 0.7303 (p0) REVERT: P 200 LEU cc_start: 0.7733 (mp) cc_final: 0.7307 (mp) REVERT: Q 38 MET cc_start: 0.8692 (mmp) cc_final: 0.8434 (mmp) REVERT: Q 69 MET cc_start: 0.8646 (mmm) cc_final: 0.8363 (mmp) REVERT: Q 104 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7954 (tt) REVERT: Q 174 ASN cc_start: 0.8359 (t0) cc_final: 0.8045 (t0) REVERT: R 32 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8402 (mmtm) REVERT: R 36 GLU cc_start: 0.7962 (mp0) cc_final: 0.7615 (mp0) REVERT: R 72 GLU cc_start: 0.7784 (tt0) cc_final: 0.7491 (pp20) REVERT: R 90 TYR cc_start: 0.8685 (m-80) cc_final: 0.8230 (m-80) REVERT: R 117 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7882 (mp0) REVERT: S 76 LYS cc_start: 0.8505 (tttm) cc_final: 0.8138 (tttt) REVERT: S 136 LYS cc_start: 0.8817 (mmmm) cc_final: 0.8520 (tptt) REVERT: S 144 MET cc_start: 0.8491 (mmm) cc_final: 0.7835 (mmm) REVERT: S 162 GLU cc_start: 0.8402 (pm20) cc_final: 0.8070 (tp30) REVERT: T 26 MET cc_start: 0.7480 (mtp) cc_final: 0.7023 (mtp) REVERT: T 110 MET cc_start: 0.8263 (mtp) cc_final: 0.7944 (mmm) REVERT: T 126 ASP cc_start: 0.8466 (t0) cc_final: 0.7597 (p0) REVERT: T 127 MET cc_start: 0.7926 (ttp) cc_final: 0.7319 (ttm) REVERT: T 173 MET cc_start: 0.8517 (mmm) cc_final: 0.8079 (tpp) REVERT: T 179 ARG cc_start: 0.6353 (OUTLIER) cc_final: 0.5857 (pmt100) REVERT: T 180 ASP cc_start: 0.7984 (t0) cc_final: 0.7692 (t0) REVERT: T 210 ASP cc_start: 0.8253 (m-30) cc_final: 0.7915 (t0) REVERT: g 24 GLN cc_start: 0.6151 (mm-40) cc_final: 0.5762 (mm110) REVERT: g 73 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.7927 (p) REVERT: g 80 MET cc_start: 0.7572 (mmm) cc_final: 0.7180 (mmm) REVERT: g 83 MET cc_start: 0.8134 (mtm) cc_final: 0.7649 (mpp) REVERT: g 131 MET cc_start: 0.7165 (mtp) cc_final: 0.6653 (mtt) REVERT: g 138 MET cc_start: 0.8673 (ttm) cc_final: 0.8194 (ttp) REVERT: g 206 LEU cc_start: 0.7657 (mp) cc_final: 0.7232 (tp) REVERT: g 215 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8453 (mt) REVERT: h 39 LYS cc_start: 0.8163 (tmtt) cc_final: 0.7714 (ttpp) REVERT: h 51 LYS cc_start: 0.7304 (mttt) cc_final: 0.7004 (mttt) REVERT: h 79 MET cc_start: 0.1069 (OUTLIER) cc_final: 0.0515 (mtp) REVERT: h 109 GLN cc_start: 0.8344 (mm110) cc_final: 0.7885 (mt0) REVERT: h 119 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8163 (tm-30) REVERT: h 181 ASP cc_start: 0.8132 (p0) cc_final: 0.7884 (t70) REVERT: h 182 LEU cc_start: 0.7625 (mt) cc_final: 0.6867 (pt) REVERT: h 183 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7696 (tp30) REVERT: h 207 ASN cc_start: 0.7902 (m-40) cc_final: 0.7120 (t0) REVERT: h 214 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7796 (p0) REVERT: i 151 ASP cc_start: 0.7997 (m-30) cc_final: 0.7773 (m-30) REVERT: i 174 MET cc_start: 0.8529 (ttm) cc_final: 0.7991 (mmm) REVERT: i 209 GLU cc_start: 0.8855 (mp0) cc_final: 0.8612 (mp0) REVERT: i 228 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8535 (pt) REVERT: j 17 PHE cc_start: 0.6735 (t80) cc_final: 0.6035 (t80) REVERT: j 23 GLN cc_start: 0.7636 (mt0) cc_final: 0.7208 (mm-40) REVERT: j 30 SER cc_start: 0.7325 (m) cc_final: 0.6906 (t) REVERT: j 31 THR cc_start: 0.7131 (OUTLIER) cc_final: 0.6673 (m) REVERT: j 161 ILE cc_start: 0.6044 (OUTLIER) cc_final: 0.5296 (pp) REVERT: k 59 MET cc_start: 0.7808 (mtt) cc_final: 0.7347 (mtm) REVERT: k 69 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: k 95 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8768 (tm-30) REVERT: k 113 THR cc_start: 0.9233 (OUTLIER) cc_final: 0.9011 (p) REVERT: k 148 GLU cc_start: 0.6843 (mp0) cc_final: 0.6494 (pm20) REVERT: l 6 TYR cc_start: 0.5211 (p90) cc_final: 0.4817 (p90) REVERT: l 12 VAL cc_start: 0.8842 (t) cc_final: 0.8619 (p) REVERT: l 61 LYS cc_start: 0.7996 (pttm) cc_final: 0.7356 (mmmm) REVERT: l 154 PHE cc_start: 0.7743 (m-10) cc_final: 0.7463 (m-10) REVERT: m 114 ARG cc_start: 0.7968 (mmm160) cc_final: 0.7483 (mmt180) REVERT: m 136 MET cc_start: 0.8341 (mtt) cc_final: 0.8095 (mtt) REVERT: m 184 MET cc_start: 0.8141 (ptp) cc_final: 0.7581 (ptp) REVERT: n 62 GLN cc_start: 0.8781 (mt0) cc_final: 0.8398 (tp40) REVERT: n 69 GLU cc_start: 0.8277 (tm-30) cc_final: 0.8047 (tm-30) REVERT: n 87 CYS cc_start: 0.8568 (t) cc_final: 0.8351 (t) REVERT: n 138 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.7616 (t80) REVERT: o 127 MET cc_start: 0.7280 (mtp) cc_final: 0.6924 (mtm) REVERT: o 135 MET cc_start: 0.7314 (tpp) cc_final: 0.6729 (tpp) REVERT: o 150 GLU cc_start: 0.8986 (tt0) cc_final: 0.8745 (tt0) REVERT: o 165 ASN cc_start: 0.7993 (t0) cc_final: 0.7554 (m110) REVERT: o 167 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6740 (tp) REVERT: o 182 LYS cc_start: 0.8573 (ttpt) cc_final: 0.8215 (pptt) REVERT: o 202 TYR cc_start: 0.7065 (m-80) cc_final: 0.6792 (m-80) REVERT: p 122 CYS cc_start: 0.7981 (p) cc_final: 0.7700 (p) REVERT: p 203 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7448 (ttt180) REVERT: q 1 MET cc_start: 0.7349 (tmm) cc_final: 0.7089 (tmm) REVERT: q 20 VAL cc_start: 0.8755 (t) cc_final: 0.8318 (m) REVERT: q 27 GLN cc_start: 0.8290 (mt0) cc_final: 0.7666 (pp30) REVERT: r 45 MET cc_start: 0.7387 (ttm) cc_final: 0.7068 (mtp) REVERT: r 89 GLN cc_start: 0.8783 (mt0) cc_final: 0.8449 (mp10) REVERT: r 97 MET cc_start: 0.8621 (tmm) cc_final: 0.8257 (ppp) REVERT: r 132 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.6715 (t) REVERT: r 153 TYR cc_start: 0.8542 (m-10) cc_final: 0.8244 (m-80) REVERT: s 72 LEU cc_start: 0.8837 (mt) cc_final: 0.8541 (mp) REVERT: s 115 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7768 (pp20) REVERT: s 159 GLN cc_start: 0.7765 (tp-100) cc_final: 0.6911 (pt0) REVERT: s 205 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7606 (mt-10) REVERT: t 157 GLN cc_start: 0.7769 (tt0) cc_final: 0.7490 (tp40) REVERT: t 173 MET cc_start: 0.8613 (mmm) cc_final: 0.8198 (mmm) REVERT: t 180 ASP cc_start: 0.7564 (t0) cc_final: 0.7181 (t0) outliers start: 244 outliers final: 181 residues processed: 823 average time/residue: 0.4347 time to fit residues: 609.2982 Evaluate side-chains 812 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 605 time to evaluate : 4.