Starting phenix.real_space_refine on Mon Feb 19 12:22:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef2_9044/02_2024/6ef2_9044_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef2_9044/02_2024/6ef2_9044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef2_9044/02_2024/6ef2_9044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef2_9044/02_2024/6ef2_9044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef2_9044/02_2024/6ef2_9044_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef2_9044/02_2024/6ef2_9044_updated.pdb" } resolution = 4.27 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 89 5.16 5 C 15527 2.51 5 N 4289 2.21 5 O 4738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 4": "NH1" <-> "NH2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 6": "NH1" <-> "NH2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 107": "NH1" <-> "NH2" Residue "F PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 202": "NH1" <-> "NH2" Residue "G TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 234": "NH1" <-> "NH2" Residue "H TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 289": "NH1" <-> "NH2" Residue "H ARG 346": "NH1" <-> "NH2" Residue "H ARG 357": "NH1" <-> "NH2" Residue "H ARG 403": "NH1" <-> "NH2" Residue "I ARG 246": "NH1" <-> "NH2" Residue "I ARG 291": "NH1" <-> "NH2" Residue "I ARG 343": "NH1" <-> "NH2" Residue "J TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 212": "NH1" <-> "NH2" Residue "J ARG 231": "NH1" <-> "NH2" Residue "J ARG 238": "NH1" <-> "NH2" Residue "J ARG 306": "NH1" <-> "NH2" Residue "J ARG 309": "NH1" <-> "NH2" Residue "K ARG 185": "NH1" <-> "NH2" Residue "K ARG 262": "NH1" <-> "NH2" Residue "K ARG 333": "NH1" <-> "NH2" Residue "K ARG 344": "NH1" <-> "NH2" Residue "L PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 191": "NH1" <-> "NH2" Residue "L TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 261": "NH1" <-> "NH2" Residue "M ARG 233": "NH1" <-> "NH2" Residue "M ARG 290": "NH1" <-> "NH2" Residue "M ARG 425": "NH1" <-> "NH2" Residue "M PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24659 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1835 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1816 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 12, 'TRANS': 236} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1795 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 235} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1782 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 230} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "E" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1869 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 242} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1739 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 225} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "G" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1778 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 9, 'TRANS': 236} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "H" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1986 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 13, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "I" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1958 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 249} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "J" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1976 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 250} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "K" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1956 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 247} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "L" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1860 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 14, 'TRANS': 249} Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 136 Chain: "M" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2035 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 259} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "s" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 96 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.03, per 1000 atoms: 0.53 Number of scatterers: 24659 At special positions: 0 Unit cell: (136.99, 138.02, 125.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 89 16.00 P 16 15.00 O 4738 8.00 N 4289 7.00 C 15527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.47 Conformation dependent library (CDL) restraints added in 4.6 seconds 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6070 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 27 sheets defined 35.