Starting phenix.real_space_refine on Mon Mar 25 15:03:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td5_10463/03_2024/6td5_10463_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td5_10463/03_2024/6td5_10463.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td5_10463/03_2024/6td5_10463_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td5_10463/03_2024/6td5_10463_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td5_10463/03_2024/6td5_10463_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td5_10463/03_2024/6td5_10463.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td5_10463/03_2024/6td5_10463.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td5_10463/03_2024/6td5_10463_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td5_10463/03_2024/6td5_10463_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 326 5.16 5 B 6 2.79 5 C 31062 2.51 5 N 8518 2.21 5 O 9494 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "F ARG 215": "NH1" <-> "NH2" Residue "F ARG 404": "NH1" <-> "NH2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G ARG 115": "NH1" <-> "NH2" Residue "G ARG 222": "NH1" <-> "NH2" Residue "H ARG 73": "NH1" <-> "NH2" Residue "H ARG 112": "NH1" <-> "NH2" Residue "H TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "I PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 224": "NH1" <-> "NH2" Residue "I ARG 228": "NH1" <-> "NH2" Residue "I ARG 246": "NH1" <-> "NH2" Residue "K ARG 71": "NH1" <-> "NH2" Residue "K ARG 75": "NH1" <-> "NH2" Residue "K ARG 97": "NH1" <-> "NH2" Residue "K ARG 159": "NH1" <-> "NH2" Residue "L PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 168": "NH1" <-> "NH2" Residue "L ARG 243": "NH1" <-> "NH2" Residue "M ARG 225": "NH1" <-> "NH2" Residue "M TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 127": "NH1" <-> "NH2" Residue "a ARG 56": "NH1" <-> "NH2" Residue "a ARG 80": "NH1" <-> "NH2" Residue "a TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 175": "NH1" <-> "NH2" Residue "b ARG 225": "NH1" <-> "NH2" Residue "c ARG 8": "NH1" <-> "NH2" Residue "c ARG 147": "NH1" <-> "NH2" Residue "c ARG 222": "NH1" <-> "NH2" Residue "c ARG 245": "NH1" <-> "NH2" Residue "c ARG 251": "NH1" <-> "NH2" Residue "c ARG 265": "NH1" <-> "NH2" Residue "d ARG 57": "NH1" <-> "NH2" Residue "d ARG 60": "NH1" <-> "NH2" Residue "d ARG 109": "NH1" <-> "NH2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "e ARG 153": "NH1" <-> "NH2" Residue "f ARG 215": "NH1" <-> "NH2" Residue "f ARG 404": "NH1" <-> "NH2" Residue "g ARG 72": "NH1" <-> "NH2" Residue "g ARG 115": "NH1" <-> "NH2" Residue "g ARG 222": "NH1" <-> "NH2" Residue "h ARG 73": "NH1" <-> "NH2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "h TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 61": "NH1" <-> "NH2" Residue "i PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 224": "NH1" <-> "NH2" Residue "i ARG 228": "NH1" <-> "NH2" Residue "i ARG 246": "NH1" <-> "NH2" Residue "k ARG 71": "NH1" <-> "NH2" Residue "k ARG 75": "NH1" <-> "NH2" Residue "k ARG 97": "NH1" <-> "NH2" Residue "k ARG 159": "NH1" <-> "NH2" Residue "l PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 168": "NH1" <-> "NH2" Residue "l ARG 243": "NH1" <-> "NH2" Residue "m ARG 225": "NH1" <-> "NH2" Residue "m TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 127": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49408 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1861 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 12, 'TRANS': 232} Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1753 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "C" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2155 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 11, 'TRANS': 260} Chain: "D" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1882 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 4, 'TRANS': 235} Chain: "E" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1802 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain: "F" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "G" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1741 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 7, 'TRANS': 222} Chain: "H" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1709 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "I" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "J" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "K" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "L" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1573 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "M" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "N" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "a" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1861 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 12, 'TRANS': 232} Chain: "b" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1753 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "c" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2155 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 11, 'TRANS': 260} Chain: "d" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1882 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 4, 'TRANS': 235} Chain: "e" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1802 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain: "f" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "g" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1741 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 7, 'TRANS': 222} Chain: "h" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1709 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "i" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "j" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "k" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "l" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1573 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "m" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "n" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'BO2': 1, 'N2E': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'BO2': 1, 'N2E': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 24.53, per 1000 atoms: 0.50 Number of scatterers: 49408 At special positions: 0 Unit cell: (138.46, 184.9, 135.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 326 16.00 F 2 9.00 O 9494 8.00 N 8518 7.00 C 31062 6.00 B 6 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.37 Conformation dependent library (CDL) restraints added in 8.7 seconds 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11716 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 150 helices and 75 sheets defined 31.9% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.37 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 removed outlier: 3.627A pdb=" N ALA A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 28 " --> pdb=" O TYR A 24 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 102 removed outlier: 3.523A pdb=" N ARG A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 removed outlier: 3.677A pdb=" N LYS A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 119 " --> pdb=" O MET A 115 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 195 through 210 removed outlier: 3.584A pdb=" N MET A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 removed outlier: 3.511A pdb=" N GLU A 240 " --> pdb=" O ASN A 236 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 28 removed outlier: 3.529A pdb=" N THR B 25 " --> pdb=" O GLU B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 99 removed outlier: 3.505A pdb=" N ARG B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 96 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 removed outlier: 3.619A pdb=" N ILE B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 175 removed outlier: 3.769A pdb=" N PHE B 171 " --> pdb=" O ASP B 167 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 189 Processing helix chain 'B' and resid 191 through 196 removed outlier: 3.800A pdb=" N GLU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 191 through 196' Processing helix chain 'B' and resid 221 through 228 removed outlier: 3.900A pdb=" N TYR B 227 " --> pdb=" O GLN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 19 through 29 Processing helix chain 'C' and resid 86 through 107 removed outlier: 4.113A pdb=" N TYR C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 129 removed outlier: 3.512A pdb=" N CYS C 121 " --> pdb=" O CYS C 117 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU C 123 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN C 129 " --> pdb=" O GLN C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 183 removed outlier: 3.930A pdb=" N ALA C 179 " --> pdb=" O GLN C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 205 removed outlier: 3.541A pdb=" N LYS C 204 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR C 205 " --> pdb=" O VAL C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 267 Proline residue: C 256 - end of helix removed outlier: 4.059A pdb=" N ARG C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 261 " --> pdb=" O HIS C 257 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 27 removed outlier: 3.501A pdb=" N GLU D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 25 " --> pdb=" O TYR D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 96 removed outlier: 3.633A pdb=" N ARG D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.565A pdb=" N THR D 119 " --> pdb=" O GLN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 171 removed outlier: 3.705A pdb=" N ILE D 169 " --> pdb=" O ASP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 193 removed outlier: 3.536A pdb=" N VAL D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 240 removed outlier: 3.678A pdb=" N LYS D 224 " --> pdb=" O GLU D 220 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 227 " --> pdb=" O GLN D 223 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 228 " --> pdb=" O LYS D 224 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D 235 " --> pdb=" O LYS D 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 132 removed outlier: 3.675A pdb=" N GLU E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA E 130 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS E 132 " --> pdb=" O VAL E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 183 through 203 removed outlier: 4.316A pdb=" N ILE E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL E 194 " --> pdb=" O GLU E 190 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 217 Processing helix chain 'E' and resid 272 through 282 removed outlier: 4.443A pdb=" N GLU E 275 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ALA E 276 " --> pdb=" O GLY E 273 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN E 278 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER E 279 " --> pdb=" O ALA E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 304 removed outlier: 3.544A pdb=" N ALA E 298 " --> pdb=" O GLY E 294 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP E 300 " --> pdb=" O THR E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 removed outlier: 4.030A pdb=" N ALA E 337 " --> pdb=" O THR E 333 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE E 338 " --> pdb=" O GLU E 334 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET E 339 " --> pdb=" O ILE E 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 195 removed outlier: 3.928A pdb=" N GLU F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA F 192 " --> pdb=" O TYR F 188 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN F 194 " --> pdb=" O ASN F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 264 removed outlier: 3.808A pdb=" N VAL F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 280 removed outlier: 3.599A pdb=" N ASP F 275 " --> pdb=" O ASN F 271 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY F 278 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU F 279 " --> pdb=" O ASP F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 339 removed outlier: 4.126A pdb=" N ARG F 339 " --> pdb=" O THR F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 343 No H-bonds generated for 'chain 'F' and resid 341 through 343' Processing helix chain 'F' and resid 349 through 363 removed outlier: 3.627A pdb=" N THR F 354 " --> pdb=" O ASP F 350 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER F 362 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA F 363 " --> pdb=" O ALA F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 398 removed outlier: 4.098A pdb=" N LYS F 396 " --> pdb=" O SER F 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 32 removed outlier: 3.622A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 101 removed outlier: 3.857A pdb=" N ALA G 87 " --> pdb=" O PRO G 83 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE G 88 " --> pdb=" O ASP G 84 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN G 94 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 121 removed outlier: 3.556A pdb=" N GLU G 118 " --> pdb=" O ASN G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 176 Processing helix chain 'G' and resid 186 through 200 removed outlier: 4.084A pdb=" N VAL G 190 " --> pdb=" O CYS G 186 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU G 199 " --> pdb=" O SER G 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 124 removed outlier: 3.561A pdb=" N LEU H 109 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 removed outlier: 3.625A pdb=" N LEU H 136 " --> pdb=" O THR H 132 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE H 137 " --> pdb=" O ALA H 133 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN H 138 " --> pdb=" O ALA H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 188 No H-bonds generated for 'chain 'H' and resid 186 through 188' Processing helix chain 'H' and resid 190 through 196 removed outlier: 3.660A pdb=" N ALA H 195 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 220 removed outlier: 3.551A pdb=" N ALA H 208 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG H 220 " --> pdb=" O HIS H 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 99 removed outlier: 3.811A pdb=" N MET I 87 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU I 98 " --> pdb=" O LEU I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 118 removed outlier: 3.571A pdb=" N HIS I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 170 removed outlier: 3.537A pdb=" N ALA I 165 " --> pdb=" O ILE I 161 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA I 169 " --> pdb=" O ALA I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 192 removed outlier: 3.578A pdb=" N ARG I 189 " --> pdb=" O ALA I 185 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS I 190 " --> pdb=" O SER I 186 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 77 removed outlier: 3.804A pdb=" N ALA J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET J 73 " --> pdb=" O PHE J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 97 removed outlier: 3.652A pdb=" N SER J 93 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU J 95 " --> pdb=" O ILE J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 151 removed outlier: 4.244A pdb=" N GLY J 148 " --> pdb=" O GLU J 144 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU J 151 " --> pdb=" O HIS J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 175 removed outlier: 3.562A pdb=" N PHE J 164 " --> pdb=" O PRO J 160 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU J 165 " --> pdb=" O GLU J 161 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 70 removed outlier: 3.836A pdb=" N VAL K 55 " --> pdb=" O ASN K 51 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN K 56 " --> pdb=" O GLY K 52 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR K 60 " --> pdb=" O ASN K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 91 removed outlier: 3.649A pdb=" N CYS K 89 " --> pdb=" O PHE K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 157 removed outlier: 4.185A pdb=" N CYS K 148 " --> pdb=" O TYR K 145 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR K 151 " --> pdb=" O CYS K 148 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA K 152 " --> pdb=" O PHE K 149 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP K 155 " --> pdb=" O ALA K 152 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU K 157 " --> pdb=" O LEU K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 181 removed outlier: 3.831A pdb=" N VAL K 178 " --> pdb=" O CYS K 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 169 removed outlier: 3.646A pdb=" N ARG L 156 " --> pdb=" O GLN L 152 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG L 163 " --> pdb=" O GLY L 159 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU L 166 " --> pdb=" O CYS L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 189 removed outlier: 3.855A pdb=" N LYS L 180 " --> pdb=" O ALA L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 231 through 241 removed outlier: 4.325A pdb=" N GLY L 236 " --> pdb=" O ILE L 232 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL L 237 " --> pdb=" O TYR L 233 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU L 238 " --> pdb=" O ALA L 234 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR L 240 " --> pdb=" O GLY L 236 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY L 241 " --> pdb=" O VAL L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 263 removed outlier: 3.554A pdb=" N PHE L 260 " --> pdb=" O ARG L 256 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA L 262 " --> pdb=" O SER L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 298 No H-bonds generated for 'chain 'L' and resid 295 through 298' Processing helix chain 'M' and resid 183 through 203 removed outlier: 3.599A pdb=" N GLN M 188 " --> pdb=" O ALA M 184 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL M 197 " --> pdb=" O LEU M 193 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS M 198 " --> pdb=" O LYS M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 