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 214 ASN Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 19 TYR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 202 ASP Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 123 PHE Chi-restraints excluded: chain K residue 162 PHE Chi-restraints excluded: chain K residue 214 ASN Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 14 PHE Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 161 TRP Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 198 TYR Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 229 LYS Chi-restraints excluded: chain M residue 231 ILE Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 134 TYR Chi-restraints excluded: chain N residue 138 TYR Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 24 MET Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 90 TYR Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain O residue 172 ASN Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain P residue 76 LEU Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 186 ASN Chi-restraints excluded: chain R residue 63 CYS Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 182 ASP Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain T residue 5 MET Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 179 ARG Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 78 CYS Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 210 PHE Chi-restraints excluded: chain g residue 215 ILE Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain h residue 42 ASN Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 79 MET Chi-restraints excluded: chain h residue 85 VAL Chi-restraints excluded: chain h residue 174 LEU Chi-restraints excluded: chain h residue 212 ILE Chi-restraints excluded: chain h residue 214 ASN Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 110 LEU Chi-restraints excluded: chain i residue 134 LEU Chi-restraints excluded: chain i residue 149 GLN Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 93 SER Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 161 ILE Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain j residue 177 THR Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 47 CYS Chi-restraints excluded: chain k residue 68 VAL Chi-restraints excluded: chain k residue 69 GLU Chi-restraints excluded: chain k residue 84 ASP Chi-restraints excluded: chain k residue 109 VAL Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain k residue 162 PHE Chi-restraints excluded: chain k residue 163 VAL Chi-restraints excluded: chain k residue 202 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 88 MET Chi-restraints excluded: chain l residue 94 ASP Chi-restraints excluded: chain l residue 179 PHE Chi-restraints excluded: chain l residue 222 THR Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 128 VAL Chi-restraints excluded: chain m residue 175 GLU Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain m residue 213 LEU Chi-restraints excluded: chain n residue 24 SER Chi-restraints excluded: chain n residue 51 ASP Chi-restraints excluded: chain n residue 134 TYR Chi-restraints excluded: chain n residue 138 TYR Chi-restraints excluded: chain n residue 140 ASP Chi-restraints excluded: chain n residue 165 GLU Chi-restraints excluded: chain n residue 173 VAL Chi-restraints excluded: chain o residue 25 VAL Chi-restraints excluded: chain o residue 44 CYS Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 167 LEU Chi-restraints excluded: chain o residue 197 THR Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain p residue 116 THR Chi-restraints excluded: chain p residue 127 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 78 THR Chi-restraints excluded: chain q residue 87 ASN Chi-restraints excluded: chain q residue 88 LEU Chi-restraints excluded: chain q residue 160 LEU Chi-restraints excluded: chain q residue 164 LEU Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 58 LEU Chi-restraints excluded: chain r residue 63 CYS Chi-restraints excluded: chain r residue 100 MET Chi-restraints excluded: chain r residue 132 SER Chi-restraints excluded: chain r residue 139 MET Chi-restraints excluded: chain r residue 148 GLU Chi-restraints excluded: chain r residue 175 ASN Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 200 SER Chi-restraints excluded: chain s residue 13 LEU Chi-restraints excluded: chain s residue 27 THR Chi-restraints excluded: chain s residue 39 ASP Chi-restraints excluded: chain s residue 54 CYS Chi-restraints excluded: chain s residue 84 THR Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 127 VAL Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain s residue 191 ASP Chi-restraints excluded: chain s residue 207 THR Chi-restraints excluded: chain t residue 25 ASP Chi-restraints excluded: chain t residue 49 THR Chi-restraints excluded: chain t residue 117 ASP Chi-restraints excluded: chain t residue 175 VAL Chi-restraints excluded: chain t residue 179 ARG Chi-restraints excluded: chain t residue 200 GLU