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'A' and resid 27 through 33 Processing helix chain 'A' and resid 87 through 108 removed outlier: 4.570A pdb=" N ARG A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.539A pdb=" N TYR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.997A pdb=" N GLU A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 214 removed outlier: 3.563A pdb=" N VAL A 203 " --> pdb=" O TRP A 199 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA A 213 " --> pdb=" O HIS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 246 No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'B' and resid 21 through 30 removed outlier: 3.949A pdb=" N THR B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 27 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 96 removed outlier: 4.081A pdb=" N VAL B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 101 No H-bonds generated for 'chain 'B' and resid 98 through 101' Processing helix chain 'B' and resid 108 through 118 removed outlier: 4.475A pdb=" N GLU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 Processing helix chain 'B' and resid 186 through 196 removed outlier: 4.163A pdb=" N LEU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'C' and resid 20 through 26 Processing helix chain 'C' and resid 28 through 31 Processing helix chain 'C' and resid 82 through 102 removed outlier: 4.436A pdb=" N ILE C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN C 96 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR C 101 " --> pdb=" O ASN C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 116 removed outlier: 3.614A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 177 removed outlier: 3.737A pdb=" N THR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 197 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 236 through 240 removed outlier: 3.833A pdb=" N VAL C 240 " --> pdb=" O LYS C 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 236 through 240' Processing helix chain 'D' and resid 23 through 29 removed outlier: 3.694A pdb=" N ARG D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 100 removed outlier: 3.871A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 117 Processing helix chain 'D' and resid 119 through 122 No H-bonds generated for 'chain 'D' and resid 119 through 122' Processing helix chain 'D' and resid 168 through 178 removed outlier: 3.779A pdb=" N GLU D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU D 176 " --> pdb=" O ARG D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing helix chain 'D' and resid 188 through 195 Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.959A pdb=" N GLU D 201 " --> pdb=" O SER D 198 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D 203 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 238 removed outlier: 3.688A pdb=" N ILE D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 31 removed outlier: 3.633A pdb=" N LEU E 28 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA E 30 " --> pdb=" O TYR E 26 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 82 through 92 removed outlier: 4.246A pdb=" N ARG E 86 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N HIS E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 102 removed outlier: 3.882A pdb=" N ASN E 100 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 123 removed outlier: 3.560A pdb=" N GLN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU E 121 " --> pdb=" O CYS E 117 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE E 123 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 185 removed outlier: 4.230A pdb=" N LEU E 184 " --> pdb=" O GLN E 180 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASN E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 206 removed outlier: 3.535A pdb=" N LEU E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 247 removed outlier: 3.639A pdb=" N LEU E 239 " --> pdb=" O LYS E 235 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE E 240 " --> pdb=" O THR E 236 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS E 244 " --> pdb=" O ILE E 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 27 removed outlier: 4.573A pdb=" N GLU F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 79 through 91 removed outlier: 3.903A pdb=" N VAL F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 121 removed outlier: 3.893A pdb=" N GLY F 109 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP F 114 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 175 removed outlier: 3.742A pdb=" N THR F 170 " --> pdb=" O GLN F 166 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N TYR F 171 " --> pdb=" O GLY F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 197 removed outlier: 3.978A pdb=" N LYS F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'F' and resid 227 through 229 No H-bonds generated for 'chain 'F' and resid 227 through 229' Processing helix chain 'G' and resid 22 through 33 removed outlier: 4.355A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU G 32 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 96 removed outlier: 3.843A pdb=" N VAL G 89 " --> pdb=" O GLY G 85 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG G 91 " --> pdb=" O HIS G 87 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 103 No H-bonds generated for 'chain 'G' and resid 100 through 103' Processing helix chain 'G' and resid 109 through 124 removed outlier: 4.708A pdb=" N GLN G 121 " --> pdb=" O GLY G 117 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 175 removed outlier: 3.678A pdb=" N ALA G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 182 removed outlier: 3.692A pdb=" N ASP G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 removed outlier: 3.938A pdb=" N LYS G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA G 197 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LYS G 198 " --> pdb=" O LYS G 194 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE G 199 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU G 205 " --> pdb=" O TYR G 201 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN G 207 " --> pdb=" O