211 through 224 removed outlier: 3.968A pdb=" N TYR M 223 " --> pdb=" O SER M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 268 through 278 Proline residue: M 273 - end of helix removed outlier: 3.505A pdb=" N LEU M 278 " --> pdb=" O LEU M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 311 removed outlier: 3.707A pdb=" N ASN M 303 " --> pdb=" O ALA M 299 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA M 304 " --> pdb=" O MET M 300 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE M 305 " --> pdb=" O LEU M 301 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU M 310 " --> pdb=" O THR M 306 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG M 311 " --> pdb=" O GLY M 307 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 73 removed outlier: 3.510A pdb=" N LYS N 61 " --> pdb=" O GLN N 57 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE N 67 " --> pdb=" O VAL N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 97 removed outlier: 3.679A pdb=" N SER N 86 " --> pdb=" O SER N 82 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS N 95 " --> pdb=" O SER N 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 151 removed outlier: 3.740A pdb=" N ALA N 149 " --> pdb=" O LEU N 145 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU N 150 " --> pdb=" O LEU N 146 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU N 151 " --> pdb=" O ARG N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 176 removed outlier: 3.633A pdb=" N ILE N 165 " --> pdb=" O GLU N 161 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU N 166 " --> pdb=" O ALA N 162 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL N 172 " --> pdb=" O ASP N 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 20 through 30 removed outlier: 3.627A pdb=" N ALA a 25 " --> pdb=" O GLN a 21 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS a 27 " --> pdb=" O GLU a 23 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA a 28 " --> pdb=" O TYR a 24 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL a 29 " --> pdb=" O ALA a 25 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR a 30 " --> pdb=" O PHE a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 81 through 102 removed outlier: 3.523A pdb=" N ARG a 85 " --> pdb=" O ALA a 81 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 122 removed outlier: 3.679A pdb=" N LYS a 118 " --> pdb=" O ARG a 114 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL a 121 " --> pdb=" O ASP a 117 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG a 122 " --> pdb=" O LYS a 118 " (cutoff:3.500A) Processing helix chain 'a' and resid 174 through 185 Processing helix chain 'a' and resid 195 through 210 removed outlier: 3.584A pdb=" N MET a 200 " --> pdb=" O LYS a 196 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE a 201 " --> pdb=" O GLU a 197 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA a 209 " --> pdb=" O ALA a 205 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE a 210 " --> pdb=" O LEU a 206 " (cutoff:3.500A) Processing helix chain 'a' and resid 236 through 247 removed outlier: 3.511A pdb=" N GLU a 240 " --> pdb=" O ASN a 236 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU a 241 " --> pdb=" O SER a 237 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP a 242 " --> pdb=" O GLU a 238 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA a 245 " --> pdb=" O GLU a 241 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 28 removed outlier: 3.528A pdb=" N THR b 25 " --> pdb=" O GLU b 21 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 99 removed outlier: 3.505A pdb=" N ARG b 82 " --> pdb=" O GLY b 78 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL b 83 " --> pdb=" O PRO b 79 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU b 84 " --> pdb=" O ASP b 80 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR b 95 " --> pdb=" O ASN b 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS b 96 " --> pdb=" O CYS b 92 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET b 98 " --> pdb=" O GLN b 94 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 119 removed outlier: 3.620A pdb=" N ILE b 115 " --> pdb=" O LYS b 111 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU b 118 " --> pdb=" O ALA b 114 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE b 119 " --> pdb=" O ILE b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 166 through 175 removed outlier: 3.769A pdb=" N PHE b 171 " --> pdb=" O ASP b 167 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS b 174 " --> pdb=" O ALA b 170 " (cutoff:3.500A) Processing helix chain 'b' and resid 182 through 189 Processing helix chain 'b' and resid 191 through 196 removed outlier: 3.801A pdb=" N GLU b 195 " --> pdb=" O LEU b 191 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLY b 196 " --> pdb=" O THR b 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 191 through 196' Processing helix chain 'b' and resid 221 through 228 removed outlier: 3.899A pdb=" N TYR b 227 " --> pdb=" O GLN b 223 " (cutoff:3.500A) Processing helix chain 'c' and resid 3 through 5 No H-bonds generated for 'chain 'c' and resid 3 through 5' Processing helix chain 'c' and resid 19 through 29 Processing helix chain 'c' and resid 86 through 107 removed outlier: 4.114A pdb=" N TYR c 90 " --> pdb=" O THR c 86 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA c 91 " --> pdb=" O SER c 87 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU c 92 " --> pdb=" O ASP c 88 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN c 104 " --> pdb=" O ALA c 100 " (cutoff:3.500A) Processing helix chain 'c' and resid 113 through 129 removed outlier: 3.511A pdb=" N CYS c 121 " --> pdb=" O CYS c 117 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU c 123 " --> pdb=" O ILE c 119 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR c 127 " --> pdb=" O GLU c 123 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR c 128 " --> pdb=" O LYS c 124 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN c 129 " --> pdb=" O GLN c 125 " (cutoff:3.500A) Processing helix chain 'c' and resid 174 through 183 removed outlier: 3.930A pdb=" N ALA c 179 " --> pdb=" O GLN c 175 " (cutoff:3.500A) Processing helix chain 'c' and resid 191 through 205 removed outlier: 3.541A pdb=" N LYS c 204 " --> pdb=" O ARG c 200 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR c 205 " --> pdb=" O VAL c 201 " (cutoff:3.500A) Processing helix chain 'c' and resid 251 through 267 Proline residue: c 256 - end of helix removed outlier: 4.059A pdb=" N ARG c 260 " --> pdb=" O PRO c 256 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA c 261 " --> pdb=" O HIS c 257 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP c 262 " --> pdb=" O ALA c 258 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN c 263 " --> pdb=" O GLU c 259 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 27 removed outlier: 3.501A pdb=" N GLU d 24 " --> pdb=" O GLU d 20 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA d 25 " --> pdb=" O TYR d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 96 removed outlier: 3.633A pdb=" N ARG d 81 " --> pdb=" O SER d 77 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN d 92 " --> pdb=" O GLN d 88 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU d 96 " --> pdb=" O GLN d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 104 through 119 removed outlier: 3.565A pdb=" N THR d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 171 removed outlier: 3.705A pdb=" N ILE d 169 " --> pdb=" O ASP d 165 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 193 removed outlier: 3.535A pdb=" N VAL d 186 " --> pdb=" O ARG d 182 " (cutoff:3.500A) Processing helix chain 'd' and resid 219 through 240 removed outlier: 3.678A pdb=" N LYS d 224 " --> pdb=" O GLU d 220 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE d 225 " --> pdb=" O GLU d 221 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL d 227 " --> pdb=" O GLN d 223 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU d 228 " --> pdb=" O LYS d 224 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU d 232 " --> pdb=" O GLU d 228 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU d 235 " --> pdb=" O LYS d 231 " (cutoff:3.500A) Processing helix chain 'e' and resid 122 through 132 removed outlier: 3.675A pdb=" N GLU e 129 " --> pdb=" O GLU e 125 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA e 130 " --> pdb=" O TYR e 126 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE e 131 " --> pdb=" O ALA e 127 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS e 132 " --> pdb=" O VAL e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 163 No H-bonds generated for 'chain 'e' and resid 161 through 163' Processing helix chain 'e' and resid 183 through 203 removed outlier: 4.317A pdb=" N ILE e 187 " --> pdb=" O ALA e 183 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU e 188 " --> pdb=" O ASP e 184 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL e 194 " --> pdb=" O GLU e 190 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG e 200 " --> pdb=" O SER e 196 " (cutoff:3.500A) Processing helix chain 'e' and resid 209 through 217 Processing helix chain 'e' and resid 272 through 282 removed outlier: 4.442A pdb=" N GLU e 275 " --> pdb=" O GLY e 272 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA e 276 " --> pdb=" O GLY e 273 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN e 278 " --> pdb=" O GLU e 275 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER e 279 " --> pdb=" O ALA e 276 " (cutoff:3.500A) Processing helix chain 'e' and resid 291 through 304 removed outlier: 3.545A pdb=" N ALA e 298 " --> pdb=" O GLY e 294 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP e 300 " --> pdb=" O THR e 296 " (cutoff:3.500A) Processing helix chain 'e' and resid 332 through 339 removed outlier: 4.030A pdb=" N ALA e 337 " --> pdb=" O THR e 333 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE e 338 " --> pdb=" O GLU e 334 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET e 339 " --> pdb=" O ILE e 335 " (cutoff:3.500A) Processing helix chain 'f' and resid 184 through 195 removed outlier: 3.928A pdb=" N GLU f 191 " --> pdb=" O GLU f 187 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA f 192 " --> pdb=" O TYR f 188 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL f 193 " --> pdb=" O ALA f 189 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN f 194 " --> pdb=" O ASN f 190 " (cutoff:3.500A) Processing helix chain 'f' and resid 243 through 264 removed outlier: 3.807A pdb=" N VAL f 248 " --> pdb=" O ALA f 244 " (cutoff:3.500A) Processing helix chain 'f' and resid 270 through 280 removed outlier: 3.598A pdb=" N ASP f 275 " --> pdb=" O ASN f 271 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY f 278 " --> pdb=" O ALA f 274 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU f 279 " --> pdb=" O ASP f 275 " (cutoff:3.500A) Processing helix chain 'f' and resid 331 through 339 removed outlier: 4.126A pdb=" N ARG f 339 " --> pdb=" O THR f 335 " (cutoff:3.500A) Processing helix chain 'f' and resid 341 through 343 No H-bonds generated for 'chain 'f' and resid 341 through 343' Processing helix chain 'f' and resid 349 through 363 removed outlier: 3.628A pdb=" N THR f 354 " --> pdb=" O ASP f 350 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER f 362 " --> pdb=" O LYS f 358 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA f 363 " --> pdb=" O ALA f 359 " (cutoff:3.500A) Processing helix chain 'f' and resid 393 through 398 removed outlier: 4.098A pdb=" N LYS f 396 " --> pdb=" O SER f 393 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 32 removed outlier: 3.622A pdb=" N LYS g 29 " --> pdb=" O GLU g 25 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA g 30 " --> pdb=" O TYR g 26 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL g 31 " --> pdb=" O ALA g 27 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 101 removed outlier: 3.858A pdb=" N ALA g 87 " --> pdb=" O PRO g 83 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE g 88 " --> pdb=" O ASP g 84 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN g 94 " --> pdb=" O SER g 90 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER g 99 " --> pdb=" O GLU g 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 109 through 121 removed outlier: 3.555A pdb=" N GLU g 118 " --> pdb=" O ASN g 114 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 176 Processing helix chain 'g' and resid 186 through 200 removed outlier: 4.084A pdb=" N VAL g 190 " --> pdb=" O CYS g 186 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY g 191 " --> pdb=" O ASP g 187 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU g 199 " --> pdb=" O SER g 195 " (cutoff:3.500A) Processing helix chain 'h' and resid 105 through 124 removed outlier: 3.561A pdb=" N LEU h 109 " --> pdb=" O ASP h 105 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN h 115 " --> pdb=" O GLU h 111 " (cutoff:3.500A) Processing helix chain 'h' and resid 130 through 142 removed outlier: 3.625A pdb=" N LEU h 136 " --> pdb=" O THR h 132 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE h 137 " --> pdb=" O ALA h 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN h 138 " --> pdb=" O ALA h 134 " (cutoff:3.500A) Processing helix chain 'h' and resid 186 through 188 No H-bonds generated for 'chain 'h' and resid 186 through 188' Processing helix chain 'h' and resid 190 through 196 removed outlier: 3.660A pdb=" N ALA h 195 " --> pdb=" O SER h 191 " (cutoff:3.500A) Processing helix chain 'h' and resid 203 through 220 removed outlier: 3.551A pdb=" N ALA h 208 " --> pdb=" O SER h 204 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG h 220 " --> pdb=" O HIS h 216 " (cutoff:3.500A) Processing helix chain 'i' and resid 78 through 99 removed outlier: 3.810A pdb=" N MET i 87 " --> pdb=" O ALA i 83 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU i 98 " --> pdb=" O LEU i 94 " (cutoff:3.500A) Processing helix chain 'i' and resid 105 through 118 removed outlier: 3.571A pdb=" N HIS i 115 " --> pdb=" O LEU i 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 160 through 170 removed outlier: 3.537A pdb=" N ALA i 165 " --> pdb=" O ILE i 161 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA i 169 " --> pdb=" O ALA i 165 " (cutoff:3.500A) Processing helix chain 'i' and resid 177 through 192 removed outlier: 3.577A pdb=" N ARG i 189 " --> pdb=" O ALA i 185 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS i 190 " --> pdb=" O SER i 186 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY i 191 " --> pdb=" O ALA i 187 " (cutoff:3.500A) Processing helix chain 'j' and resid 57 through 77 removed outlier: 3.804A pdb=" N ALA j 64 " --> pdb=" O GLN j 60 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET j 73 " --> pdb=" O PHE j 69 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 97 removed outlier: 3.652A pdb=" N SER j 93 " --> pdb=" O ALA j 89 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU j 95 " --> pdb=" O ILE j 91 " (cutoff:3.500A) Processing helix chain 'j' and resid 143 through 151 removed outlier: 4.245A pdb=" N GLY j 148 " --> pdb=" O GLU j 144 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET j 149 " --> pdb=" O SER j 145 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU j 151 " --> pdb=" O HIS j 147 " (cutoff:3.500A) Processing helix chain 'j' and resid 160 through 175 removed outlier: 3.563A pdb=" N PHE j 164 " --> pdb=" O PRO j 160 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU j 165 " --> pdb=" O GLU j 161 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE j 166 " --> pdb=" O GLU j 162 " (cutoff:3.500A) Processing helix chain 'k' and resid 51 through 70 removed outlier: 3.837A pdb=" N VAL k 55 " --> pdb=" O ASN k 51 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN k 56 " --> pdb=" O GLY k 52 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR k 60 " --> pdb=" O ASN k 56 " (cutoff:3.500A) Processing helix chain 'k' and resid 79 through 91 removed outlier: 3.650A pdb=" N CYS k 89 " --> pdb=" O PHE k 85 " (cutoff:3.500A) Processing helix chain 'k' and resid 145 through 157 removed outlier: 4.186A pdb=" N CYS k 148 " --> pdb=" O TYR k 145 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR k 151 " --> pdb=" O CYS k 148 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA k 152 " --> pdb=" O PHE k 149 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP k 155 " --> pdb=" O ALA k 152 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU k 157 " --> pdb=" O LEU k 154 " (cutoff:3.500A) Processing helix chain 'k' and resid 166 through 181 removed outlier: 3.831A pdb=" N VAL k 178 " --> pdb=" O CYS k 174 " (cutoff:3.500A) Processing helix chain 'l' and resid 148 through 169 removed outlier: 3.538A pdb=" N TRP l 154 " --> pdb=" O ASP l 150 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG l 156 " --> pdb=" O GLN l 152 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG l 163 " --> pdb=" O GLY l 159 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU l 166 " --> pdb=" O CYS l 162 " (cutoff:3.500A) Processing helix chain 'l' and resid 175 through 189 removed outlier: 3.841A pdb=" N LYS l 180 " --> pdb=" O ALA l 176 " (cutoff:3.500A) Processing helix chain 'l' and resid 231 through 241 removed outlier: 4.304A pdb=" N GLY l 236 " --> pdb=" O ILE l 232 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL l 237 " --> pdb=" O TYR l 233 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU l 238 " --> pdb=" O ALA l 234 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR l 240 " --> pdb=" O GLY l 236 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY l 241 " --> pdb=" O VAL l 237 " (cutoff:3.500A) Processing helix chain 'l' and resid 248 through 263 removed outlier: 3.507A pdb=" N PHE l 260 " --> pdb=" O ARG l 256 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA l 262 " --> pdb=" O SER l 258 " (cutoff:3.500A) Processing helix chain 'l' and resid 295 through 298 No H-bonds generated for 'chain 'l' and resid 295 through 298' Processing helix chain 'm' and