Chi-restraints excluded: chain t residue 205 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 534 optimal weight: 9.9990 chunk 563 optimal weight: 10.0000 chunk 513 optimal weight: 0.9990 chunk 547 optimal weight: 2.9990 chunk 329 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 430 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 495 optimal weight: 3.9990 chunk 518 optimal weight: 4.9990 chunk 545 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 75 ASN H 166 ASN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 ASN ** O 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 HIS S 160 ASN ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 23 GLN ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 48137 Z= 0.200 Angle : 0.635 12.337 65219 Z= 0.331 Chirality : 0.045 0.290 7399 Planarity : 0.004 0.066 8467 Dihedral : 5.465 71.870 6812 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.47 % Allowed : 20.62 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.77 (0.11), residues: 6155 helix: 1.20 (0.11), residues: 2238 sheet: -0.53 (0.14), residues: 1331 loop : -2.09 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP m 215 HIS 0.009 0.001 HIS L 65 PHE 0.024 0.001 PHE k 22 TYR 0.027 0.001 TYR I 19 ARG 0.005 0.000 ARG N 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 662 time to evaluate : 4.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 19 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7899 (pp20) REVERT: G 21 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6058 (ttt180) REVERT: I 10 THR cc_start: 0.6080 (OUTLIER) cc_final: 0.5560 (p) REVERT: I 48 GLU cc_start: 0.7693 (tt0) cc_final: 0.6673 (tm-30) REVERT: I 114 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8380 (tp) REVERT: I 174 MET cc_start: 0.7536 (mtp) cc_final: 0.7308 (mtp) REVERT: J 20 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7842 (tm-30) REVERT: J 21 TYR cc_start: 0.7738 (m-80) cc_final: 0.7304 (m-80) REVERT: J 38 ARG cc_start: 0.7429 (tpt170) cc_final: 0.6614 (mmp80) REVERT: J 105 GLU cc_start: 0.7948 (tp30) cc_final: 0.7641 (tp30) REVERT: J 146 GLN cc_start: 0.7648 (pt0) cc_final: 0.7322 (pt0) REVERT: J 231 GLU cc_start: 0.7547 (pt0) cc_final: 0.7002 (pp20) REVERT: K 71 ASP cc_start: 0.8066 (m-30) cc_final: 0.7650 (m-30) REVERT: K 79 SER cc_start: 0.6966 (OUTLIER) cc_final: 0.6700 (p) REVERT: K 219 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7942 (t) REVERT: L 6 TYR cc_start: 0.7724 (m-80) cc_final: 0.7204 (m-80) REVERT: L 123 TYR cc_start: 0.8221 (t80) cc_final: 0.7925 (t80) REVERT: L 176 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8377 (ttt) REVERT: L 178 GLU cc_start: 0.8732 (mp0) cc_final: 0.8501 (mp0) REVERT: M 85 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7347 (mtm-85) REVERT: M 135 PHE cc_start: 0.8215 (p90) cc_final: 0.8006 (p90) REVERT: M 136 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.6487 (mpp) REVERT: M 150 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.6707 (tpt) REVERT: M 161 TRP cc_start: 0.8029 (OUTLIER) cc_final: 0.5720 (m-90) REVERT: M 169 ARG cc_start: 0.8551 (ttp80) cc_final: 0.8030 (ttp80) REVERT: M 184 MET cc_start: 0.6662 (ptp) cc_final: 0.6373 (ptp) REVERT: M 188 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8168 (p0) REVERT: M 191 LYS cc_start: 0.8606 (pttp) cc_final: 0.8109 (mtpt) REVERT: M 226 ILE cc_start: 0.8893 (pt) cc_final: 0.8643 (mp) REVERT: M 241 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7529 (tm-30) REVERT: N 57 ASP cc_start: 0.8504 (m-30) cc_final: 0.7899 (t0) REVERT: O 86 MET cc_start: 0.8809 (tmm) cc_final: 0.8079 (tmm) REVERT: O 167 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7294 (mm) REVERT: O 172 ASN cc_start: 0.6497 (OUTLIER) cc_final: 0.6031 (m-40) REVERT: P 14 MET cc_start: 0.8088 (ttm) cc_final: 0.7606 (ttm) REVERT: P 59 ASP cc_start: 0.8176 (m-30) cc_final: 0.7808 (m-30) REVERT: P 86 THR cc_start: 0.9043 (m) cc_final: 0.8785 (p) REVERT: P 88 MET cc_start: 0.8645 (ttp) cc_final: 0.8249 (ttp) REVERT: P 89 SER cc_start: 0.8450 (m) cc_final: 0.8040 (t) REVERT: P 122 CYS cc_start: 0.7639 (p) cc_final: 0.7188 (p) REVERT: P 135 ASP cc_start: 0.7783 (p0) cc_final: 0.7337 (p0) REVERT: P 200 LEU cc_start: 0.7646 (mp) cc_final: 0.7254 (mp) REVERT: Q 38 MET cc_start: 0.8667 (mmp) cc_final: 0.8433 (mmp) REVERT: Q 69 MET cc_start: 0.8613 (mmm) cc_final: 0.8350 (mmp) REVERT: Q 118 MET cc_start: 0.9027 (tpp) cc_final: 0.8579 (tpp) REVERT: Q 162 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6444 (ttpt) REVERT: Q 174 ASN cc_start: 0.8337 (t0) cc_final: 0.8033 (t0) REVERT: R 32 LYS cc_start: 0.8956 (mtpt) cc_final: 0.8263 (mmtm) REVERT: R 36 GLU cc_start: 0.7963 (mp0) cc_final: 0.7621 (mp0) REVERT: R 72 GLU cc_start: 0.7729 (tt0) cc_final: 0.7519 (pp20) REVERT: R 90 TYR cc_start: 0.8740 (m-80) cc_final: 0.8248 (m-80) REVERT: R 117 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7869 (mp0) REVERT: R 175 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7607 (p0) REVERT: S 76 LYS cc_start: 0.8516 (tttm) cc_final: 0.8067 (tptt) REVERT: S 136 LYS cc_start: 0.8797 (mmmm) cc_final: 0.8509 (tptt) REVERT: S 162 GLU cc_start: 0.8419 (pm20) cc_final: 0.8056 (tp30) REVERT: T 26 MET cc_start: 0.7467 (mtp) cc_final: 0.7026 (mtp) REVERT: T 50 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7912 (ptp) REVERT: T 108 ASN cc_start: 0.8126 (t0) cc_final: 0.7783 (t0) REVERT: T 110 MET cc_start: 0.8177 (mtp) cc_final: 0.7920 (mmm) REVERT: T 126 ASP cc_start: 0.8477 (t0) cc_final: 0.7573 (p0) REVERT: T 127 MET cc_start: 0.7887 (ttp) cc_final: 0.7288 (ttm) REVERT: T 173 MET cc_start: 0.8500 (mmm) cc_final: 0.8040 (tpp) REVERT: T 179 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5814 (pmt100) REVERT: T 180 ASP cc_start: 0.7897 (t0) cc_final: 0.7563 (t0) REVERT: T 210 ASP cc_start: 0.8177 (m-30) cc_final: 0.7841 (t0) REVERT: g 24 GLN cc_start: 0.6156 (mm-40) cc_final: 0.5822 (mm-40) REVERT: g 69 LEU cc_start: 0.8572 (mm) cc_final: 0.8276 (tp) REVERT: g 73 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.7999 (p) REVERT: g 80 MET cc_start: 0.7605 (mmm) cc_final: 0.7161 (mmm) REVERT: g 131 MET cc_start: 0.7085 (mtp) cc_final: 0.6628 (mtt) REVERT: g 138 MET cc_start: 0.8692 (ttm) cc_final: 0.8225 (ttp) REVERT: g 172 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7277 (pm20) REVERT: g 180 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7828 (tm-30) REVERT: g 206 LEU cc_start: 0.7684 (mp) cc_final: 0.7174 (tp) REVERT: g 215 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8409 (mt) REVERT: h 39 LYS cc_start: 0.8155 (tmtt) cc_final: 0.7749 (ttpp) REVERT: h 51 LYS cc_start: 0.7251 (mttt) cc_final: 0.6359 (mttt) REVERT: h 79 MET cc_start: 0.1024 (mmt) cc_final: 0.0486 (mtp) REVERT: h 109 GLN cc_start: 0.8330 (mm110) cc_final: 0.7843 (mt0) REVERT: h 119 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8195 (tm-30) REVERT: h 181 ASP cc_start: 0.8143 (p0) cc_final: 0.7888 (t70) REVERT: h 182 LEU cc_start: 0.7600 (mt) cc_final: 0.6901 (pt) REVERT: h 183 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7725 (tp30) REVERT: h 207 ASN cc_start: 0.7982 (m-40) cc_final: 0.7542 (t0) REVERT: i 151 ASP cc_start: 0.7975 (m-30) cc_final: 0.7747 (m-30) REVERT: i 174 MET cc_start: 0.8509 (ttm) cc_final: 0.7921 (mmm) REVERT: i 209 GLU cc_start: 0.8829 (mp0) cc_final: 0.8593 (mp0) REVERT: i 228 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8518 (pt) REVERT: i 249 ARG cc_start: 0.7411 (tpm170) cc_final: 0.7208 (tpm170) REVERT: j 17 PHE cc_start: 0.6866 (t80) cc_final: 0.6173 (t80) REVERT: j 23 GLN cc_start: 0.7592 (mt0) cc_final: 0.7188 (mm-40) REVERT: j 30 SER cc_start: 0.7281 (m) cc_final: 0.6882 (t) REVERT: j 31 THR cc_start: 0.7111 (OUTLIER) cc_final: 0.6866 (m) REVERT: j 118 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.6035 (t80) REVERT: j 161 ILE cc_start: 0.5875 (OUTLIER) cc_final: 0.5078 (pp) REVERT: k 59 MET cc_start: 0.7796 (mtt) cc_final: 0.7333 (mtm) REVERT: k 69 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: k 148 GLU cc_start: 0.6829 (mp0) cc_final: 0.6480 (pm20) REVERT: l 6 TYR cc_start: 0.5059 (p90) cc_final: 0.4784 (p90) REVERT: l 12 VAL cc_start: 0.8840 (t) cc_final: 0.8640 (p) REVERT: l 61 LYS cc_start: 0.7983 (pttm) cc_final: 0.7337 (mmmm) REVERT: l 154 PHE cc_start: 0.7653 (m-10) cc_final: 0.7374 (m-10) REVERT: m 114 ARG cc_start: 0.7961 (mmm160) cc_final: 0.7500 (mmt180) REVERT: m 136 MET cc_start: 0.8209 (mtt) cc_final: 0.7904 (mtt) REVERT: m 184 MET cc_start: 0.8184 (ptp) cc_final: 0.7709 (ptp) REVERT: n 62 GLN cc_start: 0.8765 (mt0) cc_final: 0.8408 (tp40) REVERT: n 69 GLU cc_start: 0.8248 (tm-30) cc_final: 0.8034 (tm-30) REVERT: n 87 CYS cc_start: 0.8614 (t) cc_final: 0.8405 (t) REVERT: o 24 MET cc_start: 0.8564 (tpp) cc_final: 0.8353 (tpp) REVERT: o 127 MET cc_start: 0.7198 (mtp) cc_final: 0.6831 (mtm) REVERT: o 135 MET cc_start: 0.7320 (tpp) cc_final: 0.6739 (tpp) REVERT: o 165 ASN cc_start: 0.8006 (t0) cc_final: 0.7485 (m110) REVERT: o 167 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6778 (tp) REVERT: o 182 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8055 (pptt) REVERT: o 184 ASP cc_start: 0.7238 (m-30) cc_final: 0.6182 (p0) REVERT: o 202 TYR cc_start: 0.6986 (m-80) cc_final: 0.6726 (m-80) REVERT: p 203 ARG cc_start: 0.8075 (mtp85) cc_final: 0.7694 (ttm170) REVERT: q 20 VAL cc_start: 0.8733 (t) cc_final: 0.8385 (m) REVERT: q 165 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6913 (mm-30) REVERT: r 45 MET cc_start: 0.7340 (ttm) cc_final: 0.7066 (mtp) REVERT: r 89 GLN cc_start: 0.8739 (mt0) cc_final: 0.8479 (mp10) REVERT: r 97 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8288 (ppp) REVERT: r 132 SER cc_start: 0.7597 (OUTLIER) cc_final: 0.6551 (t) REVERT: r 148 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7265 (tp30) REVERT: r 153 TYR cc_start: 0.8540 (m-10) cc_final: 0.8285 (m-80) REVERT: s 72 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8567 (mp) REVERT: s 115 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7776 (pp20) REVERT: s 116 GLU cc_start: 0.7895 (mp0) cc_final: 0.7556 (mp0) REVERT: s 159 GLN cc_start: 0.7713 (tp-100) cc_final: 0.7254 (mt0) REVERT: s 205 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7568 (mt-10) REVERT: t 157 GLN cc_start: 0.7775 (tt0) cc_final: 0.7463 (tp-100) REVERT: t 173 MET cc_start: 0.8609 (mmm) cc_final: 0.8176 (mmm) REVERT: t 180 ASP cc_start: 0.7265 (t0) cc_final: 0.6902 (t0) outliers start: 218 outliers final: 171 residues processed: 826 average time/residue: 0.4596 time to fit residues: 638.6028 Evaluate side-chains 821 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 620 time to evaluate : 4.