ALA G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 239 No H-bonds generated for 'chain 'G' and resid 236 through 239' Processing helix chain 'G' and resid 241 through 247 removed outlier: 4.409A pdb=" N GLU G 246 " --> pdb=" O PHE G 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 198 No H-bonds generated for 'chain 'H' and resid 195 through 198' Processing helix chain 'H' and resid 217 through 224 removed outlier: 3.637A pdb=" N LEU H 221 " --> pdb=" O GLN H 217 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU H 223 " --> pdb=" O GLU H 219 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL H 224 " --> pdb=" O LYS H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 230 Processing helix chain 'H' and resid 232 through 238 removed outlier: 3.775A pdb=" N LEU H 238 " --> pdb=" O ARG H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 267 removed outlier: 4.314A pdb=" N ALA H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG H 266 " --> pdb=" O ALA H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 300 removed outlier: 3.508A pdb=" N ARG H 292 " --> pdb=" O ALA H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 313 No H-bonds generated for 'chain 'H' and resid 311 through 313' Processing helix chain 'H' and resid 328 through 340 removed outlier: 3.903A pdb=" N THR H 332 " --> pdb=" O GLU H 328 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU H 335 " --> pdb=" O ARG H 331 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU H 336 " --> pdb=" O THR H 332 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE H 337 " --> pdb=" O MET H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 360 No H-bonds generated for 'chain 'H' and resid 358 through 360' Processing helix chain 'H' and resid 382 through 392 removed outlier: 4.039A pdb=" N ASN H 387 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG H 390 " --> pdb=" O ALA H 386 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE H 391 " --> pdb=" O ASN H 387 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS H 392 " --> pdb=" O ILE H 388 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 410 Processing helix chain 'H' and resid 418 through 432 removed outlier: 3.595A pdb=" N VAL H 422 " --> pdb=" O GLU H 418 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N CYS H 423 " --> pdb=" O LEU H 419 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA H 430 " --> pdb=" O ALA H 426 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE H 431 " --> pdb=" O GLY H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 451 removed outlier: 3.527A pdb=" N LYS H 445 " --> pdb=" O LYS H 441 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS H 449 " --> pdb=" O LYS H 445 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL H 450 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE H 451 " --> pdb=" O VAL H 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 197 removed outlier: 3.513A pdb=" N LYS I 195 " --> pdb=" O ILE I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 204 No H-bonds generated for 'chain 'I' and resid 201 through 204' Processing helix chain 'I' and resid 206 through 211 removed outlier: 3.604A pdb=" N MET I 211 " --> pdb=" O LEU I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 238 removed outlier: 3.560A pdb=" N ASN I 238 " --> pdb=" O LYS I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 273 removed outlier: 3.561A pdb=" N CYS I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG I 265 " --> pdb=" O PRO I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 286 No H-bonds generated for 'chain 'I' and resid 284 through 286' Processing helix chain 'I' and resid 300 through 303 No H-bonds generated for 'chain 'I' and resid 300 through 303' Processing helix chain 'I' and resid 305 through 313 removed outlier: 4.068A pdb=" N LEU I 309 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU I 310 " --> pdb=" O MET I 306 " (cutoff:3.500A) Processing helix chain 'I' and resid 355 through 365 removed outlier: 3.735A pdb=" N LYS I 359 " --> pdb=" O LEU I 355 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS I 360 " --> pdb=" O SER I 356 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY I 363 " --> pdb=" O LYS I 359 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS I 365 " --> pdb=" O ILE I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 380 No H-bonds generated for 'chain 'I' and resid 377 through 380' Processing helix chain 'I' and resid 391 through 404 removed outlier: 3.635A pdb=" N GLY I 400 " --> pdb=" O CYS I 396 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU I 401 " --> pdb=" O THR I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 413 through 423 removed outlier: 3.675A pdb=" N ALA I 419 " --> pdb=" O ASP I 415 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 160 No H-bonds generated for 'chain 'J' and resid 157 through 160' Processing helix chain 'J' and resid 165 through 169 Processing helix chain 'J' and resid 172 through 176 Processing helix chain 'J' and resid 195 through 205 removed outlier: 3.614A pdb=" N ALA J 199 " --> pdb=" O LYS J 195 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA J 203 " --> pdb=" O ALA J 199 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS J 204 " --> pdb=" O ARG J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 238 removed outlier: 3.865A pdb=" N LEU J 233 " --> pdb=" O MET J 229 