resid 183 through 203 removed outlier: 3.598A pdb=" N GLN m 188 " --> pdb=" O ALA m 184 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL m 197 " --> pdb=" O LEU m 193 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS m 198 " --> pdb=" O LYS m 194 " (cutoff:3.500A) Processing helix chain 'm' and resid 211 through 224 removed outlier: 3.968A pdb=" N TYR m 223 " --> pdb=" O SER m 219 " (cutoff:3.500A) Processing helix chain 'm' and resid 268 through 278 Proline residue: m 273 - end of helix removed outlier: 3.504A pdb=" N LEU m 278 " --> pdb=" O LEU m 274 " (cutoff:3.500A) Processing helix chain 'm' and resid 294 through 311 removed outlier: 3.708A pdb=" N ASN m 303 " --> pdb=" O ALA m 299 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA m 304 " --> pdb=" O MET m 300 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE m 305 " --> pdb=" O LEU m 301 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU m 310 " --> pdb=" O THR m 306 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG m 311 " --> pdb=" O GLY m 307 " (cutoff:3.500A) Processing helix chain 'n' and resid 53 through 73 removed outlier: 3.510A pdb=" N LYS n 61 " --> pdb=" O GLN n 57 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE n 67 " --> pdb=" O VAL n 63 " (cutoff:3.500A) Processing helix chain 'n' and resid 81 through 97 removed outlier: 3.680A pdb=" N SER n 86 " --> pdb=" O SER n 82 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS n 95 " --> pdb=" O SER n 91 " (cutoff:3.500A) Processing helix chain 'n' and resid 142 through 151 removed outlier: 3.739A pdb=" N ALA n 149 " --> pdb=" O LEU n 145 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU n 150 " --> pdb=" O LEU n 146 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU n 151 " --> pdb=" O ARG n 147 " (cutoff:3.500A) Processing helix chain 'n' and resid 159 through 176 removed outlier: 3.632A pdb=" N ILE n 165 " --> pdb=" O GLU n 161 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU n 166 " --> pdb=" O ALA n 162 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL n 172 " --> pdb=" O ASP n 168 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 167 through 171 removed outlier: 5.524A pdb=" N LEU A 35 " --> pdb=" O GLN A 50 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 162 through 164 removed outlier: 6.693A pdb=" N CYS A 75 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU A 68 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N MET A 77 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 66 " --> pdb=" O MET A 77 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.522A pdb=" N VAL B 42 " --> pdb=" O VAL B 211 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 63 through 65 Processing sheet with id= E, first strand: chain 'B' and resid 74 through 76 removed outlier: 3.705A pdb=" N SER B 131 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 135 through 138 removed outlier: 3.650A pdb=" N GLY B 141 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 167 through 170 removed outlier: 3.796A pdb=" N ARG C 222 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 82 through 84 Processing sheet with id= I, first strand: chain 'C' and resid 143 through 146 removed outlier: 3.572A pdb=" N GLY C 144 " --> pdb=" O GLN C 152 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 71 through 75 removed outlier: 6.530A pdb=" N ILE C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.608A pdb=" N VAL D 42 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 69 through 75 removed outlier: 3.802A pdb=" N ASN D 137 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 267 through 270 removed outlier: 3.845A pdb=" N ALA E 149 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 167 through 169 removed outlier: 4.285A pdb=" N LEU E 253 " --> pdb=" O TYR E 265 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 323 through 326 removed outlier: 3.549A pdb=" N ILE F 377 " --> pdb=" O PHE F 389 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 235 through 237 Processing sheet with id= Q, first strand: chain 'F' and resid 310 through 312 Processing sheet with id= R, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.675A pdb=" N VAL G 163 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS G 217 " --> pdb=" O LYS G 223 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS G 223 " --> pdb=" O CYS G 217 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.550A pdb=" N ALA G 142 " --> pdb=" O GLY G 145 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 179 through 183 removed outlier: 6.561A pdb=" N THR H 56 " --> pdb=" O ASP H 71 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU H 239 " --> pdb=" O THR H 232 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 95 through 101 removed outlier: 3.503A pdb=" N ILE H 153 " --> pdb=" O CYS H 98 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL H 165 " --> pdb=" O LEU H 177 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 74 through 76 removed outlier: 6.579A pdb=" N SER H 76 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 153 through 156 removed outlier: 3.996A pdb=" N GLY I 40 " --> pdb=" O TYR I 37 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 63 through 65 Processing sheet with id= Y, first strand: chain 'J' and resid 136 through 140 removed outlier: 6.483A pdb=" N SER J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 42 through 44 Processing sheet with id= AA, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.488A pdb=" N GLU J 30 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR J 34 " --> pdb=" O GLU J 30 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'K' and resid 140 through 143 Processing sheet with id= AC, first strand: chain 'K' and resid 36 through 38 removed outlier: 4.507A pdb=" N CYS K 105 " --> pdb=" O MET K 129 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'K' and resid 22 through 24 removed outlier: 4.118A pdb=" N ASN K 22 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE K 24 " --> pdb=" O LYS K 28 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LYS K 28 " --> pdb=" O PHE K 24 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 224 through 226 removed outlier: 6.850A pdb=" N HIS L 277 " --> pdb=" O LYS L 285 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS L 285 " --> pdb=" O HIS L 277 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N HIS L 279 " --> pdb=" O TRP L 283 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TRP L 283 " --> pdb=" O HIS L 279 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'L' and resid 140 through 142 removed outlier: 3.719A pdb=" N VAL L 200 " --> pdb=" O TYR L 211 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY L 202 " --> pdb=" O SER L 209 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER L 209 " --> pdb=" O GLY L 202 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU L 210 " --> pdb=" O GLN L 222 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN L 222 " --> pdb=" O LEU L 210 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'M' and resid 261 through 265 removed outlier: 5.295A pdb=" N THR M 135 " --> pdb=" O ASP M 150 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY M 149 " --> pdb=" O SER M 320 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'M' and resid 168 through 170 removed outlier: 3.516A pdb=" N GLY M 238 " --> pdb=" O VAL M 246 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'N' and resid 132 through 135 removed outlier: 3.613A pdb=" N GLY N 15 " --> pdb=" O TYR N 12 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'N' and resid 39 through 41 removed outlier: 3.510A pdb=" N SER N 45 " --> pdb=" O LEU N 41 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'N' and resid 24 through 26 removed outlier: 3.788A pdb=" N TRP N 32 " --> pdb=" O LEU N 24 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR N 26 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ALA N 30 " --> pdb=" O TYR N 26 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'a' and resid 167 through 171 removed outlier: 5.524A pdb=" N LEU a 35 " --> pdb=" O GLN a 50 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'a' and resid 162 through 164 removed outlier: 6.693A pdb=" N CYS a 75 " --> pdb=" O GLU a 68 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU a 68 " --> pdb=" O CYS a 75 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N MET a 77 " --> pdb=" O LEU a 66 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU a 66 " --> pdb=" O MET a 77 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'b' and resid 158 through 161 removed outlier: 3.522A pdb=" N VAL b 42 " --> pdb=" O VAL b 211 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'b' and resid 63 through 65 Processing sheet with id= AP, first strand: chain 'b' and resid 74 through 76 removed outlier: 3.705A pdb=" N SER b 131 " --> pdb=" O SER b 75 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'b' and resid 135 through 138 removed outlier: 3.650A pdb=" N GLY b 141 " --> pdb=" O ASP b 138 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'c' and resid 167 through 170 removed outlier: 3.797A pdb=" N ARG c 222 " --> pdb=" O ARG c 245 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'c' and resid 82 through 84 Processing sheet with id= AT, first strand: chain 'c' and resid 143 through 146 removed outlier: 3.572A pdb=" N GLY c 144 " --> pdb=" O GLN c 152 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'c' and resid 71 through 75 removed outlier: 6.530A pdb=" N ILE c 78 " --> pdb=" O ILE c 74 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'd' and resid 158 through 161 removed outlier: 3.609A pdb=" N VAL d 42 " --> pdb=" O VAL d 35 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'd' and resid 69 through 75 removed outlier: 3.801A pdb=" N ASN d 137 " --> pdb=" O LYS d 141 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LYS d 141 " --> pdb=" O ASN d 137 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'e' and resid 267 through 270 removed outlier: 3.844A pdb=" N ALA e 149 " --> pdb=" O LEU e 138 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'e' and resid 167 through 169 removed outlier: 4.286A pdb=" N LEU e 253 " --> pdb=" O TYR e 265 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'f' and resid 323 through 326 removed outlier: 3.548A pdb=" N ILE f 377 " --> pdb=" O PHE f 389 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'f' and resid 235 through 237 Processing sheet with id= BB, first strand: chain 'f' and resid 310 through 312 Processing sheet with id= BC, first strand: chain 'g' and resid 162 through 165 removed outlier: 3.676A pdb=" N VAL g 163 " --> pdb=" O ALA g 39 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS g 217 " --> pdb=" O LYS g 223 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS g 223 " --> pdb=" O CYS g 217 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'g' and resid 67 through 69 removed outlier: 3.550A pdb=" N ALA g 142 " --> pdb=" O GLY g 145 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'h' and resid 179 through 183 removed outlier: 6.560A pdb=" N THR h 56 " --> pdb=" O ASP h 71 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU h 239 " --> pdb=" O THR h 232 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'h' and resid 95 through 101 removed outlier: 3.503A pdb=" N ILE h 153 " --> pdb=" O CYS h 98 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL h 165 " --> pdb=" O LEU h 177 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'h' and resid 74 through 76 removed outlier: 6.579A pdb=" N SER h 76 " --> pdb=" O VAL h 80 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL h 80 " --> pdb=" O SER h 76 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'i' and resid 153 through 156 removed outlier: 3.995A pdb=" N GLY i 40 " --> pdb=" O TYR i 37 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'i' and resid 63 through 65 Processing sheet with id= BJ, first strand: chain 'j' and resid 136 through 140 removed outlier: 6.483A pdb=" N SER j 10 " --> pdb=" O ASP j 25 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'j' and resid 42 through 44 Processing sheet with id= BL, first strand: chain 'j' and resid 28 through 30 removed outlier: 6.488A pdb=" N GLU j 30 " --> pdb=" O THR j 34 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR j 34 " --> pdb=" O GLU j 30 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'k' and resid 140 through 143 Processing sheet with id= BN, first strand: chain 'k' and resid 36 through 38 removed outlier: 4.506A pdb=" N CYS k 105 " --> pdb=" O MET k 129 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'k' and resid 22 through 24 removed outlier: 4.118A pdb=" N ASN k 22 " --> pdb=" O THR k 30 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE k 24 " --> pdb=" O LYS k 28 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LYS k 28 " --> pdb=" O PHE k 24 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'l' and resid 224 through 228 removed outlier: 6.841A pdb=" N HIS l 277 " --> pdb=" O LYS l 285 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LYS l 285 " --> pdb=" O HIS l 277 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS l 279 " --> pdb=" O TRP l 283 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TRP l 283 " --> pdb=" O HIS l 279 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'l' and resid 140 through 142 removed outlier: 3.690A pdb=" N VAL l 200 " --> pdb=" O TYR l 211 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY l 202 " --> pdb=" O SER l 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY l 207 " --> pdb=" O ASP l 204 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU l 210 " --> pdb=" O GLN l 222 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN l 222 " --> pdb=" O LEU l 210 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'l' and resid 119 through 121 removed outlier: 6.191A pdb=" N THR l 121 " --> pdb=" O ILE l 125 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ILE l 125 " --> pdb=" O THR l 121 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'm' and resid 261 through 265 removed outlier: 5.295A pdb=" N THR m 135 " --> pdb=" O ASP m 150 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY m 149 " --> pdb=" O SER m 320 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'm' and resid 168 through 170 removed outlier: 3.517A pdb=" N GLY m 238 " --> pdb=" O VAL m 246 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'n' and resid 132 through 135 removed outlier: 3.614A pdb=" N GLY n 15 " --> pdb=" O TYR n 12 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'n' and resid 39 through 41 removed outlier: 3.509A pdb=" N SER n 45 " --> pdb=" O LEU n 41 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'n' and resid 24 through 26 removed outlier: 3.788A pdb=" N TRP n 32 " --> pdb=" O LEU n 24 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR n 26 " --> pdb=" O ALA n 30 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ALA n 30 " --> pdb=" O TYR n 26 " (cutoff:3.500A) 1949 hydrogen bonds defined for protein. 5526 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: 19.62 Time building geometry restraints manager: 18.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 15542 1.34 - 1.46: 8574 1.46 - 1.58: 25720 1.58 - 1.70: 6 1.70 - 1.82: 512 Bond restraints: 50354 Sorted by residual: bond pdb=" B26 BO2 i 301 " pdb=" O27 BO2 i 301 " ideal model delta sigma weight residual 1.362 1.545 -0.183 2.00e-02 2.50e+03 8.38e+01 bond pdb=" B26 BO2 I 301 " pdb=" O27 BO2 I 301 " ideal model delta sigma weight residual 1.362 1.545 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" B26 BO2 H 301 " pdb=" O28 BO2 H 301 " ideal model delta sigma weight residual 1.356 1.535 -0.179 2.00e-02 2.50e+03 8.04e+01 bond pdb=" B26 BO2 h 301 " pdb=" O28 BO2 h 301 " ideal model delta sigma weight residual 1.356 1.535 -0.179 2.00e-02 2.50e+03 8.00e+01 bond pdb=" B26 BO2 I 301 " pdb=" O28 BO2 I 301 " ideal model delta sigma weight residual 1.356 1.533 -0.177 2.00e-02 2.50e+03 7.82e+01 ... (remaining 50349 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.54: 930 105.54 - 113.27: 27034 113.27 - 121.00: 24868 121.00 - 128.73: 14990 128.73 - 136.46: 294 Bond angle restraints: 68116 Sorted by residual: angle pdb=" C21 BO2 I 301 " pdb=" B26 BO2 I 301 " pdb=" O27 BO2 I 301 " ideal model delta sigma weight residual 121.29 102.54 18.75 3.00e+00 1.11e-01 3.91e+01 angle pdb=" C21 BO2 i 301 " pdb=" B26 BO2 i 301 " pdb=" O27 BO2 i 301 " ideal model delta sigma weight residual 121.29 102.57 18.72 3.00e+00 1.11e-01 3.89e+01 angle pdb=" C GLY i 199 " pdb=" N THR i 200 " pdb=" CA THR i 200 " ideal model delta sigma weight residual 121.54 133.40 -11.86 1.91e+00 2.74e-01 3.85e+01 angle pdb=" C GLY I 199 " pdb=" N THR I 200 " pdb=" CA THR I 200 " ideal model delta sigma weight residual 121.54 133.38 -11.84 1.91e+00 2.74e-01 3.84e+01 angle pdb=" O27 BO2 i 301 " pdb=" B26 BO2 i 301 " pdb=" O28 BO2 i 301 " ideal model delta sigma weight residual 119.22 101.86 17.36 3.00e+00 1.11e-01 3.35e+01 ... (remaining 68111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 29085 17.70 - 35.40: 890 35.40 - 53.10: 183 53.10 - 70.80: 29 70.80 - 88.50: 33 Dihedral angle restraints: 30220 sinusoidal: 11874 harmonic: 18346 Sorted by residual: dihedral pdb=" CA LYS D 47 " pdb=" C LYS D 47 " pdb=" N LYS D 48 " pdb=" CA LYS D 48 " ideal model delta harmonic sigma weight residual 180.00 -149.00 -31.00 0 5.00e+00 4.00e-02 3.84e+01 dihedral pdb=" CA LYS d 47 " pdb=" C LYS d 47 " pdb=" N LYS d 48 " pdb=" CA LYS d 48 " ideal model delta harmonic sigma weight residual -180.00 -149.01 -30.99 0 5.00e+00 4.00e-02 3.84e+01 dihedral pdb=" CA GLY J 101 " pdb=" C GLY J 101 " pdb=" N PRO J 102 " pdb=" CA PRO J 102 " ideal model delta harmonic sigma weight residual -180.00 -149.48 -30.52 0 5.00e+00 4.00e-02 3.73e+01 ... (remaining 30217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 5549 0.052 - 0.104: 1533 0.104 - 0.156: 423 0.156 - 0.208: 34 0.208 - 0.260: 21 Chirality restraints: 7560 Sorted by residual: chirality pdb=" CB VAL k 138 " pdb=" CA VAL k 138 " pdb=" CG1 VAL k 138 " pdb=" CG2 VAL k 138 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE J 23 " pdb=" CA ILE J 23 " pdb=" CG1 ILE J 23 " pdb=" CG2 ILE J 23 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB VAL K 138 " pdb=" CA VAL K 138 " pdb=" CG1 VAL K 138 " pdb=" CG2 VAL K 138 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 7557 not shown) Planarity restraints: 8826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BO2 L 401 " -0.165 2.00e-02 2.50e+03 2.31e-01 6.65e+02 pdb=" C18 BO2 L 401 " 0.072 2.00e-02 2.50e+03 pdb=" C21 BO2 L 401 " -0.269 2.00e-02 2.50e+03 pdb=" N20 BO2 L 401 " 0.400 2.00e-02 2.50e+03 pdb=" O19 BO2 L 401 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 i 301 " 0.179 2.00e-02 2.50e+03 2.10e-01 5.51e+02 pdb=" C18 BO2 i 301 " -0.075 2.00e-02 2.50e+03 pdb=" C21 BO2 i 301 " 0.255 2.00e-02 2.50e+03 pdb=" N20 BO2 i 301 " -0.342 2.00e-02 2.50e+03 pdb=" O19 BO2 i 301 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 I 301 " -0.179 2.00e-02 2.50e+03 2.10e-01 5.50e+02 pdb=" C18 BO2 I 301 " 0.075 2.00e-02 2.50e+03 pdb=" C21 BO2 I 301 " -0.255 2.00e-02 2.50e+03 pdb=" N20 BO2 I 301 " 0.342 2.00e-02 2.50e+03 pdb=" O19 BO2 I 301 " 0.016 2.00e-02 2.50e+03 ... (remaining 8823 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 858 2.67 - 3.23: 42850 3.23 - 3.78: 75153 3.78 - 4.34: 108250 4.34 - 4.90: 178473 Nonbonded interactions: 405584 Sorted by model distance: nonbonded pdb=" ND2 ASN f 266 " pdb=" OE2 GLU n 83 " model vdw 2.109 2.520 nonbonded pdb=" OE2 GLU d 46 " pdb=" NH2 ARG d 163 " model vdw 2.135 2.520 nonbonded pdb=" OE2 GLU D 46 " pdb=" NH2 ARG D 163 " model vdw 2.136 2.520 nonbonded pdb=" ND2 ASN F 266 " pdb=" OE2 GLU N 83 " model vdw 2.176 2.520 nonbonded pdb=" OE2 GLU D 90 " pdb=" NH2 ARG D 93 " model vdw 2.185 2.520 ... (remaining 405579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 8.440 Check model and map are aligned: 0.720 Set scattering table: 0.470 Process input model: 124.040 Find NCS groups from input model: 5.150 Set up NCS constraints: 0.540 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.006 0.183 50354 Z= 0.386 Angle : 0.965 18.752 68116 Z= 0.536 Chirality : 0.053 0.260 7560 Planarity : 0.008 0.231 8826 Dihedral : 10.269 88.495 18504 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.15 % Allowed : 3.55 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -4.67 (0.08), residues: 6304 helix: -4.40 (0.05), residues: 2218 sheet: -1.76 (0.13), residues: 1492 loop : -2.46 (0.10), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP C 185 HIS 0.014 0.002 HIS f 234 PHE 0.022 0.002 PHE J 20 TYR 0.035 0.003 TYR h 96 ARG 0.008 0.001 ARG d 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1848 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1840 time to evaluate : 5.688 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: A 42 LYS cc_start: 0.7976 (ttpp) cc_final: 0.7590 (tptt) REVERT: A 215 LYS cc_start: 0.7803 (mtpt) cc_final: 0.7430 (mmtm) REVERT: C 29 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7215 (mm-40) REVERT: C 50 MET cc_start: 0.6406 (pmt) cc_final: 0.6004 (ttm) REVERT: C 57 ASP cc_start: 0.7907 (t0) cc_final: 0.7501 (t0) REVERT: C 206 MET cc_start: 0.6860 (ptt) cc_final: 0.6569 (ptt) REVERT: C 262 ASP cc_start: 0.7884 (p0) cc_final: 0.7170 (p0) REVERT: D 4 ASP cc_start: 0.7357 (p0) cc_final: 0.6594 (p0) REVERT: D 102 MET cc_start: 0.6175 (ttt) cc_final: 0.5819 (ptm) REVERT: D 183 ASP cc_start: 0.7374 (m-30) cc_final: 0.6794 (m-30) REVERT: D 223 GLN cc_start: 0.6878 (mm110) cc_final: 0.6610 (tp40) REVERT: E 140 ILE cc_start: 0.8833 (mm) cc_final: 0.8600 (mm) REVERT: E 293 GLU cc_start: 0.7735 (tt0) cc_final: 0.7197 (tp30) REVERT: E 301 ILE cc_start: 0.7824 (mt) cc_final: 0.7561 (mt) REVERT: E 314 ASN cc_start: 0.6833 (t0) cc_final: 0.6490 (t0) REVERT: F 214 LYS cc_start: 0.7390 (pttt) cc_final: 0.7115 (pttt) REVERT: F 227 LYS cc_start: 0.7514 (mmtp) cc_final: 0.7303 (mtpt) REVERT: F 396 LYS cc_start: 0.7725 (ptmt) cc_final: 0.7283 (mttp) REVERT: G 18 GLU cc_start: 0.7784 (pm20) cc_final: 0.7516 (pm20) REVERT: G 32 ASP cc_start: 0.8477 (m-30) cc_final: 0.8077 (m-30) REVERT: G 101 ASP cc_start: 0.7409 (m-30) cc_final: 0.7157 (m-30) REVERT: G 105 THR cc_start: 0.8680 (t) cc_final: 0.8411 (p) REVERT: G 118 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7830 (mt-10) REVERT: G 201 HIS cc_start: 0.5810 (t-90) cc_final: 0.5384 (t70) REVERT: H 149 SER cc_start: 0.8227 (t) cc_final: 0.7941 (p) REVERT: H 234 ASP cc_start: 0.8476 (p0) cc_final: 0.8112 (p0) REVERT: I 120 GLN cc_start: 0.7734 (mt0) cc_final: 0.6965 (mm-40) REVERT: I 197 TYR cc_start: 0.8689 (m-80) cc_final: 0.8486 (m-10) REVERT: I 212 THR cc_start: 0.9013 (t) cc_final: 0.8504 (m) REVERT: I 214 LEU cc_start: 0.8362 (tp) cc_final: 0.8147 (tt) REVERT: J 111 SER cc_start: 0.8951 (p) cc_final: 0.8659 (t) REVERT: J 189 ILE cc_start: 0.7855 (pt) cc_final: 0.7618 (mp) REVERT: K 41 THR cc_start: 0.8970 (p) cc_final: 0.8760 (p) REVERT: M 174 TYR cc_start: 0.7873 (m-10) cc_final: 0.7548 (m-80) REVERT: M 207 LYS cc_start: 0.8269 (ttpm) cc_final: 0.7900 (tptm) REVERT: M 293 THR cc_start: 0.7873 (p) cc_final: 0.7619 (m) REVERT: a 42 LYS cc_start: 0.7939 (ttpp) cc_final: 0.7484 (tptt) REVERT: a 55 ASP cc_start: 0.7006 (t0) cc_final: 0.6773 (t0) REVERT: a 215 LYS cc_start: 0.7722 (mtpt) cc_final: 0.7287 (mmtm) REVERT: c 29 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7300 (mm-40) REVERT: c 50 MET cc_start: 0.6398 (pmt) cc_final: 0.5862 (mtt) REVERT: c 57 ASP cc_start: 0.7969 (t0) cc_final: 0.7660 (t0) REVERT: c 172 GLN cc_start: 0.7301 (mt0) cc_final: 0.7043 (mm-40) REVERT: c 262 ASP cc_start: 0.7982 (p0) cc_final: 0.7187 (p0) REVERT: d 4 ASP cc_start: 0.7372 (p0) cc_final: 0.6552 (p0) REVERT: d 33 VAL cc_start: 0.8908 (t) cc_final: 0.8600 (p) REVERT: d 47 LYS cc_start: 0.7591 (ttpp) cc_final: 0.7244 (ttmt) REVERT: d 92 GLN cc_start: 0.5910 (mm110) cc_final: 0.5637 (tm-30) REVERT: d 102 MET cc_start: 0.6023 (ttt) cc_final: 0.5756 (ptm) REVERT: d 139 ASP cc_start: 0.8092 (p0) cc_final: 0.7701 (p0) REVERT: d 181 SER cc_start: 0.7883 (p) cc_final: 0.7348 (t) REVERT: d 183 ASP cc_start: 0.7632 (m-30) cc_final: 0.7205 (m-30) REVERT: e 109 ASP cc_start: 0.6072 (p0) cc_final: 0.5841 (m-30) REVERT: e 162 SER cc_start: 0.7508 (p) cc_final: 0.7121 (t) REVERT: f 214 LYS cc_start: 0.7383 (pttt) cc_final: 0.7168 (pttt) REVERT: f 260 TYR cc_start: 0.8754 (t80) cc_final: 0.8533 (t80) REVERT: f 290 LYS cc_start: 0.6927 (mtpp) cc_final: 0.6704 (mmtm) REVERT: f 396 LYS cc_start: 0.7842 (ptmt) cc_final: 0.7283 (mttp) REVERT: g 32 ASP cc_start: 0.8666 (m-30) cc_final: 0.8393 (m-30) REVERT: g 64 ASN cc_start: 0.8450 (m-40) cc_final: 0.8172 (m110) REVERT: g 101 ASP cc_start: 0.7451 (m-30) cc_final: 0.7183 (m-30) REVERT: g 105 THR cc_start: 0.8658 (t) cc_final: 0.8437 (p) REVERT: g 173 LYS cc_start: 0.7806 (tmtp) cc_final: 0.7486 (tppt) REVERT: g 215 TRP cc_start: 0.8026 (p90) cc_final: 0.7783 (p90) REVERT: h 271 SER cc_start: 0.8499 (t) cc_final: 0.8215 (p) REVERT: i 212 THR cc_start: 0.8982 (t) cc_final: 0.8441 (m) REVERT: i 214 LEU cc_start: 0.8558 (tp) cc_final: 0.8338 (tt) REVERT: j 59 ASP cc_start: 0.8541 (m-30) cc_final: 0.8287 (m-30) REVERT: j 81 ASP cc_start: 0.7204 (m-30) cc_final: 0.6970 (m-30) REVERT: k 40 ASP cc_start: 0.7507 (t0) cc_final: 0.7232 (t0) REVERT: l 229 SER cc_start: 0.8372 (t) cc_final: 0.8135 (p) REVERT: m 174 TYR cc_start: 0.7741 (m-10) cc_final: 0.7505 (m-80) REVERT: m 270 PHE cc_start: 0.8302 (m-80) cc_final: 0.8074 (m-10) REVERT: m 294 LYS cc_start: 0.8417 (mtmt) cc_final: 0.8193 (mtpt) REVERT: n 115 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6402 (mm-30) outliers start: 8 outliers final: 2 residues processed: 1846 average time/residue: 0.7414 time to fit residues: 2125.8232 Evaluate side-chains 1081 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1079 time to evaluate : 5.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain j residue 190 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 525 optimal weight: 8.9990 chunk 471 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 318 optimal weight: 0.8980 chunk 251 optimal weight: 8.9990 chunk 487 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 296 optimal weight: 0.7980 chunk 362 optimal weight: 8.9990 chunk 564 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 125 GLN A 228 ASN B 207 GLN B 223 GLN C 65 ASN C 108 GLN D 97 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 GLN ** E 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN F 225 GLN F 271 ASN F 281 HIS G 114 ASN G 201 HIS H 264 GLN H 266 GLN J 60 GLN K 22 ASN K 43 GLN K 125 GLN L 152 GLN L 184 ASN L 222 GLN L 277 HIS L 279 HIS ** M 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 185 GLN a 21 GLN a 89 GLN a 125 GLN ** a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 228 ASN ** b 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 65 ASN c 108 GLN d 92 GLN d 97 ASN ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 120 GLN ** d 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 168 ASN f 195 ASN f 225 GLN f 271 ASN f 281 HIS g 114 ASN h 107 GLN h 264 GLN h 266 GLN ** i 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 60 GLN k 42 HIS k 43 GLN k 125 GLN l 108 ASN l 152 GLN l 184 ASN l 222 GLN l 277 HIS l 279 HIS m 190 GLN ** m 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 185 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 50354 Z= 0.192 Angle : 0.595 13.007 68116 Z= 0.315 Chirality : 0.045 0.381 7560 Planarity : 0.005 0.050 8826 Dihedral : 7.059 87.170 7102 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.71 % Allowed : 9.75 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.09), residues: 6304 helix: -2.08 (0.09), residues: 2164 sheet: -1.22 (0.13), residues: 1492 loop : -1.92 (0.10), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 215 HIS 0.005 0.001 HIS f 343 PHE 0.014 0.001 PHE L 225 TYR 0.032 0.001 TYR H 218 ARG 0.007 0.001 ARG g 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1296 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1154 time to evaluate : 5.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7907 (ttpp) cc_final: 0.7629 (tptt) REVERT: A 70 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7644 (p) REVERT: A 94 GLU cc_start: 0.7198 (tp30) cc_final: 0.6942 (tp30) REVERT: B 175 ARG cc_start: 0.7823 (mmm160) cc_final: 0.7313 (mmt-90) REVERT: B 184 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7739 (m-30) REVERT: B 200 GLN cc_start: 0.6142 (OUTLIER) cc_final: 0.5255 (mm-40) REVERT: B 205 ASN cc_start: 0.8109 (t0) cc_final: 0.7757 (t0) REVERT: B 217 GLU cc_start: 0.7599 (pp20) cc_final: 0.7286 (pp20) REVERT: B 225 ARG cc_start: 0.6671 (ttm110) cc_final: 0.6395 (ttp-110) REVERT: C 29 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7336 (mm110) REVERT: C 57 ASP cc_start: 0.7889 (t0) cc_final: 0.7543 (t0) REVERT: C 196 LEU cc_start: 0.7723 (mt) cc_final: 0.7456 (mt) REVERT: C 262 ASP cc_start: 0.7603 (p0) cc_final: 0.7188 (p0) REVERT: D 4 ASP cc_start: 0.7273 (p0) cc_final: 0.6513 (p0) REVERT: D 102 MET cc_start: 0.6173 (ttt) cc_final: 0.5806 (ptm) REVERT: D 183 ASP cc_start: 0.7412 (m-30) cc_final: 0.7086 (m-30) REVERT: E 293 GLU cc_start: 0.7637 (tt0) cc_final: 0.6940 (tp30) REVERT: E 314 ASN cc_start: 0.6564 (t0) cc_final: 0.6312 (t0) REVERT: F 186 ILE cc_start: 0.8681 (mm) cc_final: 0.8338 (mm) REVERT: F 290 LYS cc_start: 0.8022 (mmtm) cc_final: 0.6773 (mtmt) REVERT: F 333 SER cc_start: 0.8560 (t) cc_final: 0.8273 (p) REVERT: F 396 LYS cc_start: 0.7740 (ptmt) cc_final: 0.7301 (mttp) REVERT: G 32 ASP cc_start: 0.8501 (m-30) cc_final: 0.8236 (m-30) REVERT: G 101 ASP cc_start: 0.7391 (m-30) cc_final: 0.6985 (m-30) REVERT: G 105 THR cc_start: 0.8677 (t) cc_final: 0.8463 (p) REVERT: G 114 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7715 (m-40) REVERT: G 212 GLU cc_start: 0.7811 (tt0) cc_final: 0.7574 (tt0) REVERT: H 234 ASP cc_start: 0.8341 (p0) cc_final: 0.8073 (p0) REVERT: I 120 GLN cc_start: 0.7927 (mt0) cc_final: 0.7377 (mp10) REVERT: I 168 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7715 (mm-30) REVERT: I 181 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8292 (mtmm) REVERT: I 214 LEU cc_start: 0.8517 (tp) cc_final: 0.8231 (tt) REVERT: J 79 GLU cc_start: 0.7182 (mp0) cc_final: 0.6632 (mt-10) REVERT: J 189 ILE cc_start: 0.7994 (pt) cc_final: 0.7698 (mp) REVERT: K 69 ARG cc_start: 0.6924 (mtt180) cc_final: 0.6562 (mtp180) REVERT: L 229 SER cc_start: 0.8351 (OUTLIER) cc_final: 0.8001 (p) REVERT: M 174 TYR cc_start: 0.7798 (m-10) cc_final: 0.7473 (m-80) REVERT: M 194 LYS cc_start: 0.8717 (tttt) cc_final: 0.8327 (tttm) REVERT: M 195 TYR cc_start: 0.8033 (m-80) cc_final: 0.7678 (m-80) REVERT: M 225 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7746 (ttp-170) REVERT: a 42 LYS cc_start: 0.7826 (ttpp) cc_final: 0.7518 (tptt) REVERT: a 55 ASP cc_start: 0.6970 (t0) cc_final: 0.6669 (t0) REVERT: a 70 THR cc_start: 0.7885 (OUTLIER) cc_final: 0.7552 (p) REVERT: a 94 GLU cc_start: 0.7148 (tp30) cc_final: 0.6871 (tp30) REVERT: a 215 LYS cc_start: 0.7726 (mtpt) cc_final: 0.7265 (mmtm) REVERT: b 21 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7177 (mm-30) REVERT: b 200 GLN cc_start: 0.6113 (OUTLIER) cc_final: 0.5250 (mm-40) REVERT: b 217 GLU cc_start: 0.7585 (pp20) cc_final: 0.7211 (pp20) REVERT: b 231 ILE cc_start: 0.5002 (OUTLIER) cc_final: 0.4782 (pp) REVERT: c 29 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7281 (mm110) REVERT: c 57 ASP cc_start: 0.7918 (t0) cc_final: 0.7637 (t0) REVERT: c 109 GLU cc_start: 0.7761 (pt0) cc_final: 0.7286 (pt0) REVERT: c 172 GLN cc_start: 0.7364 (mt0) cc_final: 0.7157 (mm-40) REVERT: c 196 LEU cc_start: 0.7791 (mt) cc_final: 0.7526 (mt) REVERT: c 262 ASP cc_start: 0.7646 (p0) cc_final: 0.7175 (p0) REVERT: d 4 ASP cc_start: 0.7258 (p0) cc_final: 0.6503 (p0) REVERT: d 47 LYS cc_start: 0.7608 (ttpp) cc_final: 0.7390 (ttmt) REVERT: d 92 GLN cc_start: 0.6312 (mm-40) cc_final: 0.5549 (tm-30) REVERT: d 102 MET cc_start: 0.6099 (ttt) cc_final: 0.5751 (ptm) REVERT: d 167 THR cc_start: 0.8941 (m) cc_final: 0.8738 (p) REVERT: d 181 SER cc_start: 0.7952 (p) cc_final: 0.7637 (t) REVERT: d 183 ASP cc_start: 0.7325 (m-30) cc_final: 0.6990 (m-30) REVERT: e 278 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7674 (mm-40) REVERT: e 314 ASN cc_start: 0.7098 (t0) cc_final: 0.6836 (t0) REVERT: e 316 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6783 (mt-10) REVERT: f 186 ILE cc_start: 0.8637 (mm) cc_final: 0.8324 (mm) REVERT: f 290 LYS cc_start: 0.6932 (mtpp) cc_final: 0.6612 (mmtm) REVERT: f 333 SER cc_start: 0.8660 (t) cc_final: 0.8430 (p) REVERT: f 396 LYS cc_start: 0.7809 (ptmt) cc_final: 0.7251 (mttp) REVERT: g 64 ASN cc_start: 0.8548 (m-40) cc_final: 0.8313 (m-40) REVERT: g 101 ASP cc_start: 0.7405 (m-30) cc_final: 0.6971 (m-30) REVERT: g 105 THR cc_start: 0.8658 (t) cc_final: 0.8452 (p) REVERT: g 173 LYS cc_start: 0.7754 (tmtp) cc_final: 0.7360 (tppt) REVERT: g 188 GLU cc_start: 0.5868 (pt0) cc_final: 0.5648 (pt0) REVERT: h 234 ASP cc_start: 0.8302 (p0) cc_final: 0.8052 (p0) REVERT: j 59 ASP cc_start: 0.8573 (m-30) cc_final: 0.8211 (m-30) REVERT: k 129 MET cc_start: 0.7618 (mtp) cc_final: 0.7407 (ttm) REVERT: m 174 TYR cc_start: 0.7752 (m-10) cc_final: 0.7518 (m-80) REVERT: m 195 TYR cc_start: 0.8045 (m-80) cc_final: 0.7603 (m-80) REVERT: n 31 LYS cc_start: 0.8093 (mtpt) cc_final: 0.7887 (mttm) REVERT: n 65 ASP cc_start: 0.7766 (m-30) cc_final: 0.7365 (m-30) outliers start: 142 outliers final: 88 residues processed: 1245 average time/residue: 0.6402 time to fit residues: 1283.6443 Evaluate side-chains 1113 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1017 time to evaluate : 5.