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 214 ASN Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 19 TYR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 202 ASP Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 123 PHE Chi-restraints excluded: chain K residue 162 PHE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 14 PHE Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 122 TYR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 161 TRP Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 198 TYR Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 229 LYS Chi-restraints excluded: chain M residue 231 ILE Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 134 TYR Chi-restraints excluded: chain N residue 138 TYR Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 24 MET Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain O residue 172 ASN Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain P residue 76 LEU Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 162 LYS Chi-restraints excluded: chain Q residue 186 ASN Chi-restraints excluded: chain R residue 63 CYS Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 182 ASP Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain T residue 5 MET Chi-restraints excluded: chain T residue 50 MET Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 179 ARG Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 78 CYS Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain g residue 125 TYR Chi-restraints excluded: chain g residue 172 GLN Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 210 PHE Chi-restraints excluded: chain g residue 215 ILE Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain h residue 42 ASN Chi-restraints excluded: chain h residue 85 VAL Chi-restraints excluded: chain h residue 174 LEU Chi-restraints excluded: chain h residue 212 ILE Chi-restraints excluded: chain i residue 59 VAL Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 134 LEU Chi-restraints excluded: chain i residue 149 GLN Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 118 TYR Chi-restraints excluded: chain j residue 161 ILE Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain j residue 177 THR Chi-restraints excluded: chain k residue 47 CYS Chi-restraints excluded: chain k residue 69 GLU Chi-restraints excluded: chain k residue 84 ASP Chi-restraints excluded: chain k residue 107 MET Chi-restraints excluded: chain k residue 109 VAL Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain k residue 162 PHE Chi-restraints excluded: chain k residue 163 VAL Chi-restraints excluded: chain k residue 202 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 88 MET Chi-restraints excluded: chain l residue 94 ASP Chi-restraints excluded: chain l residue 179 PHE Chi-restraints excluded: chain l residue 202 GLU Chi-restraints excluded: chain l residue 222 THR Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 128 VAL Chi-restraints excluded: chain m residue 175 GLU Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain m residue 211 LEU Chi-restraints excluded: chain m residue 213 LEU Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 24 SER Chi-restraints excluded: chain n residue 51 ASP Chi-restraints excluded: chain n residue 134 TYR Chi-restraints excluded: chain n residue 140 ASP Chi-restraints excluded: chain n residue 173 VAL Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 25 VAL Chi-restraints excluded: chain o residue 44 CYS Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 167 LEU Chi-restraints excluded: chain o residue 197 THR Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain p residue 116 THR Chi-restraints excluded: chain p residue 127 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 78 THR Chi-restraints excluded: chain q residue 87 ASN Chi-restraints excluded: chain q residue 88 LEU Chi-restraints excluded: chain q residue 160 LEU Chi-restraints excluded: chain q residue 164 LEU Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 58 LEU Chi-restraints excluded: chain r residue 63 CYS Chi-restraints excluded: chain r residue 97 MET Chi-restraints excluded: chain r residue 100 MET Chi-restraints excluded: chain r residue 132 SER Chi-restraints excluded: chain r residue 139 MET Chi-restraints excluded: chain r residue 148 GLU Chi-restraints excluded: chain r residue 175 ASN Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 200 SER Chi-restraints excluded: chain s residue 13 LEU Chi-restraints excluded: chain s residue 27 THR Chi-restraints excluded: chain s residue 54 CYS Chi-restraints excluded: chain s residue 72 LEU Chi-restraints excluded: chain s residue 84 THR Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 127 VAL Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain s residue 191 ASP Chi-restraints excluded: chain s residue 207 THR Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain t residue 25 ASP Chi-restraints excluded: chain t residue 49 THR Chi-restraints excluded: chain t residue 117 ASP Chi-restraints excluded: chain t residue 175 VAL Chi-restraints excluded: chain t residue 179 ARG Chi-restraints excluded: chain t residue 200 GLU Chi-restraints excluded: chain t residue 205 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 359 optimal weight: 10.0000 chunk 579 optimal weight: 10.0000 chunk 353 optimal weight: 0.0270 chunk 274 optimal weight: 1.9990 chunk 402 optimal weight: 8.9990 chunk 607 optimal weight: 10.0000 chunk 559 optimal weight: 10.0000 chunk 483 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 373 optimal weight: 8.9990 chunk 296 optimal weight: 7.9990 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 166 ASN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 HIS ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 127 GLN ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 48137 Z= 0.285 Angle : 0.681 12.454 65219 Z= 0.354 Chirality : 0.046 0.316 7399 Planarity : 0.005 0.097 8467 Dihedral : 5.562 72.293 6812 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.47 % Allowed : 20.58 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.86 (0.11), residues: 6155 helix: 1.13 (0.11), residues: 2237 sheet: -0.58 (0.14), residues: 1349 loop : -2.15 (0.12), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 189 HIS 0.008 0.001 HIS L 65 PHE 0.028 0.002 PHE G 163 TYR 0.027 0.002 TYR I 19 ARG 0.013 0.001 ARG h 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12310 Ramachandran restraints generated. 