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL J 235 " --> pdb=" O ARG J 231 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET J 236 " --> pdb=" O GLU J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 275 removed outlier: 4.009A pdb=" N ARG J 270 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU J 274 " --> pdb=" O ARG J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 284 removed outlier: 3.664A pdb=" N GLU J 283 " --> pdb=" O LEU J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 305 No H-bonds generated for 'chain 'J' and resid 302 through 305' Processing helix chain 'J' and resid 321 through 331 removed outlier: 3.579A pdb=" N ILE J 327 " --> pdb=" O ALA J 323 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU J 328 " --> pdb=" O ARG J 324 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG J 329 " --> pdb=" O ALA J 325 " (cutoff:3.500A) Processing helix chain 'J' and resid 344 through 347 No H-bonds generated for 'chain 'J' and resid 344 through 347' Processing helix chain 'J' and resid 356 through 370 Processing helix chain 'J' and resid 380 through 389 Processing helix chain 'J' and resid 392 through 394 No H-bonds generated for 'chain 'J' and resid 392 through 394' Processing helix chain 'K' and resid 180 through 187 removed outlier: 4.233A pdb=" N ILE K 184 " --> pdb=" O GLN K 180 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG K 185 " --> pdb=" O LYS K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 193 Processing helix chain 'K' and resid 196 through 201 Processing helix chain 'K' and resid 220 through 228 removed outlier: 4.035A pdb=" N LYS K 224 " --> pdb=" O THR K 220 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 242 Processing helix chain 'K' and resid 249 through 263 Processing helix chain 'K' and resid 288 through 303 removed outlier: 4.055A pdb=" N GLN K 293 " --> pdb=" O ASP K 289 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG K 294 " --> pdb=" O ARG K 290 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU K 299 " --> pdb=" O ILE K 295 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN K 302 " --> pdb=" O GLU K 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 359 removed outlier: 3.564A pdb=" N GLY K 354 " --> pdb=" O ARG K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 381 through 397 removed outlier: 3.504A pdb=" N ALA K 394 " --> pdb=" O ALA K 390 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL K 395 " --> pdb=" O GLY K 391 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS K 397 " --> pdb=" O ARG K 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 408 through 414 removed outlier: 3.587A pdb=" N ALA K 412 " --> pdb=" O GLU K 408 " (cutoff:3.500A) Processing helix chain 'K' and resid 421 through 423 No H-bonds generated for 'chain 'K' and resid 421 through 423' Processing helix chain 'L' and resid 172 through 174 No H-bonds generated for 'chain 'L' and resid 172 through 174' Processing helix chain 'L' and resid 188 through 196 removed outlier: 3.680A pdb=" N GLU L 195 " --> pdb=" O ARG L 191 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL L 196 " --> pdb=" O GLU L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 202 Processing helix chain 'L' and resid 204 through 210 removed outlier: 3.664A pdb=" N ARG L 209 " --> pdb=" O GLU L 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 239 Processing helix chain 'L' and resid 248 through 250 No H-bonds generated for 'chain 'L' and resid 248 through 250' Processing helix chain 'L' and resid 260 through 272 Processing helix chain 'L' and resid 283 through 285 No H-bonds generated for 'chain 'L' and resid 283 through 285' Processing helix chain 'L' and resid 295 through 312 removed outlier: 4.580A pdb=" N GLU L 300 " --> pdb=" O SER L 296 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN L 302 " --> pdb=" O ASP L 298 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG L 303 " --> pdb=" O ARG L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 364 removed outlier: 4.539A pdb=" N LEU L 358 " --> pdb=" O GLU L 354 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU L 359 " --> pdb=" O ALA L 355 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE L 363 " --> pdb=" O GLU L 359 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS L 364 " --> pdb=" O ILE L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 382 No H-bonds generated for 'chain 'L' and resid 379 through 382' Processing helix chain 'L' and resid 388 through 402 removed outlier: 3.715A pdb=" N ALA L 402 " --> pdb=" O ALA L 398 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 422 removed outlier: 3.904A pdb=" N ARG L 420 " --> pdb=" O MET L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 425 through 428 No H-bonds generated for 'chain 'L' and resid 425 through 428' Processing helix chain 'M' and resid 187 through 197 removed outlier: 3.746A pdb=" N GLU M 191 " --> pdb=" O ASP M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 202 No H-bonds generated for 'chain 'M' and resid 199 through 202' Processing helix chain 'M' and resid 206 through 209 No H-bonds generated for 'chain 'M' and resid 206 through 209' Processing helix chain 'M' and resid 228 through 239 removed outlier: 3.645A pdb=" N ALA M 232 " --> pdb=" O LYS M 228 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG M 233 " --> pdb=" O THR M 229 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 252 Processing helix chain 