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 229 SER Chi-restraints excluded: chain L residue 291 GLN Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 200 GLN Chi-restraints excluded: chain b residue 231 ILE Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 209 LEU Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 146 VAL Chi-restraints excluded: chain e residue 164 MET Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 78 ILE Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 170 THR Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 48 THR Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 71 LYS Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 151 GLU Chi-restraints excluded: chain n residue 192 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 313 optimal weight: 5.9990 chunk 175 optimal weight: 0.3980 chunk 470 optimal weight: 9.9990 chunk 384 optimal weight: 10.0000 chunk 155 optimal weight: 0.7980 chunk 565 optimal weight: 0.9990 chunk 611 optimal weight: 0.9980 chunk 503 optimal weight: 9.9990 chunk 561 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 453 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN A 232 GLN B 19 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN H 266 GLN J 68 GLN J 147 HIS K 84 ASN K 125 GLN L 152 GLN L 222 GLN L 277 HIS N 62 GLN a 232 GLN b 19 GLN ** c 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 252 GLN f 266 ASN f 311 GLN g 198 HIS k 125 GLN k 197 ASN l 108 ASN l 152 GLN l 222 GLN l 277 HIS ** m 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 94 GLN n 148 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 50354 Z= 0.177 Angle : 0.534 10.305 68116 Z= 0.281 Chirality : 0.043 0.209 7560 Planarity : 0.004 0.051 8826 Dihedral : 6.676 86.307 7102 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.05 % Allowed : 11.85 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.10), residues: 6304 helix: -0.67 (0.10), residues: 2178 sheet: -0.92 (0.13), residues: 1510 loop : -1.71 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 185 HIS 0.004 0.001 HIS i 95 PHE 0.025 0.001 PHE a 180 TYR 0.029 0.001 TYR H 218 ARG 0.006 0.001 ARG L 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1055 time to evaluate : 5.542 Fit side-chains revert: symmetry clash REVERT: A 70 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7599 (p) REVERT: B 184 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: B 200 GLN cc_start: 0.6278 (OUTLIER) cc_final: 0.5440 (mm-40) REVERT: B 205 ASN cc_start: 0.8082 (t0) cc_final: 0.7762 (t0) REVERT: B 217 GLU cc_start: 0.7647 (pp20) cc_final: 0.7432 (pp20) REVERT: C 29 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7476 (mm-40) REVERT: C 57 ASP cc_start: 0.7796 (t0) cc_final: 0.7500 (t0) REVERT: C 196 LEU cc_start: 0.7730 (mt) cc_final: 0.7461 (mt) REVERT: C 262 ASP cc_start: 0.7509 (p0) cc_final: 0.7140 (p0) REVERT: D 4 ASP cc_start: 0.7285 (p0) cc_final: 0.6563 (p0) REVERT: D 46 GLU cc_start: 0.6599 (tm-30) cc_final: 0.6302 (tm-30) REVERT: D 102 MET cc_start: 0.6236 (ttt) cc_final: 0.5800 (ptm) REVERT: D 182 ARG cc_start: 0.7226 (tmm-80) cc_final: 0.6513 (tmm160) REVERT: D 183 ASP cc_start: 0.7185 (m-30) cc_final: 0.6387 (m-30) REVERT: E 293 GLU cc_start: 0.7513 (tt0) cc_final: 0.6899 (tp30) REVERT: E 314 ASN cc_start: 0.6577 (t0) cc_final: 0.6348 (t0) REVERT: E 316 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6766 (mt-10) REVERT: F 186 ILE cc_start: 0.8651 (mm) cc_final: 0.8334 (mm) REVERT: F 290 LYS cc_start: 0.7952 (mmtm) cc_final: 0.6748 (mtmt) REVERT: F 396 LYS cc_start: 0.7747 (ptmt) cc_final: 0.7299 (mttp) REVERT: G 32 ASP cc_start: 0.8455 (m-30) cc_final: 0.8228 (m-30) REVERT: G 64 ASN cc_start: 0.8617 (m-40) cc_final: 0.8322 (m-40) REVERT: G 101 ASP cc_start: 0.7442 (m-30) cc_final: 0.7094 (m-30) REVERT: G 105 THR cc_start: 0.8670 (t) cc_final: 0.8423 (p) REVERT: G 212 GLU cc_start: 0.7787 (tt0) cc_final: 0.7565 (tt0) REVERT: H 105 ASP cc_start: 0.8242 (m-30) cc_final: 0.7700 (m-30) REVERT: H 139 LYS cc_start: 0.8250 (mmtp) cc_final: 0.8006 (mmmm) REVERT: H 234 ASP cc_start: 0.8257 (p0) cc_final: 0.8001 (p0) REVERT: I 181 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8323 (mtmm) REVERT: I 214 LEU cc_start: 0.8583 (tp) cc_final: 0.8371 (tt) REVERT: J 79 GLU cc_start: 0.7141 (mp0) cc_final: 0.6566 (mt-10) REVERT: J 106 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7820 (mt-10) REVERT: J 189 ILE cc_start: 0.7942 (pt) cc_final: 0.7624 (mp) REVERT: K 69 ARG cc_start: 0.6841 (mtt180) cc_final: 0.6614 (mtp180) REVERT: M 174 TYR cc_start: 0.7835 (m-10) cc_final: 0.7607 (m-80) REVERT: M 195 TYR cc_start: 0.8013 (m-80) cc_final: 0.7754 (m-80) REVERT: N 31 LYS cc_start: 0.8107 (mttt) cc_final: 0.7881 (mttm) REVERT: a 55 ASP cc_start: 0.7061 (t0) cc_final: 0.6779 (t0) REVERT: a 215 LYS cc_start: 0.7760 (mtpt) cc_final: 0.7260 (mmtm) REVERT: b 21 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7074 (mm-30) REVERT: b 200 GLN cc_start: 0.6027 (OUTLIER) cc_final: 0.5129 (mm-40) REVERT: b 217 GLU cc_start: 0.7610 (pp20) cc_final: 0.7386 (pp20) REVERT: b 231 ILE cc_start: 0.5208 (OUTLIER) cc_final: 0.4863 (pp) REVERT: c 29 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7224 (mm110) REVERT: c 50 MET cc_start: 0.6617 (pmm) cc_final: 0.6331 (ptp) REVERT: c 57 ASP cc_start: 0.7905 (t0) cc_final: 0.7643 (t0) REVERT: c 196 LEU cc_start: 0.7734 (mt) cc_final: 0.7483 (mt) REVERT: c 262 ASP cc_start: 0.7497 (p0) cc_final: 0.7081 (p0) REVERT: d 4 ASP cc_start: 0.7243 (p0) cc_final: 0.6451 (p0) REVERT: d 92 GLN cc_start: 0.5805 (mm-40) cc_final: 0.5334 (tm-30) REVERT: d 102 MET cc_start: 0.6170 (ttt) cc_final: 0.5762 (ptm) REVERT: d 167 THR cc_start: 0.8922 (m) cc_final: 0.8711 (p) REVERT: e 266 ASP cc_start: 0.8342 (m-30) cc_final: 0.7928 (m-30) REVERT: e 278 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7593 (mm-40) REVERT: e 314 ASN cc_start: 0.7055 (t0) cc_final: 0.6787 (t0) REVERT: f 186 ILE cc_start: 0.8600 (mm) cc_final: 0.8313 (mm) REVERT: f 290 LYS cc_start: 0.6911 (mtpp) cc_final: 0.6540 (mmtm) REVERT: f 333 SER cc_start: 0.8691 (t) cc_final: 0.8368 (p) REVERT: f 373 LYS cc_start: 0.8263 (mmtm) cc_final: 0.8053 (mmtm) REVERT: f 396 LYS cc_start: 0.7834 (ptmt) cc_final: 0.7319 (mttp) REVERT: g 64 ASN cc_start: 0.8615 (m-40) cc_final: 0.8366 (m-40) REVERT: g 101 ASP cc_start: 0.7449 (m-30) cc_final: 0.6978 (m-30) REVERT: g 105 THR cc_start: 0.8689 (t) cc_final: 0.8446 (p) REVERT: g 173 LYS cc_start: 0.7760 (tmtp) cc_final: 0.7151 (ttmm) REVERT: h 102 SER cc_start: 0.8697 (t) cc_final: 0.8118 (t) REVERT: h 105 ASP cc_start: 0.8232 (m-30) cc_final: 0.7673 (m-30) REVERT: h 234 ASP cc_start: 0.8280 (p0) cc_final: 0.8076 (p0) REVERT: j 4 MET cc_start: 0.8248 (mmm) cc_final: 0.7599 (mmm) REVERT: j 106 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7684 (mt-10) REVERT: j 203 ARG cc_start: 0.8243 (mtp85) cc_final: 0.8019 (mtp85) REVERT: k 129 MET cc_start: 0.7725 (mtp) cc_final: 0.7444 (ttm) REVERT: k 173 LYS cc_start: 0.7943 (mtmm) cc_final: 0.7738 (mtpp) REVERT: m 195 TYR cc_start: 0.8035 (m-80) cc_final: 0.7718 (m-80) REVERT: m 207 LYS cc_start: 0.8033 (tttp) cc_final: 0.7183 (tptm) REVERT: n 31 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7962 (mttm) REVERT: n 137 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.6702 (t80) outliers start: 160 outliers final: 121 residues processed: 1160 average time/residue: 0.6649 time to fit residues: 1258.5436 Evaluate side-chains 1127 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1000 time to evaluate : 5.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain L residue 292 THR Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 200 GLN Chi-restraints excluded: chain b residue 231 ILE Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 60 SER Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 79 ASP Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 146 VAL Chi-restraints excluded: chain e residue 164 MET Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 178 MET Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 78 ILE Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain h residue 175 VAL Chi-restraints excluded: chain h residue 271 SER Chi-restraints excluded: chain i residue 53 SER Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 158 SER Chi-restraints excluded: chain i residue 203 ASP Chi-restraints excluded: chain i residue 214 LEU Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 147 HIS Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain j residue 193 ASP Chi-restraints excluded: chain k residue 48 THR Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 289 ASP Chi-restraints excluded: chain l residue 292 THR Chi-restraints excluded: chain m residue 145 VAL Chi-restraints excluded: chain m residue 293 THR Chi-restraints excluded: chain m residue 325 THR Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 103 LEU Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 137 TYR Chi-restraints excluded: chain n residue 151 GLU Chi-restraints excluded: chain n residue 192 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 559 optimal weight: 4.9990 chunk 425 optimal weight: 0.4980 chunk 293 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 270 optimal weight: 6.9990 chunk 379 optimal weight: 2.9990 chunk 567 optimal weight: 6.9990 chunk 601 optimal weight: 7.9990 chunk 296 optimal weight: 9.9990 chunk 538 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 HIS J 60 GLN K 125 GLN L 128 GLN L 152 GLN N 148 GLN ** a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 228 ASN a 232 GLN b 143 HIS ** c 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 252 GLN f 225 GLN ** j 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 147 HIS k 125 GLN l 128 GLN l 222 GLN ** m 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 50354 Z= 0.240 Angle : 0.550 10.188 68116 Z= 0.288 Chirality : 0.044 0.202 7560 Planarity : 0.004 0.052 8826 Dihedral : 6.703 81.517 7102 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.68 % Allowed : 12.73 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.10), residues: 6304 helix: 0.03 (0.11), residues: 2186 sheet: -0.79 (0.13), residues: 1526 loop : -1.53 (0.11), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 185 HIS 0.005 0.001 HIS c 103 PHE 0.019 0.001 PHE A 231 TYR 0.037 0.002 TYR H 218 ARG 0.013 0.001 ARG f 395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1006 time to evaluate : 5.909 Fit side-chains REVERT: A 172 LYS cc_start: 0.8299 (tppt) cc_final: 0.8045 (tttt) REVERT: B 184 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: B 200 GLN cc_start: 0.6339 (OUTLIER) cc_final: 0.5571 (mm-40) REVERT: B 205 ASN cc_start: 0.8047 (t0) cc_final: 0.7731 (t0) REVERT: C 29 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7457 (mm-40) REVERT: C 57 ASP cc_start: 0.7853 (t0) cc_final: 0.7463 (t0) REVERT: C 196 LEU cc_start: 0.7750 (mt) cc_final: 0.7480 (mt) REVERT: C 262 ASP cc_start: 0.7458 (p0) cc_final: 0.7177 (p0) REVERT: D 4 ASP cc_start: 0.7427 (p0) cc_final: 0.6690 (p0) REVERT: D 46 GLU cc_start: 0.6576 (tm-30) cc_final: 0.6206 (tm-30) REVERT: D 102 MET cc_start: 0.6393 (ttt) cc_final: 0.5863 (ptm) REVERT: D 182 ARG cc_start: 0.7358 (tmm-80) cc_final: 0.6488 (tmm160) REVERT: D 183 ASP cc_start: 0.7182 (m-30) cc_final: 0.6506 (m-30) REVERT: D 187 HIS cc_start: 0.7730 (t-90) cc_final: 0.7480 (t-90) REVERT: E 293 GLU cc_start: 0.7524 (tt0) cc_final: 0.6925 (tp30) REVERT: E 300 ASP cc_start: 0.7204 (t70) cc_final: 0.6987 (t70) REVERT: E 314 ASN cc_start: 0.6560 (t0) cc_final: 0.6319 (t0) REVERT: F 186 ILE cc_start: 0.8683 (mm) cc_final: 0.8368 (mm) REVERT: F 290 LYS cc_start: 0.8072 (mmtm) cc_final: 0.6752 (mtmt) REVERT: G 32 ASP cc_start: 0.8462 (m-30) cc_final: 0.8224 (m-30) REVERT: G 64 ASN cc_start: 0.8679 (m-40) cc_final: 0.8379 (m-40) REVERT: G 101 ASP cc_start: 0.7512 (m-30) cc_final: 0.7144 (m-30) REVERT: G 105 THR cc_start: 0.8715 (t) cc_final: 0.8410 (p) REVERT: H 139 LYS cc_start: 0.8320 (mmtp) cc_final: 0.8092 (mmmm) REVERT: I 181 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8315 (mtmm) REVERT: I 214 LEU cc_start: 0.8699 (tp) cc_final: 0.8457 (tt) REVERT: J 32 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.6636 (mt) REVERT: J 106 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7861 (mt-10) REVERT: J 189 ILE cc_start: 0.7888 (pt) cc_final: 0.7616 (mp) REVERT: K 69 ARG cc_start: 0.6816 (mtt180) cc_final: 0.6612 (mtp180) REVERT: L 128 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8404 (tp-100) REVERT: M 182 MET cc_start: 0.8127 (ttt) cc_final: 0.7594 (ttt) REVERT: M 195 TYR cc_start: 0.8112 (m-80) cc_final: 0.7812 (m-80) REVERT: M 225 ARG cc_start: 0.8183 (mtp180) cc_final: 0.7737 (ttp-170) REVERT: N 31 LYS cc_start: 0.8114 (mttt) cc_final: 0.7905 (mttm) REVERT: N 40 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8325 (pp) REVERT: a 215 LYS cc_start: 0.7769 (mtpt) cc_final: 0.7377 (mmtm) REVERT: b 21 GLU cc_start: 0.7273 (mm-30) cc_final: 0.7057 (mm-30) REVERT: b 200 GLN cc_start: 0.6227 (OUTLIER) cc_final: 0.5293 (mm-40) REVERT: c 29 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7430 (mm-40) REVERT: c 57 ASP cc_start: 0.7819 (t0) cc_final: 0.7507 (t0) REVERT: c 196 LEU cc_start: 0.7724 (mt) cc_final: 0.7462 (mt) REVERT: c 262 ASP cc_start: 0.7466 (p0) cc_final: 0.7142 (p0) REVERT: d 4 ASP cc_start: 0.7264 (p0) cc_final: 0.6482 (p0) REVERT: d 46 GLU cc_start: 0.6125 (tm-30) cc_final: 0.5535 (tm-30) REVERT: d 92 GLN cc_start: 0.5797 (mm-40) cc_final: 0.5233 (tm-30) REVERT: d 102 MET cc_start: 0.6315 (ttt) cc_final: 0.5919 (ptm) REVERT: d 167 THR cc_start: 0.8959 (m) cc_final: 0.8736 (p) REVERT: e 266 ASP cc_start: 0.8392 (m-30) cc_final: 0.8010 (m-30) REVERT: e 278 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7588 (mm-40) REVERT: e 314 ASN cc_start: 0.7009 (t0) cc_final: 0.6721 (t0) REVERT: f 186 ILE cc_start: 0.8648 (mm) cc_final: 0.8356 (mm) REVERT: g 64 ASN cc_start: 0.8655 (m-40) cc_final: 0.8369 (m-40) REVERT: g 101 ASP cc_start: 0.7455 (m-30) cc_final: 0.7172 (m-30) REVERT: g 105 THR cc_start: 0.8722 (t) cc_final: 0.8401 (p) REVERT: g 173 LYS cc_start: 0.7726 (tmtp) cc_final: 0.7256 (ttmm) REVERT: g 175 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8172 (mt-10) REVERT: h 102 SER cc_start: 0.8784 (t) cc_final: 0.8170 (t) REVERT: h 105 ASP cc_start: 0.8282 (m-30) cc_final: 0.7709 (m-30) REVERT: h 139 LYS cc_start: 0.7976 (tttm) cc_final: 0.7422 (mmmm) REVERT: h 234 ASP cc_start: 0.8245 (p0) cc_final: 0.7998 (p0) REVERT: i 71 MET cc_start: 0.8035 (mmt) cc_final: 0.7818 (mmt) REVERT: i 181 LYS cc_start: 0.8592 (ttmt) cc_final: 0.8286 (mtmm) REVERT: j 32 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.6771 (mt) REVERT: j 106 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7859 (mt-10) REVERT: k 129 MET cc_start: 0.7666 (mtp) cc_final: 0.7356 (ttm) REVERT: l 128 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8773 (tp-100) REVERT: m 174 TYR cc_start: 0.7962 (m-80) cc_final: 0.7728 (m-80) REVERT: m 182 MET cc_start: 0.8155 (ttt) cc_final: 0.7649 (ttt) REVERT: m 195 TYR cc_start: 0.8132 (m-80) cc_final: 0.7730 (m-80) REVERT: m 225 ARG cc_start: 0.8145 (mtp180) cc_final: 0.7649 (ttp-170) REVERT: n 31 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7989 (mttm) REVERT: n 137 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.6793 (t80) outliers start: 193 outliers final: 146 residues processed: 1136 average time/residue: 0.6233 time to fit residues: 1152.8115 Evaluate side-chains 1113 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 958 time to evaluate : 5.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain L residue 292 THR Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 330 GLN Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain N residue 215 LYS Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 200 GLN Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 60 SER Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 79 ASP Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 169 ILE Chi-restraints excluded: chain d residue 209 LEU Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 146 VAL Chi-restraints excluded: chain e residue 164 MET Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 178 MET Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 78 ILE Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 170 THR Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain h residue 175 VAL Chi-restraints excluded: chain h residue 271 SER Chi-restraints excluded: chain i residue 77 THR Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 158 SER Chi-restraints excluded: chain i residue 214 LEU Chi-restraints excluded: chain i residue 219 ASP Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 71 THR Chi-restraints excluded: chain j residue 147 HIS Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 48 THR Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain k residue 163 SER Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 128 GLN Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 247 SER Chi-restraints excluded: chain l residue 287 SER Chi-restraints excluded: chain l residue 289 ASP Chi-restraints excluded: chain l residue 292 THR Chi-restraints excluded: chain m residue 145 VAL Chi-restraints excluded: chain m residue 293 THR Chi-restraints excluded: chain m residue 325 THR Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 103 LEU Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 137 TYR Chi-restraints excluded: chain n residue 151 GLU Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain n residue 215 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 500 optimal weight: 2.9990 chunk 341 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 447 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 513 optimal weight: 8.9990 chunk 415 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 539 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN K 73 HIS K 125 GLN L 128 GLN ** L 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN ** c 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 223 GLN ** e 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 60 GLN j 147 HIS l 128 GLN l 222 GLN ** m 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 234 ASN ** m 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 50354 Z= 0.257 Angle : 0.552 10.244 68116 Z= 0.289 Chirality : 0.044 0.205 7560 Planarity : 0.004 0.052 8826 Dihedral : 6.748 83.709 7102 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.74 % Allowed : 13.99 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.10), residues: 6304 helix: 0.39 (0.11), residues: 2178 sheet: -0.71 (0.13), residues: 1536 loop : -1.44 (0.11), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 185 HIS 0.008 0.001 HIS j 147 PHE 0.026 0.001 PHE A 180 TYR 0.035 0.002 TYR H 218 ARG 0.009 0.001 ARG F 395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 972 time to evaluate : 5.795 Fit side-chains revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8317 (tppt) cc_final: 0.8107 (tttt) REVERT: B 200 GLN cc_start: 0.6133 (OUTLIER) cc_final: 0.5376 (mm-40) REVERT: B 205 ASN cc_start: 0.8052 (t0) cc_final: 0.7735 (t0) REVERT: C 29 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7414 (mm-40) REVERT: C 57 ASP cc_start: 0.7788 (t0) cc_final: 0.7428 (t0) REVERT: C 196 LEU cc_start: 0.7756 (mt) cc_final: 0.7476 (mt) REVERT: C 262 ASP cc_start: 0.7439 (p0) cc_final: 0.6979 (p0) REVERT: C 263 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7330 (mm110) REVERT: D 4 ASP cc_start: 0.7399 (p0) cc_final: 0.6663 (p0) REVERT: D 46 GLU cc_start: 0.6584 (tm-30) cc_final: 0.6170 (tm-30) REVERT: D 182 ARG cc_start: 0.7360 (tmm-80) cc_final: 0.6539 (tmm160) REVERT: D 183 ASP cc_start: 0.7183 (m-30) cc_final: 0.6803 (m-30) REVERT: D 187 HIS cc_start: 0.7732 (t-90) cc_final: 0.7467 (t-90) REVERT: E 162 SER cc_start: 0.8033 (p) cc_final: 0.7638 (t) REVERT: E 278 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7384 (mm110) REVERT: E 293 GLU cc_start: 0.7390 (tt0) cc_final: 0.6848 (tp30) REVERT: E 314 ASN cc_start: 0.6581 (t0) cc_final: 0.6248 (t0) REVERT: F 186 ILE cc_start: 0.8706 (mm) cc_final: 0.8410 (mm) REVERT: F 290 LYS cc_start: 0.8041 (mmtm) cc_final: 0.6734 (mtmt) REVERT: G 32 ASP cc_start: 0.8471 (m-30) cc_final: 0.8238 (m-30) REVERT: G 64 ASN cc_start: 0.8697 (m-40) cc_final: 0.8380 (m-40) REVERT: G 101 ASP cc_start: 0.7521 (m-30) cc_final: 0.7192 (m-30) REVERT: G 105 THR cc_start: 0.8709 (t) cc_final: 