6155 Oldfield, 0 Emsley, 6155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 624 time to evaluate : 4.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 19 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7698 (pp20) REVERT: G 21 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6063 (ttt180) REVERT: G 128 ASN cc_start: 0.7565 (t0) cc_final: 0.6480 (p0) REVERT: I 10 THR cc_start: 0.6127 (OUTLIER) cc_final: 0.5599 (p) REVERT: I 48 GLU cc_start: 0.7662 (tt0) cc_final: 0.6631 (tm-30) REVERT: I 114 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8427 (tp) REVERT: I 174 MET cc_start: 0.7532 (mtp) cc_final: 0.7296 (mtp) REVERT: J 20 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7884 (tm-30) REVERT: J 38 ARG cc_start: 0.7436 (tpt170) cc_final: 0.6618 (mmp80) REVERT: J 105 GLU cc_start: 0.8000 (tp30) cc_final: 0.7595 (tp30) REVERT: J 238 GLU cc_start: 0.3747 (OUTLIER) cc_final: 0.3500 (pt0) REVERT: K 71 ASP cc_start: 0.7984 (m-30) cc_final: 0.7563 (m-30) REVERT: K 78 MET cc_start: 0.7400 (ttp) cc_final: 0.7144 (ttm) REVERT: K 79 SER cc_start: 0.7018 (OUTLIER) cc_final: 0.6715 (p) REVERT: K 219 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7813 (t) REVERT: L 6 TYR cc_start: 0.7769 (m-80) cc_final: 0.7269 (m-80) REVERT: L 123 TYR cc_start: 0.8219 (t80) cc_final: 0.7900 (t80) REVERT: L 176 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8408 (ttt) REVERT: L 178 GLU cc_start: 0.8721 (mp0) cc_final: 0.8477 (mp0) REVERT: M 75 MET cc_start: 0.8741 (ptp) cc_final: 0.8480 (ptp) REVERT: M 85 ARG cc_start: 0.7711 (ttm-80) cc_final: 0.7437 (mtm-85) REVERT: M 136 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.6437 (mpp) REVERT: M 150 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.6647 (tpt) REVERT: M 161 TRP cc_start: 0.8037 (OUTLIER) cc_final: 0.5715 (m-90) REVERT: M 169 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8081 (ttp80) REVERT: M 191 LYS cc_start: 0.8590 (pttp) cc_final: 0.8138 (mtpt) REVERT: M 226 ILE cc_start: 0.8903 (pt) cc_final: 0.8662 (mp) REVERT: M 241 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7528 (tm-30) REVERT: N 57 ASP cc_start: 0.8509 (m-30) cc_final: 0.7846 (t0) REVERT: O 86 MET cc_start: 0.8786 (tmm) cc_final: 0.8095 (tmm) REVERT: O 167 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7393 (mm) REVERT: O 172 ASN cc_start: 0.6801 (OUTLIER) cc_final: 0.6082 (m-40) REVERT: P 14 MET cc_start: 0.8115 (ttm) cc_final: 0.7569 (ttm) REVERT: P 59 ASP cc_start: 0.8207 (m-30) cc_final: 0.7851 (m-30) REVERT: P 86 THR cc_start: 0.9078 (m) cc_final: 0.8841 (p) REVERT: P 88 MET cc_start: 0.8658 (ttp) cc_final: 0.8274 (ttp) REVERT: P 89 SER cc_start: 0.8445 (m) cc_final: 0.8037 (t) REVERT: P 122 CYS cc_start: 0.7695 (p) cc_final: 0.7217 (p) REVERT: P 135 ASP cc_start: 0.7838 (p0) cc_final: 0.7276 (p0) REVERT: P 200 LEU cc_start: 0.7677 (mp) cc_final: 0.7258 (mp) REVERT: Q 38 MET cc_start: 0.8666 (mmp) cc_final: 0.8430 (mmp) REVERT: Q 69 MET cc_start: 0.8651 (mmm) cc_final: 0.8380 (mmp) REVERT: Q 174 ASN cc_start: 0.8326 (t0) cc_final: 0.8016 (t0) REVERT: R 32 LYS cc_start: 0.9005 (mtpt) cc_final: 0.8615 (mmtm) REVERT: R 36 GLU cc_start: 0.7932 (mp0) cc_final: 0.7587 (mp0) REVERT: R 45 MET cc_start: 0.7348 (mtp) cc_final: 0.6040 (ppp) REVERT: R 72 GLU cc_start: 0.7759 (tt0) cc_final: 0.7500 (pp20) REVERT: R 90 TYR cc_start: 0.8673 (m-80) cc_final: 0.8210 (m-80) REVERT: R 117 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7884 (mp0) REVERT: R 175 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7599 (p0) REVERT: S 76 LYS cc_start: 0.8547 (tttm) cc_final: 0.8171 (tttt) REVERT: S 136 LYS cc_start: 0.8792 (mmmm) cc_final: 0.8488 (tptt) REVERT: S 162 GLU cc_start: 0.8411 (pm20) cc_final: 0.8057 (tp30) REVERT: T 26 MET cc_start: 0.7476 (mtp) cc_final: 0.6994 (mtp) REVERT: T 108 ASN cc_start: 0.8069 (t0) cc_final: 0.7532 (t0) REVERT: T 110 MET cc_start: 0.8241 (mtp) cc_final: 0.7669 (mmm) REVERT: T 126 ASP cc_start: 0.8478 (t0) cc_final: 0.7602 (p0) REVERT: T 127 MET cc_start: 0.7910 (ttp) cc_final: 0.7308 (ttm) REVERT: T 173 MET cc_start: 0.8528 (mmm) cc_final: 0.8076 (tpp) REVERT: T 179 ARG cc_start: 0.6361 (OUTLIER) cc_final: 0.5837 (pmt100) REVERT: T 180 ASP cc_start: 0.7939 (t0) cc_final: 0.7629 (t0) REVERT: T 210 ASP cc_start: 0.8220 (m-30) cc_final: 0.7882 (t0) REVERT: g 24 GLN cc_start: 0.6137 (mm-40) cc_final: 0.5792 (mm-40) REVERT: g 73 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.7942 (p) REVERT: g 83 MET cc_start: 0.8174 (mtm) cc_final: 0.7712 (mpp) REVERT: g 131 MET cc_start: 0.7129 (mtp) cc_final: 0.6609 (mtt) REVERT: g 138 MET cc_start: 0.8687 (ttm) cc_final: 0.8091 (ttp) REVERT: g 172 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7219 (pm20) REVERT: g 180 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7769 (tm-30) REVERT: g 206 LEU cc_start: 0.7753 (mp) cc_final: 0.7281 (tp) REVERT: g 215 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8363 (mt) REVERT: h 39 LYS cc_start: 0.8157 (tmtt) cc_final: 0.7763 (ttpp) REVERT: h 51 LYS cc_start: 0.7269 (mttt) cc_final: 0.7017 (mttt) REVERT: h 79 MET cc_start: 0.1274 (OUTLIER) cc_final: 0.0683 (mtp) REVERT: h 109 GLN cc_start: 0.8314 (mm110) cc_final: 0.7874 (mt0) REVERT: h 119 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8177 (tm-30) REVERT: h 181 ASP cc_start: 0.8132 (p0) cc_final: 0.7916 (t70) REVERT: h 182 LEU cc_start: 0.7599 (mt) cc_final: 0.6891 (pt) REVERT: h 183 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7726 (tp30) REVERT: h 207 ASN cc_start: 0.8064 (m-40) cc_final: 0.7706 (t0) REVERT: i 72 MET cc_start: 0.7797 (mtp) cc_final: 0.7431 (tpp) REVERT: i 151 ASP cc_start: 0.7993 (m-30) cc_final: 0.7778 (m-30) REVERT: i 174 MET cc_start: 0.8526 (ttm) cc_final: 0.8003 (mmm) REVERT: i 209 GLU cc_start: 0.8827 (mp0) cc_final: 0.8593 (mp0) REVERT: i 228 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8480 (pt) REVERT: j 17 PHE cc_start: 0.6854 (t80) cc_final: 0.6177 (t80) REVERT: j 23 GLN cc_start: 0.7630 (mt0) cc_final: 0.7204 (mm-40) REVERT: j 30 SER cc_start: 0.7360 (m) cc_final: 0.6938 (t) REVERT: j 31 THR cc_start: 0.7109 (OUTLIER) cc_final: 0.6693 (m) REVERT: j 71 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7773 (ptm) REVERT: j 118 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.6057 (t80) REVERT: j 161 ILE cc_start: 0.5978 (OUTLIER) cc_final: 0.5168 (pp) REVERT: k 29 GLU cc_start: 0.8086 (tp30) cc_final: 0.7473 (tt0) REVERT: k 59 MET cc_start: 0.7826 (mtt) cc_final: 0.7350 (mtm) REVERT: k 69 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7605 (mm-30) REVERT: k 148 GLU cc_start: 0.6793 (mp0) cc_final: 0.6486 (pm20) REVERT: l 6 TYR cc_start: 0.5098 (p90) cc_final: 0.4821 (p90) REVERT: l 12 VAL cc_start: 0.8850 (t) cc_final: 0.8644 (p) REVERT: l 61 LYS cc_start: 0.7955 (pttm) cc_final: 0.7343 (mmmm) REVERT: l 154 PHE cc_start: 0.7764 (m-10) cc_final: 0.7474 (m-10) REVERT: m 114 ARG cc_start: 0.7963 (mmm160) cc_final: 0.7456 (mmt180) REVERT: m 136 MET cc_start: 0.8241 (mtt) cc_final: 0.7937 (mtt) REVERT: m 184 MET cc_start: 0.8140 (ptp) cc_final: 0.7467 (ptp) REVERT: n 62 GLN cc_start: 0.8773 (mt0) cc_final: 0.8407 (tp40) REVERT: n 69 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8056 (tm-30) REVERT: n 87 CYS cc_start: 0.8565 (t) cc_final: 0.8346 (t) REVERT: o 24 MET cc_start: 0.8523 (tpp) cc_final: 0.7980 (mmt) REVERT: o 127 MET cc_start: 0.7259 (mtp) cc_final: 0.6903 (mtm) REVERT: o 135 MET cc_start: 0.7307 (tpp) cc_final: 0.6724 (tpp) REVERT: o 150 GLU cc_start: 0.8968 (tt0) cc_final: 0.8707 (tt0) REVERT: o 165 ASN cc_start: 0.7956 (t0) cc_final: 0.7504 (m110) REVERT: o 167 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6787 (tp) REVERT: o 182 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8100 (pptt) REVERT: o 184 ASP cc_start: 0.7287 (m-30) cc_final: 0.6238 (p0) REVERT: o 202 TYR cc_start: 0.7053 (m-80) cc_final: 0.6797 (m-80) REVERT: p 203 ARG cc_start: 0.8047 (mtp85) cc_final: 0.7278 (ttt180) REVERT: q 20 VAL cc_start: 0.8723 (t) cc_final: 0.8370 (m) REVERT: q 137 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8673 (m-10) REVERT: r 45 MET cc_start: 0.7380 (ttm) cc_final: 0.7057 (mtp) REVERT: r 89 GLN cc_start: 0.8719 (mt0) cc_final: 0.8441 (mp10) REVERT: r 97 MET cc_start: 0.8660 (tmm) cc_final: 0.7972 (ppp) REVERT: r 132 SER cc_start: 0.7742 (OUTLIER) cc_final: 0.6710 (t) REVERT: r 148 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7253 (tp30) REVERT: r 153 TYR cc_start: 0.8532 (m-10) cc_final: 0.8252 (m-80) REVERT: s 72 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8544 (mp) REVERT: s 115 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7803 (pp20) REVERT: s 116 GLU cc_start: 0.7933 (mp0) cc_final: 0.7559 (mp0) REVERT: s 159 GLN cc_start: 0.7821 (tp-100) cc_final: 0.7081 (pt0) REVERT: s 205 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7582 (mt-10) REVERT: t 157 GLN cc_start: 0.7789 (tt0) cc_final: 0.7503 (tp40) REVERT: t 173 MET cc_start: 0.8592 (mmm) cc_final: 0.8167 (mmm) REVERT: t 180 ASP cc_start: 0.7395 (t0) cc_final: 0.7036 (t0) outliers start: 218 outliers final: 180 residues processed: 791 average time/residue: 0.4541 time to fit residues: 606.4918 Evaluate side-chains 821 residues out of total 5169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 611 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 214 ASN Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 19 TYR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 202 ASP Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 238 GLU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 123 PHE Chi-restraints excluded: chain K residue 162 PHE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 14 PHE Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 161 TRP Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 198 TYR Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 229 LYS Chi-restraints excluded: chain M residue 231 ILE Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 134 TYR Chi-restraints excluded: chain N residue 138 TYR Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 24 MET Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain O residue 172 ASN Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain P residue 76 LEU Chi-restraints excluded: chain P residue 189 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 182 ILE Chi-restraints excluded: chain Q residue 186 ASN Chi-restraints excluded: chain R residue 63 CYS Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 182 ASP Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain T residue 5 MET Chi-restraints excluded: chain T residue 49 THR Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 179 ARG Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 78 CYS Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain g residue 172 GLN Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 210 PHE Chi-restraints excluded: chain g residue 215 ILE Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain h residue 42 ASN Chi-restraints excluded: chain h residue 79 MET Chi-restraints excluded: chain h residue 85 VAL Chi-restraints excluded: chain h residue 174 LEU Chi-restraints excluded: chain h residue 212 ILE Chi-restraints excluded: chain i residue 59 VAL Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 134 LEU Chi-restraints excluded: chain i residue 149 GLN Chi-restraints excluded: chain i residue 228 LEU Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 71 MET Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 118 TYR Chi-restraints excluded: chain j residue 161 ILE Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain j residue 177 THR Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 47 CYS Chi-restraints excluded: chain k residue 68 VAL Chi-restraints excluded: chain k residue 69 GLU Chi-restraints excluded: chain k residue 84 ASP Chi-restraints excluded: chain k residue 107 MET Chi-restraints excluded: chain k residue 109 VAL Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain k residue 162 PHE Chi-restraints excluded: chain k residue 163 VAL Chi-restraints excluded: chain k residue 202 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 88 MET Chi-restraints excluded: chain l residue 94 ASP Chi-restraints excluded: chain l residue 179 PHE Chi-restraints excluded: chain l residue 202 GLU Chi-restraints excluded: chain l residue 222 THR Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 128 VAL Chi-restraints excluded: chain m residue 175 GLU Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain m residue 211 LEU Chi-restraints excluded: chain m residue 213 LEU Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 24 SER Chi-restraints excluded: chain n residue 51 ASP Chi-restraints excluded: chain n residue 134 TYR Chi-restraints excluded: chain n residue 140 ASP Chi-restraints excluded: chain n residue 173 VAL Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 25 VAL Chi-restraints excluded: chain o residue 44 CYS Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 167 LEU Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain o residue 197 THR Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain p residue 116 THR Chi-restraints excluded: chain p residue 127 ILE Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 78 THR Chi-restraints excluded: chain q residue 87 ASN Chi-restraints excluded: chain q residue 88 LEU Chi-restraints excluded: chain q residue 137 PHE Chi-restraints excluded: chain q residue 160 LEU Chi-restraints excluded: chain q residue 164 LEU Chi-restraints excluded: chain q residue 190 ASP Chi-restraints excluded: chain r residue 37 ILE Chi-restraints excluded: chain r residue 58 LEU Chi-restraints excluded: chain r residue 63 CYS Chi-restraints excluded: chain r residue 100 MET Chi-restraints excluded: chain r residue 132 SER Chi-restraints excluded: chain r residue 139 MET Chi-restraints excluded: chain r residue 148 GLU Chi-restraints excluded: chain r residue 175 ASN Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 200 SER Chi-restraints excluded: chain s residue 13 LEU Chi-restraints excluded: chain s residue 27 THR Chi-restraints excluded: chain s residue 54 CYS Chi-restraints excluded: chain s residue 72 LEU Chi-restraints excluded: chain s residue 84 THR Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 127 VAL Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain s residue 191 ASP Chi-restraints excluded: chain s residue 207 THR Chi-restraints excluded: chain t residue 25 ASP Chi-restraints excluded: chain t residue 49 THR Chi-restraints excluded: chain t residue 117 ASP Chi-restraints excluded: chain t residue 175 VAL Chi-restraints excluded: chain t residue 179 ARG Chi-restraints excluded: chain t residue 200 GLU Chi-restraints excluded: chain t residue 205 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 384 optimal weight: 3.9990 chunk 515 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 446 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 134 optimal weight: 0.0770 chunk 484 optimal weight: 9.9990 chunk 202 optimal weight: 4.9990 chunk 497 optimal weight: 4.9990 chunk 61 optimal weight: 0.0980 chunk 89 optimal weight: 5.9990 overall best weight: 2.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 166 ASN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 HIS ** k 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.089232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.079999 restraints weight = 162668.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.081998 restraints weight = 86399.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.083334 restraints weight = 53686.630| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 48137 Z= 0.199 Angle : 0.640 12.458 65219 Z= 0.332 Chirality : 0.045 0.308 7399 Planarity : 0.004 0.066 8467 Dihedral : 5.372 69.721 6812 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.41 % Allowed : 20.83 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.68 (0.11), residues: 6155 helix: 1.30 (0.11), residues: 2244 sheet: -0.47 (0.14), residues: 1337 loop : -2.08 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP m 215 HIS 0.009 0.001 HIS L 65 PHE 0.023 0.001 PHE G 163 TYR 0.029 0.001 TYR i 19 ARG 0.009 0.000 ARG h 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11611.90 seconds wall clock time: 205 minutes 29.08 seconds (12329.08 seconds total)