'M' and resid 259 through 271 removed outlier: 3.657A pdb=" N VAL M 263 " --> pdb=" O GLY M 259 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE M 267 " --> pdb=" O VAL M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 299 through 312 removed outlier: 4.006A pdb=" N THR M 304 " --> pdb=" O GLU M 300 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU M 312 " --> pdb=" O LEU M 308 " (cutoff:3.500A) Processing helix chain 'M' and resid 354 through 363 removed outlier: 4.469A pdb=" N GLN M 359 " --> pdb=" O ASP M 355 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE M 360 " --> pdb=" O SER M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 376 through 381 Processing helix chain 'M' and resid 388 through 405 removed outlier: 3.918A pdb=" N ALA M 393 " --> pdb=" O ALA M 389 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL M 394 " --> pdb=" O GLN M 390 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY M 399 " --> pdb=" O THR M 395 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU M 403 " --> pdb=" O GLY M 399 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG M 404 " --> pdb=" O MET M 400 " (cutoff:3.500A) Processing helix chain 'M' and resid 412 through 422 Processing sheet with id= A, first strand: chain 'A' and resid 42 through 46 removed outlier: 3.715A pdb=" N LEU A 43 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 225 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 236 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR A 229 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 232 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 79 through 82 removed outlier: 3.602A pdb=" N SER A 145 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 153 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= D, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.564A pdb=" N GLY B 138 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU B 147 " --> pdb=" O TRP B 159 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 149 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= F, first strand: chain 'C' and resid 74 through 76 removed outlier: 3.707A pdb=" N GLY C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= H, first strand: chain 'D' and resid 71 through 77 removed outlier: 3.678A pdb=" N ALA D 136 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 137 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS D 146 " --> pdb=" O GLY D 137 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 151 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 46 through 49 Processing sheet with id= J, first strand: chain 'E' and resid 146 through 148 Processing sheet with id= K, first strand: chain 'E' and resid 220 through 223 removed outlier: 3.505A pdb=" N LYS E 229 " --> pdb=" O CYS E 221 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR E 223 " --> pdb=" O GLY E 227 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 159 through 161 removed outlier: 3.771A pdb=" N VAL F 45 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA F 44 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR F 223 " --> pdb=" O ILE F 215 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 72 through 76 removed outlier: 3.699A pdb=" N GLY F 131 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY F 136 " --> pdb=" O HIS F 143 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 38 through 40 removed outlier: 3.589A pdb=" N GLY G 39 " --> pdb=" O ALA G 163 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 46 through 48 removed outlier: 3.658A pdb=" N LYS G 229 " --> pdb=" O TRP G 218 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER G 220 " --> pdb=" O LEU G 227 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU G 227 " --> pdb=" O SER G 220 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 51 through 53 removed outlier: 3.580A pdb=" N LYS G 52 " --> pdb=" O GLU G 213 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 67 through 70 removed outlier: 3.686A pdb=" N ILE G 74 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER G 79 " --> pdb=" O SER G 135 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER G 135 " --> pdb=" O SER G 79 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 248 through 250 removed outlier: 6.294A pdb=" N VAL H 375 " --> pdb=" O TYR H 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'H' and resid 270 through 274 Processing sheet with id= T, first strand: chain 'I' and resid 325 through 327 removed outlier: 6.523A pdb=" N VAL I 219 " --> pdb=" O MET I 326 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG I 346 " --> pdb=" O ILE I 220 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'I' and resid 277 through 279 Processing sheet with id= V, first strand: chain 'J' and resid 186 through 188 Processing sheet with id= W, first strand: chain 'J' and resid 209 through 213 Processing sheet with id= X, first strand: chain 'K' and resid 209 through 211 removed outlier: 7.225A pdb=" N ARG K 336 " --> pdb=" O LEU K 210 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'K' and resid 268 through 270 removed outlier: 6.649A pdb=" N LYS K 313 " --> pdb=" O ILE K 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'L' and resid 345 through 347 removed outlier: 3.740A pdb=" N LEU L 219 " --> pdb=" O ARG L 345 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR L 221 " --> pdb=" O VAL L 347 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N