0.8411 (p) REVERT: I 156 MET cc_start: 0.7834 (mmm) cc_final: 0.7617 (mmt) REVERT: I 181 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8404 (mtmm) REVERT: J 12 MET cc_start: 0.7890 (ttp) cc_final: 0.7555 (ttp) REVERT: J 32 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.6639 (mt) REVERT: J 106 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7931 (mt-10) REVERT: J 189 ILE cc_start: 0.7928 (pt) cc_final: 0.7612 (mp) REVERT: L 128 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8636 (tp-100) REVERT: M 195 TYR cc_start: 0.8086 (m-80) cc_final: 0.7740 (m-80) REVERT: M 225 ARG cc_start: 0.8226 (mtp180) cc_final: 0.7681 (ttp-170) REVERT: N 31 LYS cc_start: 0.8144 (mttt) cc_final: 0.7925 (mttm) REVERT: N 40 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8314 (pp) REVERT: N 65 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7220 (m-30) REVERT: b 200 GLN cc_start: 0.6099 (OUTLIER) cc_final: 0.5343 (mm-40) REVERT: b 231 ILE cc_start: 0.5402 (OUTLIER) cc_final: 0.5136 (pp) REVERT: c 29 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7400 (mm-40) REVERT: c 57 ASP cc_start: 0.7812 (t0) cc_final: 0.7498 (t0) REVERT: c 196 LEU cc_start: 0.7725 (mt) cc_final: 0.7476 (mt) REVERT: c 262 ASP cc_start: 0.7520 (p0) cc_final: 0.7164 (p0) REVERT: c 263 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7358 (mm110) REVERT: d 4 ASP cc_start: 0.7293 (p0) cc_final: 0.6483 (p0) REVERT: d 46 GLU cc_start: 0.6189 (tm-30) cc_final: 0.5748 (tm-30) REVERT: d 92 GLN cc_start: 0.5651 (mm-40) cc_final: 0.5182 (tm-30) REVERT: d 102 MET cc_start: 0.6373 (ttt) cc_final: 0.5871 (ptm) REVERT: d 167 THR cc_start: 0.8952 (m) cc_final: 0.8739 (p) REVERT: d 213 GLU cc_start: 0.6352 (pt0) cc_final: 0.5984 (tp30) REVERT: e 266 ASP cc_start: 0.8394 (m-30) cc_final: 0.8002 (m-30) REVERT: e 314 ASN cc_start: 0.6975 (t0) cc_final: 0.6659 (t0) REVERT: f 186 ILE cc_start: 0.8699 (mm) cc_final: 0.8406 (mm) REVERT: g 32 ASP cc_start: 0.8586 (m-30) cc_final: 0.8361 (m-30) REVERT: g 64 ASN cc_start: 0.8671 (m-40) cc_final: 0.8372 (m-40) REVERT: g 101 ASP cc_start: 0.7422 (m-30) cc_final: 0.7151 (m-30) REVERT: g 105 THR cc_start: 0.8732 (t) cc_final: 0.8393 (p) REVERT: g 175 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8192 (mt-10) REVERT: h 102 SER cc_start: 0.8797 (t) cc_final: 0.8214 (t) REVERT: h 105 ASP cc_start: 0.8271 (m-30) cc_final: 0.7727 (m-30) REVERT: h 139 LYS cc_start: 0.7977 (tttm) cc_final: 0.7510 (mmtp) REVERT: i 113 LYS cc_start: 0.8600 (ptmm) cc_final: 0.8283 (pttp) REVERT: i 181 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8255 (mtmm) REVERT: j 12 MET cc_start: 0.7870 (ttp) cc_final: 0.7546 (ttp) REVERT: j 32 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.6617 (mt) REVERT: j 106 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7891 (mt-10) REVERT: k 129 MET cc_start: 0.7685 (mtp) cc_final: 0.7369 (ttm) REVERT: l 128 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8793 (tp-100) REVERT: m 195 TYR cc_start: 0.8098 (m-80) cc_final: 0.7730 (m-80) REVERT: m 207 LYS cc_start: 0.7930 (tttp) cc_final: 0.7213 (tptm) REVERT: m 225 ARG cc_start: 0.8180 (mtp180) cc_final: 0.7559 (ttp-170) REVERT: n 31 LYS cc_start: 0.8296 (mtpt) cc_final: 0.8041 (mttm) REVERT: n 137 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.6775 (t80) outliers start: 196 outliers final: 163 residues processed: 1089 average time/residue: 0.6359 time to fit residues: 1122.6131 Evaluate side-chains 1108 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 934 time to evaluate : 5.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain L residue 292 THR Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 167 LYS Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 330 GLN Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain N residue 215 LYS Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 146 ASP Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 200 GLN Chi-restraints excluded: chain b residue 231 ILE Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 60 SER Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 79 ASP Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 169 ILE Chi-restraints excluded: chain d residue 223 GLN Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 146 VAL Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 178 MET Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain g residue 11 SER Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 78 ILE Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 170 THR Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain g residue 208 LEU Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain h residue 175 VAL Chi-restraints excluded: chain h residue 204 SER Chi-restraints excluded: chain h residue 271 SER Chi-restraints excluded: chain i residue 77 THR Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 158 SER Chi-restraints excluded: chain i residue 203 ASP Chi-restraints excluded: chain i residue 214 LEU Chi-restraints excluded: chain i residue 219 ASP Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 71 THR Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 147 HIS Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain k residue 163 SER Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 128 GLN Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 247 SER Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain l residue 287 SER Chi-restraints excluded: chain l residue 289 ASP Chi-restraints excluded: chain l residue 292 THR Chi-restraints excluded: chain m residue 145 VAL Chi-restraints excluded: chain m residue 293 THR Chi-restraints excluded: chain m residue 320 SER Chi-restraints excluded: chain m residue 325 THR Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain m residue 331 GLN Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 103 LEU Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 137 TYR Chi-restraints excluded: chain n residue 151 GLU Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain n residue 215 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 202 optimal weight: 5.9990 chunk 541 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 352 optimal weight: 9.9990 chunk 148 optimal weight: 0.6980 chunk 601 optimal weight: 6.9990 chunk 499 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 315 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 ASN H 266 GLN K 125 GLN L 128 GLN ** L 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN N 185 GLN c 53 HIS ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 223 GLN ** e 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 114 ASN h 261 GLN j 147 HIS k 73 HIS l 128 GLN ** m 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 185 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 50354 Z= 0.271 Angle : 0.555 10.310 68116 Z= 0.291 Chirality : 0.045 0.212 7560 Planarity : 0.004 0.053 8826 Dihedral : 6.816 89.900 7102 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.31 % Allowed : 14.16 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.10), residues: 6304 helix: 0.54 (0.11), residues: 2184 sheet: -0.66 (0.13), residues: 1532 loop : -1.39 (0.12), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 185 HIS 0.013 0.001 HIS j 147 PHE 0.021 0.001 PHE A 180 TYR 0.035 0.002 TYR H 218 ARG 0.008 0.001 ARG F 395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1201 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 975 time to evaluate : 5.933 Fit side-chains REVERT: B 200 GLN cc_start: 0.6129 (OUTLIER) cc_final: 0.5396 (mm-40) REVERT: B 205 ASN cc_start: 0.8040 (t0) cc_final: 0.7694 (t0) REVERT: C 29 GLN cc_start: 0.7603 (mm-40) cc_final: 0.7321 (tm-30) REVERT: C 57 ASP cc_start: 0.7791 (t0) cc_final: 0.7423 (t0) REVERT: C 122 ASP cc_start: 0.7252 (m-30) cc_final: 0.7036 (m-30) REVERT: C 196 LEU cc_start: 0.7736 (mt) cc_final: 0.7489 (mt) REVERT: D 4 ASP cc_start: 0.7396 (p0) cc_final: 0.6673 (p0) REVERT: D 46 GLU cc_start: 0.6588 (tm-30) cc_final: 0.6217 (tm-30) REVERT: D 182 ARG cc_start: 0.7379 (tmm-80) cc_final: 0.6574 (tmm160) REVERT: D 183 ASP cc_start: 0.7230 (m-30) cc_final: 0.6853 (m-30) REVERT: E 162 SER cc_start: 0.8044 (p) cc_final: 0.7633 (t) REVERT: E 293 GLU cc_start: 0.7434 (tt0) cc_final: 0.6877 (tp30) REVERT: E 314 ASN cc_start: 0.6660 (t0) cc_final: 0.6260 (t0) REVERT: F 186 ILE cc_start: 0.8711 (mm) cc_final: 0.8414 (mm) REVERT: F 290 LYS cc_start: 0.8058 (mmtm) cc_final: 0.6744 (mtmt) REVERT: G 32 ASP cc_start: 0.8502 (m-30) cc_final: 0.8250 (m-30) REVERT: G 64 ASN cc_start: 0.8705 (m-40) cc_final: 0.8370 (m110) REVERT: G 101 ASP cc_start: 0.7503 (m-30) cc_final: 0.7126 (m-30) REVERT: G 105 THR cc_start: 0.8716 (t) cc_final: 0.8393 (p) REVERT: I 156 MET cc_start: 0.7803 (mmm) cc_final: 0.7505 (mmt) REVERT: J 12 MET cc_start: 0.7928 (ttp) cc_final: 0.7569 (ttp) REVERT: J 18 GLU cc_start: 0.6835 (pm20) cc_final: 0.6534 (pm20) REVERT: J 32 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.6679 (mt) REVERT: J 106 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7958 (mt-10) REVERT: J 189 ILE cc_start: 0.7884 (pt) cc_final: 0.7556 (mp) REVERT: L 128 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8699 (tp-100) REVERT: L 215 ASP cc_start: 0.6962 (p0) cc_final: 0.6735 (p0) REVERT: M 195 TYR cc_start: 0.8168 (m-80) cc_final: 0.7810 (m-80) REVERT: M 225 ARG cc_start: 0.8209 (mtp180) cc_final: 0.7596 (ttp-170) REVERT: N 24 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8732 (mp) REVERT: N 31 LYS cc_start: 0.8193 (mttt) cc_final: 0.7976 (mttm) REVERT: N 40 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8353 (pp) REVERT: N 65 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7222 (m-30) REVERT: b 200 GLN cc_start: 0.6142 (OUTLIER) cc_final: 0.5388 (mm-40) REVERT: b 213 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6992 (pt0) REVERT: b 231 ILE cc_start: 0.5447 (OUTLIER) cc_final: 0.5210 (pp) REVERT: c 29 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7296 (tm-30) REVERT: c 57 ASP cc_start: 0.7818 (t0) cc_final: 0.7508 (t0) REVERT: c 196 LEU cc_start: 0.7693 (mt) cc_final: 0.7443 (mt) REVERT: d 4 ASP cc_start: 0.7302 (p0) cc_final: 0.6494 (p0) REVERT: d 46 GLU cc_start: 0.6222 (tm-30) cc_final: 0.5743 (tm-30) REVERT: d 92 GLN cc_start: 0.5657 (mm-40) cc_final: 0.5208 (tm-30) REVERT: d 102 MET cc_start: 0.6462 (ttt) cc_final: 0.5969 (ptm) REVERT: d 167 THR cc_start: 0.8947 (m) cc_final: 0.8740 (p) REVERT: d 181 SER cc_start: 0.7996 (p) cc_final: 0.7750 (t) REVERT: d 213 GLU cc_start: 0.6463 (pt0) cc_final: 0.6052 (tp30) REVERT: d 233 ARG cc_start: 0.5582 (OUTLIER) cc_final: 0.3890 (ttt90) REVERT: e 266 ASP cc_start: 0.8394 (m-30) cc_final: 0.8012 (m-30) REVERT: e 278 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7645 (mm-40) REVERT: e 314 ASN cc_start: 0.6943 (t0) cc_final: 0.6624 (t0) REVERT: f 186 ILE cc_start: 0.8725 (mm) cc_final: 0.8429 (mm) REVERT: g 32 ASP cc_start: 0.8595 (m-30) cc_final: 0.8376 (m-30) REVERT: g 64 ASN cc_start: 0.8693 (m-40) cc_final: 0.8381 (m-40) REVERT: g 101 ASP cc_start: 0.7414 (m-30) cc_final: 0.7121 (m-30) REVERT: g 105 THR cc_start: 0.8737 (t) cc_final: 0.8378 (p) REVERT: g 175 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8208 (mt-10) REVERT: h 102 SER cc_start: 0.8850 (t) cc_final: 0.8151 (t) REVERT: h 105 ASP cc_start: 0.8317 (m-30) cc_final: 0.7757 (m-30) REVERT: h 139 LYS cc_start: 0.8029 (tttm) cc_final: 0.7547 (mmtp) REVERT: i 113 LYS cc_start: 0.8631 (ptmm) cc_final: 0.8279 (pttp) REVERT: j 4 MET cc_start: 0.8148 (mmm) cc_final: 0.7710 (mmm) REVERT: j 12 MET cc_start: 0.7900 (ttp) cc_final: 0.7541 (ttp) REVERT: j 32 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.6636 (mt) REVERT: j 106 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7863 (mt-10) REVERT: l 128 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8796 (tp-100) REVERT: m 195 TYR cc_start: 0.8194 (m-80) cc_final: 0.7801 (m-80) REVERT: m 225 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7566 (ttp-170) REVERT: n 31 LYS cc_start: 0.8320 (mtpt) cc_final: 0.8061 (mttm) REVERT: n 137 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.6728 (t80) outliers start: 226 outliers final: 182 residues processed: 1114 average time/residue: 0.6532 time to fit residues: 1187.2343 Evaluate side-chains 1140 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 945 time to evaluate : 5.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 247 SER Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain L residue 292 THR Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 167 LYS Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 330 GLN Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 153 ASN Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain N residue 215 LYS Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 200 GLN Chi-restraints excluded: chain b residue 213 GLU Chi-restraints excluded: chain b residue 231 ILE Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 60 SER Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 79 ASP Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 169 ILE Chi-restraints excluded: chain d residue 209 LEU Chi-restraints excluded: chain d residue 223 GLN Chi-restraints excluded: chain d residue 233 ARG Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 146 VAL Chi-restraints excluded: chain e residue 164 MET Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 178 MET Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain g residue 11 SER Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 78 ILE Chi-restraints excluded: chain g residue 82 LEU Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 170 THR Chi-restraints excluded: chain g residue 187 ASP Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain g residue 208 LEU Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain h residue 175 VAL Chi-restraints excluded: chain h residue 204 SER Chi-restraints excluded: chain h residue 271 SER Chi-restraints excluded: chain i residue 77 THR Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 158 SER Chi-restraints excluded: chain i residue 203 ASP Chi-restraints excluded: chain i residue 214 LEU Chi-restraints excluded: chain i residue 219 ASP Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 71 THR Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 147 HIS Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 48 THR Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain k residue 163 SER Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 128 GLN Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 247 SER Chi-restraints excluded: chain l residue 287 SER Chi-restraints excluded: chain l residue 289 ASP Chi-restraints excluded: chain l residue 292 THR Chi-restraints excluded: chain m residue 145 VAL Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 293 THR Chi-restraints excluded: chain m residue 320 SER Chi-restraints excluded: chain m residue 325 THR Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain m residue 330 GLN Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 103 LEU Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 137 TYR Chi-restraints excluded: chain n residue 151 GLU Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain n residue 215 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 580 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 342 optimal weight: 5.9990 chunk 439 optimal weight: 0.9980 chunk 340 optimal weight: 7.9990 chunk 506 optimal weight: 1.9990 chunk 336 optimal weight: 8.9990 chunk 599 optimal weight: 6.9990 chunk 375 optimal weight: 0.3980 chunk 365 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 223 GLN ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN K 125 GLN L 128 GLN ** L 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN a 228 ASN a 232 GLN ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 223 GLN ** e 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 147 HIS l 128 GLN ** m 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 50354 Z= 0.250 Angle : 0.545 10.257 68116 Z= 0.286 Chirality : 0.044 0.227 7560 Planarity : 0.004 0.053 8826 Dihedral : 6.786 89.225 7102 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.29 % Allowed : 14.68 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.10), residues: 6304 helix: 0.69 (0.11), residues: 2186 sheet: -0.60 (0.13), residues: 1526 loop : -1.37 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 185 HIS 0.010 0.001 HIS F 343 PHE 0.019 0.001 PHE A 180 TYR 0.032 0.001 TYR h 218 ARG 0.007 0.000 ARG F 395 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 971 time to evaluate : 5.669 Fit side-chains REVERT: B 200 GLN cc_start: 0.6162 (OUTLIER) cc_final: 0.5463 (mm-40) REVERT: B 205 ASN cc_start: 0.8024 (t0) cc_final: 0.7678 (t0) REVERT: C 29 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7133 (mt0) REVERT: C 57 ASP cc_start: 0.7785 (t0) cc_final: 0.7404 (t0) REVERT: C 122 ASP cc_start: 0.7244 (m-30) cc_final: 0.7030 (m-30) REVERT: C 196 LEU cc_start: 0.7740 (mt) cc_final: 0.7498 (mt) REVERT: D 4 ASP cc_start: 0.7384 (p0) cc_final: 0.6677 (p0) REVERT: D 46 GLU cc_start: 0.6650 (tm-30) cc_final: 0.6313 (tm-30) REVERT: D 182 ARG cc_start: 0.7336 (tmm-80) cc_final: 0.6530 (tmm160) REVERT: D 183 ASP cc_start: 0.7252 (m-30) cc_final: 0.6860 (m-30) REVERT: E 162 SER cc_start: 0.8064 (p) cc_final: 0.7669 (t) REVERT: E 293 GLU cc_start: 0.7345 (tt0) cc_final: 0.6797 (tp30) REVERT: E 314 ASN cc_start: 0.6695 (t0) cc_final: 0.6201 (t0) REVERT: F 186 ILE cc_start: 0.8712 (mm) cc_final: 0.8442 (mm) REVERT: F 290 LYS cc_start: 0.8035 (mmtm) cc_final: 0.6706 (mtmt) REVERT: G 32 ASP cc_start: 0.8498 (m-30) cc_final: 0.8257 (m-30) REVERT: G 64 ASN cc_start: 0.8711 (m-40) cc_final: 0.8381 (m110) REVERT: G 101 ASP cc_start: 0.7504 (m-30) cc_final: 0.7142 (m-30) REVERT: G 105 THR cc_start: 0.8717 (t) cc_final: 0.8395 (p) REVERT: G 188 GLU cc_start: 0.5729 (pt0) cc_final: 0.5404 (pt0) REVERT: I 156 MET cc_start: 0.7755 (mmm) cc_final: 0.7450 (mmt) REVERT: I 181 LYS cc_start: 0.8594 (mtmm) cc_final: 0.8333 (mtmm) REVERT: J 12 MET cc_start: 0.7972 (ttp) cc_final: 