MET L 325 " --> pdb=" O LEU L 220 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 346 through 348 removed outlier: 8.730A pdb=" N ILE M 347 " --> pdb=" O GLY M 217 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU M 219 " --> pdb=" O ILE M 347 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N ALA M 218 " --> pdb=" O VAL M 321 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL M 323 " --> pdb=" O ALA M 218 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N MET M 220 " --> pdb=" O VAL M 323 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA M 325 " --> pdb=" O MET M 220 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR M 276 " --> pdb=" O LYS M 322 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N LEU M 324 " --> pdb=" O THR M 276 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE M 278 " --> pdb=" O LEU M 324 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ALA M 326 " --> pdb=" O ILE M 278 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE M 280 " --> pdb=" O ALA M 326 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA 612 hydrogen bonds defined for protein. 1764 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: 6.60 Time building geometry restraints manager: 10.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8107 1.34 - 1.45: 4149 1.45 - 1.57: 12627 1.57 - 1.69: 27 1.69 - 1.81: 149 Bond restraints: 25059 Sorted by residual: bond pdb=" C4 ATP M 501 " pdb=" C5 ATP M 501 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.27e+01 bond pdb=" C4 ATP H 501 " pdb=" C5 ATP H 501 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C4 ATP I 501 " pdb=" C5 ATP I 501 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.41e+01 bond pdb=" C4 ATP J 501 " pdb=" C5 ATP J 501 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.35e+01 bond pdb=" C5 ATP J 501 " pdb=" N7 ATP J 501 " ideal model delta sigma weight residual 1.387 1.330 0.057 1.00e-02 1.00e+04 3.29e+01 ... (remaining 25054 not shown) Histogram of bond angle deviations from ideal: 97.05 - 104.82: 419 104.82 - 112.59: 12861 112.59 - 120.36: 10525 120.36 - 128.12: 10044 128.12 - 135.89: 176 Bond angle restraints: 34025 Sorted by residual: angle pdb=" PB ATP H 501 " pdb=" O3B ATP H 501 " pdb=" PG ATP H 501 " ideal model delta sigma weight residual 139.87 114.96 24.91 1.00e+00 1.00e+00 6.20e+02 angle pdb=" PB ATP M 501 " pdb=" O3B ATP M 501 " pdb=" PG ATP M 501 " ideal model delta sigma weight residual 139.87 116.27 23.60 1.00e+00 1.00e+00 5.57e+02 angle pdb=" PA ATP M 501 " pdb=" O3A ATP M 501 " pdb=" PB ATP M 501 " ideal model delta sigma weight residual 136.83 113.84 22.99 1.00e+00 1.00e+00 5.28e+02 angle pdb=" PB ATP J 501 " pdb=" O3B ATP J 501 " pdb=" PG ATP J 501 " ideal model delta sigma weight residual 139.87 118.59 21.28 1.00e+00 1.00e+00 4.53e+02 angle pdb=" PA ATP J 501 " pdb=" O3A ATP J 501 " pdb=" PB ATP J 501 " ideal model delta sigma weight residual 136.83 115.58 21.25 1.00e+00 1.00e+00 4.52e+02 ... (remaining 34020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 14319 18.09 - 36.18: 762 36.18 - 54.26: 97 54.26 - 72.35: 31 72.35 - 90.44: 13 Dihedral angle restraints: 15222 sinusoidal: 5769 harmonic: 9453 Sorted by residual: dihedral pdb=" CA PHE B 157 " pdb=" C PHE B 157 " pdb=" N PRO B 158 " pdb=" CA PRO B 158 " ideal model delta harmonic sigma weight residual 180.00 146.90 33.10 0 5.00e+00 4.00e-02 4.38e+01 dihedral pdb=" CA VAL K 401 " pdb=" C VAL K 401 " pdb=" N ILE K 402 " pdb=" CA ILE K 402 " ideal model delta harmonic sigma weight residual -180.00 -149.20 -30.80 0 5.00e+00 4.00e-02 3.79e+01 dihedral pdb=" CA PHE M 207 " pdb=" C PHE M 207 " pdb=" N LYS M 208 " pdb=" CA LYS M 208 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 15219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2169 0.041 - 0.082: 1238 0.082 - 0.123: 441 0.123 - 0.164: 117 0.164 - 0.205: 12 Chirality restraints: 3977 Sorted by residual: chirality pdb=" CB ILE K 277 " pdb=" CA ILE K 277 " pdb=" CG1 ILE K 277 " pdb=" CG2 ILE K 277 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL J 268 " pdb=" CA VAL J 268 " pdb=" CG1 VAL J 268 " pdb=" CG2 VAL J 268 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE G 40 " pdb=" CA ILE G 40 " pdb=" CG1 ILE G 40 " pdb=" CG2 ILE G 40 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 3974 not shown) Planarity restraints: 4395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 157 " -0.051 5.00e-02 4.00e+02 7.61e-02 9.26e+00 pdb=" N PRO B 158 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 158 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 158 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 14 " 0.048 5.00e-02 4.00e+02 7.37e-02 8.69e+00 pdb=" N PRO F 15 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 15 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 15 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 106 " 0.041 5.00e-02 4.00e+02 6.07e-02 5.90e+00 pdb=" N PRO C 107 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 107 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 107 " 0.034 5.00e-02 4.00e+02 ... (remaining 4392 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1063 2.69 - 3.24: 27251 3.24 - 3.80: 36569 3.80 - 4.35: 47569 4.35 - 4.90: 75702 Nonbonded interactions: 188154 Sorted by model distance: nonbonded pdb=" OD2 ASP K 304 " pdb=" NH2 ARG K 330 " model vdw 2.139 2.520 nonbonded pdb=" OG SER D 