0.7619 (ttp) REVERT: J 18 GLU cc_start: 0.6787 (pm20) cc_final: 0.6473 (pm20) REVERT: J 32 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.6718 (mt) REVERT: J 106 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7943 (mt-10) REVERT: J 189 ILE cc_start: 0.7912 (pt) cc_final: 0.7574 (mp) REVERT: L 128 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8730 (tp-100) REVERT: M 195 TYR cc_start: 0.8195 (m-80) cc_final: 0.7822 (m-80) REVERT: M 225 ARG cc_start: 0.8201 (mtp180) cc_final: 0.7536 (ttp-170) REVERT: M 293 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7833 (m) REVERT: N 24 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8766 (mp) REVERT: N 31 LYS cc_start: 0.8191 (mttt) cc_final: 0.7970 (mttm) REVERT: N 40 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8341 (pp) REVERT: N 65 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7197 (m-30) REVERT: a 141 ASP cc_start: 0.8031 (p0) cc_final: 0.7817 (p0) REVERT: b 213 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6634 (pt0) REVERT: b 231 ILE cc_start: 0.5451 (OUTLIER) cc_final: 0.5229 (pp) REVERT: c 29 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7310 (tm-30) REVERT: c 57 ASP cc_start: 0.7833 (t0) cc_final: 0.7502 (t0) REVERT: c 122 ASP cc_start: 0.7328 (m-30) cc_final: 0.7112 (m-30) REVERT: c 196 LEU cc_start: 0.7695 (mt) cc_final: 0.7450 (mt) REVERT: d 4 ASP cc_start: 0.7277 (p0) cc_final: 0.6539 (p0) REVERT: d 46 GLU cc_start: 0.6225 (tm-30) cc_final: 0.5742 (tm-30) REVERT: d 92 GLN cc_start: 0.5632 (mm-40) cc_final: 0.5203 (tm-30) REVERT: d 102 MET cc_start: 0.6468 (ttt) cc_final: 0.5983 (ptm) REVERT: d 167 THR cc_start: 0.8946 (m) cc_final: 0.8730 (p) REVERT: d 181 SER cc_start: 0.7889 (p) cc_final: 0.7677 (t) REVERT: d 213 GLU cc_start: 0.6399 (pt0) cc_final: 0.6007 (tp30) REVERT: d 233 ARG cc_start: 0.5539 (OUTLIER) cc_final: 0.3857 (ttt90) REVERT: e 266 ASP cc_start: 0.8418 (m-30) cc_final: 0.7995 (m-30) REVERT: e 278 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7661 (mm-40) REVERT: e 293 GLU cc_start: 0.7236 (tt0) cc_final: 0.6813 (tp30) REVERT: e 314 ASN cc_start: 0.7036 (t0) cc_final: 0.6691 (t0) REVERT: f 186 ILE cc_start: 0.8729 (mm) cc_final: 0.8453 (mm) REVERT: g 32 ASP cc_start: 0.8577 (m-30) cc_final: 0.8359 (m-30) REVERT: g 64 ASN cc_start: 0.8684 (m-40) cc_final: 0.8381 (m110) REVERT: g 101 ASP cc_start: 0.7432 (m-30) cc_final: 0.7098 (m-30) REVERT: g 105 THR cc_start: 0.8716 (t) cc_final: 0.8389 (p) REVERT: g 115 ARG cc_start: 0.7665 (mmt90) cc_final: 0.7022 (mtt180) REVERT: g 175 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8207 (mt-10) REVERT: h 139 LYS cc_start: 0.7976 (tttm) cc_final: 0.7577 (mmtp) REVERT: i 113 LYS cc_start: 0.8623 (ptmm) cc_final: 0.8339 (pttp) REVERT: i 181 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8288 (mtmm) REVERT: i 212 THR cc_start: 0.8803 (t) cc_final: 0.8567 (p) REVERT: j 12 MET cc_start: 0.7954 (ttp) cc_final: 0.7618 (ttp) REVERT: j 18 GLU cc_start: 0.6790 (pm20) cc_final: 0.6489 (pm20) REVERT: j 32 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.6678 (mt) REVERT: j 106 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7906 (mt-10) REVERT: l 128 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8852 (tp-100) REVERT: m 195 TYR cc_start: 0.8191 (m-80) cc_final: 0.7806 (m-80) REVERT: m 207 LYS cc_start: 0.7968 (tttp) cc_final: 0.7167 (tptm) REVERT: m 225 ARG cc_start: 0.8208 (mtp180) cc_final: 0.7511 (ttp-170) REVERT: n 31 LYS cc_start: 0.8310 (mtpt) cc_final: 0.8033 (mttm) REVERT: n 137 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.6820 (t80) outliers start: 225 outliers final: 189 residues processed: 1115 average time/residue: 0.6506 time to fit residues: 1185.3338 Evaluate side-chains 1141 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 939 time to evaluate : 6.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 247 SER Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain L residue 292 THR Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 167 LYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 330 GLN Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain N residue 215 LYS Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 133 VAL Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 213 GLU Chi-restraints excluded: chain b residue 231 ILE Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 60 SER Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 79 ASP Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 169 ILE Chi-restraints excluded: chain d residue 209 LEU Chi-restraints excluded: chain d residue 223 GLN Chi-restraints excluded: chain d residue 233 ARG Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 146 VAL Chi-restraints excluded: chain e residue 164 MET Chi-restraints excluded: chain e residue 165 SER Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 178 MET Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain g residue 11 SER Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 78 ILE Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 170 THR Chi-restraints excluded: chain g residue 187 ASP Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain h residue 175 VAL Chi-restraints excluded: chain h residue 204 SER Chi-restraints excluded: chain h residue 271 SER Chi-restraints excluded: chain i residue 66 MET Chi-restraints excluded: chain i residue 77 THR Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 158 SER Chi-restraints excluded: chain i residue 203 ASP Chi-restraints excluded: chain i residue 214 LEU Chi-restraints excluded: chain i residue 219 ASP Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 71 THR Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain k residue 163 SER Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 128 GLN Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 247 SER Chi-restraints excluded: chain l residue 287 SER Chi-restraints excluded: chain l residue 289 ASP Chi-restraints excluded: chain l residue 292 THR Chi-restraints excluded: chain m residue 145 VAL Chi-restraints excluded: chain m residue 234 ASN Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 293 THR Chi-restraints excluded: chain m residue 320 SER Chi-restraints excluded: chain m residue 325 THR Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain m residue 330 GLN Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 103 LEU Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 137 TYR Chi-restraints excluded: chain n residue 151 GLU Chi-restraints excluded: chain n residue 153 ASN Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain n residue 215 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 370 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 358 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 381 optimal weight: 6.9990 chunk 408 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 471 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 195 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 223 GLN ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN L 128 GLN ** L 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 142 GLN a 228 ASN ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 128 GLN l 152 GLN ** m 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 50354 Z= 0.322 Angle : 0.582 10.901 68116 Z= 0.305 Chirality : 0.046 0.299 7560 Planarity : 0.004 0.053 8826 Dihedral : 6.861 87.825 7102 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.48 % Allowed : 14.81 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.10), residues: 6304 helix: 0.66 (0.11), residues: 2192 sheet: -0.62 (0.13), residues: 1528 loop : -1.39 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 185 HIS 0.009 0.001 HIS K 76 PHE 0.019 0.002 PHE A 180 TYR 0.038 0.002 TYR h 218 ARG 0.008 0.001 ARG K 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 932 time to evaluate : 6.173 Fit side-chains REVERT: B 200 GLN cc_start: 0.6109 (OUTLIER) cc_final: 0.5394 (mm-40) REVERT: B 205 ASN cc_start: 0.8036 (t0) cc_final: 0.7677 (t0) REVERT: C 29 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7394 (tm-30) REVERT: C 57 ASP cc_start: 0.7821 (t0) cc_final: 0.7451 (t0) REVERT: C 196 LEU cc_start: 0.7735 (mt) cc_final: 0.7492 (mt) REVERT: D 4 ASP cc_start: 0.7405 (p0) cc_final: 0.6719 (p0) REVERT: D 46 GLU cc_start: 0.6625 (tm-30) cc_final: 0.6264 (tm-30) REVERT: E 293 GLU cc_start: 0.7329 (tt0) cc_final: 0.6748 (tp30) REVERT: E 314 ASN cc_start: 0.6807 (t0) cc_final: 0.6265 (t0) REVERT: F 186 ILE cc_start: 0.8743 (mm) cc_final: 0.8455 (mm) REVERT: F 290 LYS cc_start: 0.8080 (mmtm) cc_final: 0.6706 (mtmt) REVERT: G 32 ASP cc_start: 0.8508 (m-30) cc_final: 0.8271 (m-30) REVERT: G 64 ASN cc_start: 0.8730 (m-40) cc_final: 0.8382 (m110) REVERT: G 101 ASP cc_start: 0.7509 (m-30) cc_final: 0.7100 (m-30) REVERT: G 105 THR cc_start: 0.8748 (t) cc_final: 0.8411 (p) REVERT: G 188 GLU cc_start: 0.5726 (pt0) cc_final: 0.5419 (pt0) REVERT: I 120 GLN cc_start: 0.8075 (mt0) cc_final: 0.7864 (mt0) REVERT: I 156 MET cc_start: 0.7764 (mmm) cc_final: 0.7500 (mmt) REVERT: I 181 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8410 (mtmm) REVERT: J 12 MET cc_start: 0.8028 (ttp) cc_final: 0.7699 (ttp) REVERT: J 18 GLU cc_start: 0.6787 (pm20) cc_final: 0.6465 (pm20) REVERT: J 32 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.6756 (mt) REVERT: J 106 GLU cc_start: 0.8218 (mt-10) cc_final: 0.8003 (mt-10) REVERT: J 189 ILE cc_start: 0.7960 (pt) cc_final: 0.7584 (mp) REVERT: L 128 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8789 (tp-100) REVERT: M 195 TYR cc_start: 0.8246 (m-80) cc_final: 0.7851 (m-80) REVERT: M 225 ARG cc_start: 0.8211 (mtp180) cc_final: 0.7505 (ttp-170) REVERT: M 293 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7873 (m) REVERT: N 24 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8787 (mp) REVERT: N 31 LYS cc_start: 0.8246 (mttt) cc_final: 0.8008 (mttm) REVERT: N 40 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8477 (pp) REVERT: N 65 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7208 (m-30) REVERT: N 137 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.6819 (t80) REVERT: b 213 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6584 (pt0) REVERT: c 29 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7393 (tm-30) REVERT: c 57 ASP cc_start: 0.7809 (t0) cc_final: 0.7472 (t0) REVERT: c 122 ASP cc_start: 0.7331 (m-30) cc_final: 0.7122 (m-30) REVERT: c 192 GLU cc_start: 0.7773 (tp30) cc_final: 0.7165 (tp30) REVERT: c 196 LEU cc_start: 0.7746 (mt) cc_final: 0.7485 (mt) REVERT: d 4 ASP cc_start: 0.7303 (p0) cc_final: 0.6586 (p0) REVERT: d 46 GLU cc_start: 0.6279 (tm-30) cc_final: 0.5762 (tm-30) REVERT: d 92 GLN cc_start: 0.5693 (mm-40) cc_final: 0.5239 (tm-30) REVERT: d 102 MET cc_start: 0.6481 (ttt) cc_final: 0.6052 (ptm) REVERT: d 167 THR cc_start: 0.8954 (m) cc_final: 0.8705 (p) REVERT: d 213 GLU cc_start: 0.6420 (pt0) cc_final: 0.6029 (tp30) REVERT: d 233 ARG cc_start: 0.5513 (OUTLIER) cc_final: 0.3831 (ttt90) REVERT: e 266 ASP cc_start: 0.8469 (m-30) cc_final: 0.8079 (m-30) REVERT: e 278 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7629 (mm-40) REVERT: e 293 GLU cc_start: 0.7276 (tt0) cc_final: 0.6861 (tp30) REVERT: e 314 ASN cc_start: 0.7072 (t0) cc_final: 0.6724 (t0) REVERT: f 186 ILE cc_start: 0.8750 (mm) cc_final: 0.8464 (mm) REVERT: g 32 ASP cc_start: 0.8579 (m-30) cc_final: 0.8370 (m-30) REVERT: g 64 ASN cc_start: 0.8706 (m-40) cc_final: 0.8387 (m110) REVERT: g 101 ASP cc_start: 0.7435 (m-30) cc_final: 0.7104 (m-30) REVERT: g 105 THR cc_start: 0.8724 (t) cc_final: 0.8374 (p) REVERT: g 115 ARG cc_start: 0.7691 (mmt90) cc_final: 0.7024 (mtt180) REVERT: g 175 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8204 (mt-10) REVERT: h 139 LYS cc_start: 0.8045 (tttm) cc_final: 0.7593 (mmtp) REVERT: i 212 THR cc_start: 0.8804 (t) cc_final: 0.8565 (p) REVERT: j 12 MET cc_start: 0.8024 (ttp) cc_final: 0.7711 (ttp) REVERT: j 18 GLU cc_start: 0.6778 (pm20) cc_final: 0.6457 (pm20) REVERT: j 32 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.6739 (mt) REVERT: j 106 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7979 (mt-10) REVERT: l 128 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8899 (tp-100) REVERT: l 214 ASP cc_start: 0.7770 (t0) cc_final: 0.7524 (t0) REVERT: m 195 TYR cc_start: 0.8233 (m-80) cc_final: 0.7809 (m-80) REVERT: m 225 ARG cc_start: 0.8218 (mtp180) cc_final: 0.7502 (ttp-170) REVERT: m 293 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7854 (m) REVERT: n 31 LYS cc_start: 0.8308 (mtpt) cc_final: 0.8007 (mttm) REVERT: n 137 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.6898 (t80) outliers start: 235 outliers final: 209 residues processed: 1080 average time/residue: 0.6174 time to fit residues: 1085.9221 Evaluate side-chains 1134 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 911 time to evaluate : 6.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 247 SER Chi-restraints excluded: chain L residue 253 ASP Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain L residue 292 THR Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 167 LYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 330 GLN Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 153 ASN Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain N residue 215 LYS Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 133 VAL Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 212 VAL Chi-restraints excluded: chain b residue 213 GLU Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 60 SER Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 79 ASP Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 169 ILE Chi-restraints excluded: chain d residue 209 LEU Chi-restraints excluded: chain d residue 223 GLN Chi-restraints excluded: chain d residue 233 ARG Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 146 VAL Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 164 MET Chi-restraints excluded: chain e residue 165 SER Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 178 MET Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain f residue 199 THR Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain g residue 11 SER Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 78 ILE Chi-restraints excluded: chain g residue 82 LEU Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 170 THR Chi-restraints excluded: chain g residue 187 ASP Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain g residue 208 LEU Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain h residue 175 VAL Chi-restraints excluded: chain h residue 204 SER Chi-restraints excluded: chain h residue 234 ASP Chi-restraints excluded: chain h residue 269 SER Chi-restraints excluded: chain h residue 271 SER Chi-restraints excluded: chain i residue 66 MET Chi-restraints excluded: chain i residue 77 THR Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 124 SER Chi-restraints excluded: chain i residue 158 SER Chi-restraints excluded: chain i residue 203 ASP Chi-restraints excluded: chain i residue 214 LEU Chi-restraints excluded: chain i residue 219 ASP Chi-restraints excluded: chain i residue 225 MET Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 71 THR Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain k residue 163 SER Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 128 GLN Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 247 SER Chi-restraints excluded: chain l residue 253 ASP Chi-restraints excluded: chain l residue 287 SER Chi-restraints excluded: chain l residue 289 ASP Chi-restraints excluded: chain l residue 292 THR Chi-restraints excluded: chain m residue 145 VAL Chi-restraints excluded: chain m residue 234 ASN Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 253 VAL Chi-restraints excluded: chain m residue 293 THR Chi-restraints excluded: chain m residue 320 SER Chi-restraints excluded: chain m residue 325 THR Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain m residue 330 GLN Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 103 LEU Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 137 TYR Chi-restraints excluded: chain n residue 151 GLU Chi-restraints excluded: chain n residue 153 ASN Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain n residue 215 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 545 optimal weight: 10.0000 chunk 574 optimal weight: 9.9990 chunk 524 optimal weight: 0.0870 chunk 558 optimal weight: 10.0000 chunk 336 optimal weight: 0.3980 chunk 243 optimal weight: 5.9990 chunk 438 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 504 optimal weight: 0.6980 chunk 528 optimal weight: 4.9990 chunk 556 optimal weight: 0.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN K 125 GLN L 128 GLN ** L 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 142 GLN ** a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 223 GLN ** e 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 108 ASN l 128 GLN ** m 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 50354 Z= 0.178 Angle : 0.519 9.902 68116 Z= 0.273 Chirality : 0.043 0.256 7560 Planarity : 0.004 0.052 8826 Dihedral : 6.641 87.411 7102 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.47 % Allowed : 16.13 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.11), residues: 6304 helix: 1.00 (0.11), residues: 2180 sheet: -0.50 (0.13), residues: 1502 loop : -1.30 (0.12), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 185 HIS 0.010 0.001 HIS k 76 PHE 0.018 0.001 PHE A 180 TYR 0.023 0.001 TYR H 218 ARG 0.007 0.000 ARG K 9 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 955 time to evaluate : 5.963 Fit side-chains REVERT: B 205 ASN cc_start: 0.7978 (t0) cc_final: 0.7667 (t0) REVERT: C 29 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7055 (mt0) REVERT: C 57 ASP cc_start: 0.7739 (t0) cc_final: 0.7408 (t0) REVERT: C 196 LEU cc_start: 0.7723 (mt) cc_final: 0.7476 (mt) REVERT: D 4 ASP cc_start: 0.7334 (p0) cc_final: 0.6672 (p0) REVERT: D 46 GLU cc_start: 0.6657 (tm-30) cc_final: 0.6388 (tm-30) REVERT: D 182 ARG cc_start: 0.7341 (tmm-80) cc_final: 0.6401 (tmm160) REVERT: D 216 TYR cc_start: 0.7620 (m-80) cc_final: 0.7373 (m-80) REVERT: E 162 SER cc_start: 0.8042 (p) cc_final: 0.7641 (t) REVERT: E 278 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7441 (mm110) REVERT: E 293 GLU cc_start: 0.7238 (tt0) cc_final: 0.6661 (tp30) REVERT: E 314 ASN cc_start: 0.6604 (t0) cc_final: 0.6095 (t0) REVERT: F 186 ILE cc_start: 0.8695 (mm) cc_final: 0.8451 (mm) REVERT: F 290 LYS cc_start: 0.8029 (mmtm) cc_final: 0.6678 (mtmt) REVERT: G 32 ASP cc_start: 0.8481 (m-30) cc_final: 0.8238 (m-30) REVERT: G 41 CYS cc_start: 0.7644 (t) cc_final: 0.7282 (t) REVERT: G 64 ASN cc_start: 0.8699 (m-40) cc_final: 0.8340 (m110) REVERT: G 101 ASP cc_start: 0.7502 (m-30) cc_final: 0.7119 (m-30) REVERT: G 105 THR cc_start: 0.8711 (t) cc_final: 0.8435 (p) REVERT: H 139 LYS cc_start: 0.8295 (mmtp) cc_final: 0.7962 (mmmm) REVERT: I 156 MET cc_start: 0.7702 (mmm) cc_final: 0.7365 (mmt) REVERT: I 181 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8282 (mtmm) REVERT: I 215 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8214 (p) REVERT: J 12 MET cc_start: 0.7999 (ttp) cc_final: 0.7630 (ttp) REVERT: J 18 GLU cc_start: 0.6775 (pm20) cc_final: 0.6474 (pm20) REVERT: J 32 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.6663 (mt) REVERT: J 106 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7999 (mt-10) REVERT: J 189 ILE cc_start: 0.7929 (pt) cc_final: 0.7581 (mp) REVERT: J 203 ARG cc_start: 0.8346 (mtp85) cc_final: 0.8123 (mtp85) REVERT: L 128 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8697 (tp-100) REVERT: M 167 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8706 (ttmt) REVERT: M 195 TYR cc_start: 0.8176 (m-80) cc_final: 0.7796 (m-80) REVERT: M 225 ARG cc_start: 0.8183 (mtp180) cc_final: 0.7530 (ttp-170) REVERT: M 293 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7815 (m) REVERT: N 31 LYS cc_start: 0.8207 (mttt) cc_final: 0.7966 (mttm) REVERT: N 40 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8260 (pp) REVERT: N 65 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7214 (m-30) REVERT: N 137 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.6730 (t80) REVERT: a 156 VAL cc_start: 0.9160 (OUTLIER) cc_final: 0.8920 (t) REVERT: a 223 ARG cc_start: 0.8419 (ptt-90) cc_final: 0.8169 (ptt180) REVERT: b 213 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6291 (pt0) REVERT: c 29 GLN cc_start: 0.7560 (mm-40) cc_final: 0.7164 (mt0) REVERT: c 57 ASP cc_start: 0.7777 (t0) cc_final: 0.7445 (t0) REVERT: c 122 ASP cc_start: 0.7252 (m-30) cc_final: 0.7051 (m-30) REVERT: c 192 GLU cc_start: 0.7734 (tp30) cc_final: 0.7145 (tp30) REVERT: c 196 LEU cc_start: 0.7736 (mt) cc_final: 0.7480 (mt) REVERT: d 4 ASP cc_start: 0.7226 (p0) cc_final: 0.6558 (p0) REVERT: d 46 GLU cc_start: 0.6229 (tm-30) cc_final: 0.5782 (tm-30) REVERT: d 92 GLN cc_start: 0.5613 (mm-40) cc_final: 0.5219 (tm-30) REVERT: d 102 MET cc_start: 0.6463 (ttt) cc_final: 0.6008 (ptm) REVERT: d 167 THR cc_start: 0.8917 (m) cc_final: 0.8713 (p) REVERT: d 213 GLU cc_start: 0.6461 (pt0) cc_final: 0.6073 (tp30) REVERT: d 233 ARG cc_start: 0.5448 (OUTLIER) cc_final: 0.3776 (ttt90) REVERT: e 266 ASP cc_start: 0.8407 (m-30) cc_final: 0.8014 (m-30) REVERT: e 293 GLU cc_start: 0.7168 (tt0) cc_final: 0.6787 (tp30) REVERT: e 314 ASN cc_start: 0.6994 (t0) cc_final: 0.6652 (t0) REVERT: f 186 ILE cc_start: 0.8690 (mm) cc_final: 0.8430 (mm) REVERT: g 32 ASP cc_start: 0.8567 (m-30) cc_final: 0.8363 (m-30) REVERT: g 41 CYS cc_start: 0.7590 (t) cc_final: 0.7210 (t) REVERT: g 64 ASN cc_start: 0.8649 (m-40) cc_final: 0.8332 (m110) REVERT: g 101 ASP cc_start: 0.7415 (m-30) cc_final: 0.7084 (m-30) REVERT: g 105 THR cc_start: 0.8690 (t) cc_final: 0.8393 (p) REVERT: g 115 ARG cc_start: 0.7579 (mmt90) cc_final: 0.6975 (mtt180) REVERT: g 175 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8173 (mt-10) REVERT: h 139 LYS cc_start: 0.8049 (tttm) cc_final: 0.7608 (mmtp) REVERT: i 181 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8283 (mtmm) REVERT: i 212 THR cc_start: 0.8796 (t) cc_final: 0.8547 (p) REVERT: j 12 MET cc_start: 0.7974 (ttp) cc_final: 0.7624 (ttp) REVERT: j 18 GLU cc_start: 0.6747 (pm20) cc_final: 0.6443 (pm20) REVERT: j 32 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.6685 (mt) REVERT: j 53 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8329 (mp) REVERT: j 106 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7915 (mt-10) REVERT: j 203 ARG cc_start: 0.8340 (mtp85) cc_final: 0.8048 (mtp85) REVERT: k 129 MET cc_start: 0.7721 (mtp) cc_final: 0.7477 (ttm) REVERT: l 128 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8821 (tp-100) REVERT: m 195 TYR cc_start: 0.8172 (m-80) cc_final: 0.7760 (m-80) REVERT: m 225 ARG cc_start: 0.8187 (mtp180) cc_final: 0.7526 (ttp-170) REVERT: m 293 THR cc_start: 0.8128 (p) cc_final: 0.7789 (m) REVERT: n 31 LYS cc_start: 0.8312 (mtpt) cc_final: 0.8031 (mttm) REVERT: n 137 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.6906 (t80) outliers start: 182 outliers final: 153 residues processed: 1073 average time/residue: 0.6332 time to fit residues: 1098.7381 Evaluate side-chains 1093 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 925 time to evaluate : 5.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 247 SER Chi-restraints excluded: chain L residue 253 ASP Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 167 LYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 330 GLN Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 153 ASN Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain N residue 215 LYS Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 133 VAL Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 213 GLU Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 60 SER Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 79 ASP Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 223 GLN Chi-restraints excluded: chain d residue 233 ARG Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 146 VAL Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 164 MET Chi-restraints excluded: chain e residue 165 SER Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain e residue 178 MET Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain h residue 175 VAL Chi-restraints excluded: chain h residue 234 ASP Chi-restraints excluded: chain h residue 271 SER Chi-restraints excluded: chain i residue 66 MET Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 158 SER Chi-restraints excluded: chain i residue 203 ASP Chi-restraints excluded: chain i residue 214 LEU Chi-restraints excluded: chain i residue 219 ASP Chi-restraints excluded: chain i residue 225 MET Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain k residue 163 SER Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 128 GLN Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 247 SER Chi-restraints excluded: chain l residue 253 ASP Chi-restraints excluded: chain l residue 287 SER Chi-restraints excluded: chain l residue 289 ASP Chi-restraints excluded: chain m residue 145 VAL Chi-restraints excluded: chain m residue 234 ASN Chi-restraints excluded: chain m residue 320 SER Chi-restraints excluded: chain m residue 325 THR Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain m residue 330 GLN Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 103 LEU Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 137 TYR Chi-restraints excluded: chain n residue 151 GLU Chi-restraints excluded: chain n residue 153 ASN Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain n residue 215 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 366 optimal weight: 4.9990 chunk 590 optimal weight: 0.9980 chunk 360 optimal weight: 10.0000 chunk 280 optimal weight: 7.9990 chunk 410 optimal weight: 6.9990 chunk 619 optimal weight: 0.9980 chunk 570 optimal weight: 0.8980 chunk 493 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 381 optimal weight: 5.9990 chunk 302 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN L 128 GLN ** L 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 278 GLN h 266 GLN l 128 GLN ** m 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 50354 Z= 0.214 Angle : 0.533 10.088 68116 Z= 0.280 Chirality : 0.044 0.245 7560 Planarity : 0.004 0.069 8826 Dihedral : 6.606 87.296 7102 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.47 % Allowed : 16.28 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.11), residues: 6304 helix: 1.04 (0.11), residues: 2190 sheet: -0.48 (0.13), residues: 1512 loop : -1.28 (0.12), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 185 HIS 0.009 0.001 HIS K 76 PHE 0.022 0.001 PHE a 180 TYR 0.028 0.001 TYR H 218 ARG 0.007 0.000 ARG K 9 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 920 time to evaluate : 5.369 Fit side-chains REVERT: B 191 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8482 (mp) REVERT: B 205 ASN cc_start: 0.7983 (t0) cc_final: 0.7672 (t0) REVERT: C 29 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7135 (mt0) REVERT: C 57 ASP cc_start: 0.7746 (t0) cc_final: 0.7412 (t0) REVERT: C 196 LEU cc_start: 0.7728 (mt) cc_final: 0.7485 (mt) REVERT: D 4 ASP cc_start: 0.7342 (p0) cc_final: 0.6676 (p0) REVERT: D 46 GLU cc_start: 0.6683 (tm-30) cc_final: 0.6422 (tm-30) REVERT: D 182 ARG cc_start: 0.7348 (tmm-80) cc_final: 0.6404 (tmm160) REVERT: D 216 TYR cc_start: 0.7638 (m-80) cc_final: 0.7343 (m-80) REVERT: E 162 SER cc_start: 0.8040 (p) cc_final: 0.7638 (t) REVERT: E 278 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7433 (mm110) REVERT: E 293 GLU cc_start: 0.7228 (tt0) cc_final: 0.6699 (tp30) REVERT: E 314 ASN cc_start: 0.6650 (t0) cc_final: 0.6126 (t0) REVERT: F 186 ILE cc_start: 0.8684 (mm) cc_final: 0.8442 (mm) REVERT: F 290 LYS cc_start: 0.8063 (mmtm) cc_final: 0.6702 (mtmt) REVERT: G 32 ASP cc_start: 0.8478 (m-30) cc_final: 0.8234 (m-30) REVERT: G 41 CYS cc_start: 0.7617 (t) cc_final: 0.7258 (t) REVERT: G 64 ASN cc_start: 0.8696 (m-40) cc_final: 0.8333 (m110) REVERT: G 101 ASP cc_start: 0.7508 (m-30) cc_final: 0.7118 (m-30) REVERT: G 105 THR cc_start: 0.8726 (t) cc_final: 0.8433 (p) REVERT: H 139 LYS cc_start: 0.8307 (mmtp) cc_final: 0.7968 (mmmm) REVERT: I 156 MET cc_start: 0.7714 (mmm) cc_final: 0.7377 (mmt) REVERT: I 181 LYS cc_start: 0.8594 (mtmm) cc_final: 0.8300 (mtmm) REVERT: I 215 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8212 (p) REVERT: J 12 MET cc_start: 0.8006 (ttp) cc_final: 0.7637 (ttp) REVERT: J 18 GLU cc_start: 0.6796 (pm20) cc_final: 0.6489 (pm20) REVERT: J 32 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6647 (mt) REVERT: J 189 ILE cc_start: 0.7923 (pt) cc_final: 0.7555 (mp) REVERT: L 128 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8597 (tp-100) REVERT: L 250 ASP cc_start: 0.7963 (t0) cc_final: 0.7695 (t0) REVERT: M 195 TYR cc_start: 0.8163 (m-80) cc_final: 0.7749 (m-80) REVERT: M 225 ARG cc_start: 0.8217 (mtp180) cc_final: 0.7519 (ttp-170) REVERT: M 293 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7819 (m) REVERT: N 24 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8779 (mp) REVERT: N 31 LYS cc_start: 0.8214 (mttt) cc_final: 0.7992 (mttm) REVERT: N 40 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8313 (pp) REVERT: N 65 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7247 (m-30) REVERT: N 137 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.6730 (t80) REVERT: a 223 ARG cc_start: 0.8428 (ptt-90) cc_final: 0.8175 (ptt180) REVERT: b 213 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6187 (pt0) REVERT: c 29 GLN cc_start: 0.7515 (mm-40) cc_final: 0.7160 (mt0) REVERT: c 57 ASP cc_start: 0.7786 (t0) cc_final: 0.7456 (t0) REVERT: c 192 GLU cc_start: 0.7734 (tp30) cc_final: 0.7140 (tp30) REVERT: c 196 LEU cc_start: 0.7739 (mt) cc_final: 0.7480 (mt) REVERT: d 4 ASP cc_start: 0.7264 (p0) cc_final: 0.6572 (p0) REVERT: d 92 GLN cc_start: 0.5618 (mm-40) cc_final: 0.5241 (tm-30) REVERT: d 102 MET cc_start: 0.6485 (ttt) cc_final: 0.6020 (ptm) REVERT: d 167 THR cc_start: 0.8920 (m) cc_final: 0.8719 (p) REVERT: d 213 GLU cc_start: 0.6459 (pt0) cc_final: 0.6041 (tp30) REVERT: d 233 ARG cc_start: 0.5456 (OUTLIER) cc_final: 0.3802 (ttt90) REVERT: e 266 ASP cc_start: 0.8447 (m-30) cc_final: 0.8026 (m-30) REVERT: e 293 GLU cc_start: 0.7204 (tt0) cc_final: 0.6823 (tp30) REVERT: e 314 ASN cc_start: 0.7041 (t0) cc_final: 0.6699 (t0) REVERT: f 186 ILE cc_start: 0.8702 (mm) cc_final: 0.8441 (mm) REVERT: g 32 ASP cc_start: 0.8571 (m-30) cc_final: 0.8369 (m-30) REVERT: g 41 CYS cc_start: 0.7572 (t) cc_final: 0.7199 (t) REVERT: g 64 ASN cc_start: 0.8651 (m-40) cc_final: 0.8333 (m110) REVERT: g 101 ASP cc_start: 0.7420 (m-30) cc_final: 0.7094 (m-30) REVERT: g 105 THR cc_start: 0.8705 (t) cc_final: 0.8408 (p) REVERT: g 115 ARG cc_start: 0.7596 (mmt90) cc_final: 0.6989 (mtt180) REVERT: g 175 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8182 (mt-10) REVERT: h 139 LYS cc_start: 0.8074 (tttm) cc_final: 0.7641 (mmtp) REVERT: i 181 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8290 (mtmm) REVERT: i 212 THR cc_start: 0.8820 (t) cc_final: 0.8567 (p) REVERT: j 12 MET cc_start: 0.7981 (ttp) cc_final: 0.7634 (ttp) REVERT: j 18 GLU cc_start: 0.6778 (pm20) cc_final: 0.6480 (pm20) REVERT: j 32 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.6685 (mt) REVERT: j 53 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8362 (mp) REVERT: j 106 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7925 (mt-10) REVERT: k 129 MET cc_start: 0.7725 (mtp) cc_final: 0.7481 (ttm) REVERT: l 128 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8520 (tp-100) REVERT: m 195 TYR cc_start: 0.8210 (m-80) cc_final: 0.7821 (m-80) REVERT: m 225 ARG cc_start: 0.8204 (mtp180) cc_final: 0.7494 (ttp-170) REVERT: m 293 THR cc_start: 0.8174 (p) cc_final: 0.7831 (m) REVERT: n 31 LYS cc_start: 0.8314 (mtpt) cc_final: 0.8038 (mttm) REVERT: n 137 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.6962 (t80) outliers start: 182 outliers final: 159 residues processed: 1041 average time/residue: 0.6319 time to fit residues: 1070.6927 Evaluate side-chains 1080 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 906 time to evaluate : 5.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 247 SER Chi-restraints excluded: chain L residue 253 ASP Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 330 GLN Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 153 ASN Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain N residue 215 LYS Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 133 VAL Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 72 CYS Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 213 GLU Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 60 SER Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 79 ASP Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 233 ARG Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 146 VAL Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 164 MET Chi-restraints excluded: chain e residue 165 SER Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain e residue 178 MET Chi-restraints excluded: chain e residue 184 ASP Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain f residue 199 THR Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 170 THR Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain h residue 175 VAL Chi-restraints excluded: chain h residue 234 ASP Chi-restraints excluded: chain h residue 271 SER Chi-restraints excluded: chain i residue 66 MET Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 158 SER Chi-restraints excluded: chain i residue 203 ASP Chi-restraints excluded: chain i residue 214 LEU Chi-restraints excluded: chain i residue 219 ASP Chi-restraints excluded: chain i residue 225 MET Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain k residue 163 SER Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 128 GLN Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 227 VAL Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 247 SER Chi-restraints excluded: chain l residue 253 ASP Chi-restraints excluded: chain l residue 287 SER Chi-restraints excluded: chain l residue 289 ASP Chi-restraints excluded: chain m residue 145 VAL Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 320 SER Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain m residue 330 GLN Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 103 LEU Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 137 TYR Chi-restraints excluded: chain n residue 151 GLU Chi-restraints excluded: chain n residue 153 ASN Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain n residue 215 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 391 optimal weight: 0.9980 chunk 525 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 454 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 137 optimal weight: 0.7980 chunk 494 optimal weight: 0.9980 chunk 206 optimal weight: 7.9990 chunk 507 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 91 optimal weight: 0.0370 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN L 128 GLN ** L 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 223 GLN ** e 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 128 GLN ** m 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.155116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128376 restraints weight = 58100.719| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.73 r_work: 0.3319 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 50354 Z= 0.148 Angle : 0.503 9.538 68116 Z= 0.265 Chirality : 0.042 0.225 7560 Planarity : 0.004 0.058 8826 Dihedral : 6.459 86.525 7102 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.02 % Allowed : 16.89 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.11), residues: 6304 helix: 1.25 (0.12), residues: 2180 sheet: -0.39 (0.13), residues: 1506 loop : -1.22 (0.12), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 185 HIS 0.009 0.001 HIS K 76 PHE 0.022 0.001 PHE a 180 TYR 0.019 0.001 TYR H 218 ARG 0.007 0.000 ARG K 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18065.25 seconds wall clock time: 320 minutes 44.25 seconds (19244.25 seconds total)