153 " pdb=" OE1 GLN H 465 " model vdw 2.141 2.440 nonbonded pdb=" O ASP C 42 " pdb=" OH TYR C 146 " model vdw 2.150 2.440 nonbonded pdb=" O ILE J 330 " pdb=" NH1 ARG J 333 " model vdw 2.150 2.520 nonbonded pdb=" NH1 ARG H 385 " pdb=" O CYS H 411 " model vdw 2.153 2.520 ... (remaining 188149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.150 Check model and map are aligned: 0.390 Set scattering table: 0.220 Process input model: 61.570 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.011 0.098 25059 Z= 0.729 Angle : 1.024 24.907 34025 Z= 0.627 Chirality : 0.056 0.205 3977 Planarity : 0.006 0.076 4395 Dihedral : 12.030 90.439 9152 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 13.44 % Favored : 86.53 % Rotamer: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.80 % 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: -5.32 (0.12), residues: 3260 helix: -3.88 (0.09), residues: 1150 sheet: -3.82 (0.19), residues: 476 loop : -3.12 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP H 404 HIS 0.013 0.003 HIS G 204 PHE 0.031 0.003 PHE J 382 TYR 0.034 0.003 TYR E 26 ARG 0.015 0.002 ARG F 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 633 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 THR cc_start: 0.7838 (p) cc_final: 0.7585 (p) REVERT: B 57 MET cc_start: 0.7779 (mpp) cc_final: 0.7270 (mtm) REVERT: B 123 GLN cc_start: 0.6943 (pt0) cc_final: 0.6715 (pt0) REVERT: B 186 GLU cc_start: 0.8220 (tp30) cc_final: 0.7414 (tp30) REVERT: B 194 LEU cc_start: 0.9159 (pp) cc_final: 0.8750 (pp) REVERT: B 245 ASP cc_start: 0.8010 (p0) cc_final: 0.7686 (p0) REVERT: C 26 LEU cc_start: 0.9130 (mp) cc_final: 0.8927 (mp) REVERT: C 51 LYS cc_start: 0.8148 (tptm) cc_final: 0.7912 (tttm) REVERT: C 89 ASN cc_start: 0.7848 (m110) cc_final: 0.7623 (t0) REVERT: C 160 TRP cc_start: 0.7714 (m100) cc_final: 0.7101 (m100) REVERT: C 173 GLN cc_start: 0.8192 (mm110) cc_final: 0.7910 (mm-40) REVERT: C 194 LEU cc_start: 0.8835 (tp) cc_final: 0.8485 (tt) REVERT: C 213 PHE cc_start: 0.8838 (m-80) cc_final: 0.8633 (m-80) REVERT: D 5 ASP cc_start: 0.7838 (p0) cc_final: 0.7446 (p0) REVERT: D 22 TYR cc_start: 0.7749 (m-10) cc_final: 0.7494 (m-10) REVERT: D 102 ASP cc_start: 0.8397 (t0) cc_final: 0.8128 (t0) REVERT: E 59 LEU cc_start: 0.7876 (tt) cc_final: 0.7632 (tt) REVERT: E 122 ARG cc_start: 0.9050 (tpp80) cc_final: 0.8799 (tpp80) REVERT: E 213 ASP cc_start: 0.8420 (t70) cc_final: 0.8083 (t70) REVERT: E 221 CYS cc_start: 0.7290 (p) cc_final: 0.6904 (p) REVERT: E 232 ASP cc_start: 0.8417 (t70) cc_final: 0.7976 (p0) REVERT: F 31 GLN cc_start: 0.8774 (pt0) cc_final: 0.8566 (tt0) REVERT: F 80 ASP cc_start: 0.7839 (t70) cc_final: 0.7627 (t0) REVERT: F 145 LEU cc_start: 0.8350 (mp) cc_final: 0.8043 (mt) REVERT: G 9 ASP cc_start: 0.8186 (m-30) cc_final: 0.7580 (m-30) REVERT: G 26 TYR cc_start: 0.8062 (m-80) cc_final: 0.7587 (m-80) REVERT: G 177 GLU cc_start: 0.7599 (tp30) cc_final: 0.7337 (tp30) REVERT: G 238 GLU cc_start: 0.8407 (pp20) cc_final: 0.7973 (pp20) REVERT: H 314 VAL cc_start: 0.9141 (m) cc_final: 0.8800 (p) REVERT: I 259 ASP cc_start: 0.7695 (p0) cc_final: 0.7274 (p0) REVERT: I 265 ARG cc_start: 0.8528 (mtm110) cc_final: 0.8111 (ttp-110) REVERT: I 306 MET cc_start: 0.8589 (ttp) cc_final: 0.8320 (ttt) REVERT: I 329 ASN cc_start: 0.8232 (m-40) cc_final: 0.7987 (m-40) REVERT: J 243 SER cc_start: 0.9036 (t) cc_final: 0.8711 (m) REVERT: J 274 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7696 (tm-30) REVERT: J 404 PHE cc_start: 0.8184 (p90) cc_final: 0.7645 (p90) REVERT: K 224 LYS cc_start: 0.9044 (mtmt) cc_final: 0.7966 (tptt) REVERT: L 307 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7413 (tm-30) REVERT: M 307 GLU cc_start: 0.8533 (tt0) cc_final: 0.7896 (tp30) REVERT: M 390 GLN cc_start: 0.8717 (mp10) cc_final: 0.8308 (mp10) REVERT: s 125 ILE cc_start: 0.9319 (mm) cc_final: 0.9040 (mm) REVERT: s 127 VAL cc_start: 0.9050 (p) cc_final: 0.8792 (m) outliers start: 0 outliers final: 0 residues processed: 633 average time/residue: 0.4209 time to fit residues: 391.0522 Evaluate side-chains 390 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 253 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 293 optimal weight: 0.0170 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 92 ASN A 175 GLN C 124 GLN C 147 GLN F 21 GLN F 60 GLN F 119 ASN ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN G 68 GLN G 118 GLN G 182 HIS H 356 ASN I 418 GLN J 295 ASN J 391 ASN ** K 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25059 Z= 0.185 Angle : 0.678 10.223 34025 Z= 0.344 Chirality : 0.046 0.177 3977 Planarity : 0.005 0.043 4395 Dihedral : 9.266 89.250 3716 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.04 % Allowed : 4.41 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % 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: -4.13 (0.13), residues: 3260 helix: -2.68 (0.12), residues: 1215 sheet: -2.95 (0.21), residues: 466 loop : -2.65 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP M 376 HIS 0.012 0.001 HIS F 110 PHE 0.019 0.002 PHE B 204 TYR 0.025 0.001 TYR B 82 ARG 0.006 0.001 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 535 time to evaluate : 2.790 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: A 49 ASP cc_start: 0.8090 (p0) cc_final: 0.7711 (p0) REVERT: A 210 MET cc_start: 0.7680 (ptm) cc_final: 0.7405 (ptm) REVERT: B 57 MET cc_start: 0.7931 (mpp) cc_final: 0.7597 (mtm) REVERT: B 116 LYS cc_start: 0.8091 (mttt) cc_final: 0.7879 (ttpt) REVERT: C 68 LYS cc_start: 0.8676 (tttt) cc_final: 0.8387 (tttm) REVERT: C 160 TRP cc_start: 0.7843 (m100) cc_final: 0.7321 (m100) REVERT: C 173 GLN cc_start: 0.8319 (mm110) cc_final: 0.7969 (mm-40) REVERT: C 212 GLU cc_start: 0.8311 (pm20) cc_final: 0.8052 (pm20) REVERT: D 5 ASP cc_start: 0.7261 (p0) cc_final: 0.6755 (p0) REVERT: D 22 TYR cc_start: 0.7936 (m-10) cc_final: 0.7617 (m-80) REVERT: D 102 ASP cc_start: 0.8460 (t0) cc_final: 0.8104 (t0) REVERT: E 26 TYR cc_start: 0.8905 (m-80) cc_final: 0.8631 (m-80) REVERT: E 151 ASP cc_start: 0.7229 (p0) cc_final: 0.6838 (t0) REVERT: E 221 CYS cc_start: 0.7005 (p) cc_final: 0.6684 (p) REVERT: F 24 TYR cc_start: 0.8800 (m-10) cc_final: 0.8549 (m-10) REVERT: F 27 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7776 (mt-10) REVERT: F 31 GLN cc_start: 0.8723 (pt0) cc_final: 0.8277 (tt0) REVERT: F 42 THR cc_start: 0.8518 (p) cc_final: 0.8246 (p) REVERT: F 80 ASP cc_start: 0.7752 (t70) cc_final: 0.7551 (t0) REVERT: F 138 ASP cc_start: 0.8315 (p0) cc_final: 0.7798 (p0) REVERT: F 145 LEU cc_start: 0.8346 (mp) cc_final: 0.8091 (mt) REVERT: F 148 GLN cc_start: 0.7557 (pp30) cc_final: 0.7272 (pp30) REVERT: F 152 ASN cc_start: 0.8694 (m110) cc_final: 0.8442 (m-40) REVERT: G 9 ASP cc_start: 0.8261 (m-30) cc_final: 0.8046 (m-30) REVERT: G 26 TYR cc_start: 0.8103 (m-80) cc_final: 0.7817 (m-80) REVERT: G 238 GLU cc_start: 0.8185 (pp20) cc_final: 0.7896 (pp20) REVERT: H 314 VAL cc_start: 0.9138 (m) cc_final: 0.8934 (p) REVERT: H 320 ASP cc_start: 0.6824 (p0) cc_final: 0.6572 (p0) REVERT: I 246 ARG cc_start: 0.4055 (pmt-80) cc_final: 0.2496 (mtt90) REVERT: I 259 ASP cc_start: 0.7615 (p0) cc_final: 0.7342 (p0) REVERT: I 301 GLU cc_start: 0.7956 (mp0) cc_final: 0.7699 (mp0) REVERT: I 306 MET cc_start: 0.8590 (ttp) cc_final: 0.8360 (ttt) REVERT: I 406 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7282 (tm-30) REVERT: I 421 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7585 (tp30) REVERT: J 243 SER cc_start: 0.9346 (t) cc_final: 0.8814 (m) REVERT: J 269 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7120 (tm-30) REVERT: J 274 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8263 (tm-30) REVERT: J 370 LEU cc_start: 0.8932 (tt) cc_final: 0.8025 (tp) REVERT: K 179 MET cc_start: 0.7525 (tmm) cc_final: 0.7318 (tmm) REVERT: K 224 LYS cc_start: 0.9169 (mtmt) cc_final: 0.8198 (tptt) REVERT: L 189 GLN cc_start: 0.7056 (mp10) cc_final: 0.6742 (mm-40) REVERT: L 271 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8410 (mtpp) REVERT: M 307 GLU cc_start: 0.8277 (tt0) cc_final: 0.7737 (tp30) REVERT: M 421 GLU cc_start: 0.8308 (tt0) cc_final: 0.8099 (tt0) REVERT: s 127 VAL cc_start: 0.9020 (p) cc_final: 0.8799 (m) outliers start: 1 outliers final: 0 residues processed: 535 average time/residue: 0.3630 time to fit residues: 298.8440 Evaluate side-chains 365 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 163 optimal weight: 4.9990 chunk 91 optimal weight: 0.0570 chunk 244 optimal weight: 10.0000 chunk 199 optimal weight: 0.0370 chunk 80 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 317 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 291 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 overall best weight: 3.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN D 117 GLN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN J 295 ASN K 285 GLN ** K 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 364 HIS M 362 GLN M 412 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25059 Z= 0.349 Angle : 0.729 9.397 34025 Z= 0.374 Chirality : 0.049 0.171 3977 Planarity : 0.005 0.050 4395 Dihedral : 9.086 83.898 3716 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.04 % Allowed : 6.36 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.14), residues: 3260 helix: -2.01 (0.13), residues: 1223 sheet: -2.58 (0.21), residues: 490 loop : -2.42 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP M 376 HIS 0.008 0.002 HIS B 190 PHE 0.021 0.002 PHE F 20 TYR 0.021 0.002 TYR M 180 ARG 0.007 0.001 ARG K 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 468 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8147 (p0) cc_final: 0.7813 (p0) REVERT: A 81 MET cc_start: 0.8834 (ttp) cc_final: 0.8607 (ttp) REVERT: A 210 MET cc_start: 0.7871 (ptm) cc_final: 0.7533 (ttm) REVERT: B 57 MET cc_start: 0.7933 (mpp) cc_final: 0.7473 (mtm) REVERT: B 116 LYS cc_start: 0.8206 (mttt) cc_final: 0.7911 (ttpt) REVERT: C 18 ARG cc_start: 0.8607 (ptp-110) cc_final: 0.8283 (mtp-110) REVERT: C 173 GLN cc_start: 0.8566 (mm110) cc_final: 0.8157 (tp40) REVERT: D 5 ASP cc_start: 0.7699 (p0) cc_final: 0.7222 (p0) REVERT: D 139 ASP cc_start: 0.8455 (t0) cc_final: 0.8098 (t0) REVERT: E 134 MET cc_start: 0.8658 (mtp) cc_final: 0.7884 (mtm) REVERT: E 221 CYS cc_start: 0.7140 (p) cc_final: 0.6874 (p) REVERT: F 31 GLN cc_start: 0.9039 (pt0) cc_final: 0.8726 (pt0) REVERT: F 145 LEU cc_start: 0.8587 (mp) cc_final: 0.8332 (mt) REVERT: F 148 GLN cc_start: 0.7816 (pp30) cc_final: 0.7445 (pp30) REVERT: F 203 ASP cc_start: 0.7601 (m-30) cc_final: 0.7301 (t70) REVERT: G 125 LEU cc_start: 0.8656 (tp) cc_final: 0.8450 (tt) REVERT: G 177 GLU cc_start: 0.7455 (tp30) cc_final: 0.7214 (tp30) REVERT: G 238 GLU cc_start: 0.8313 (pp20) cc_final: 0.7913 (pp20) REVERT: H 314 VAL cc_start: 0.9348 (m) cc_final: 0.9056 (p) REVERT: H 320 ASP cc_start: 0.7208 (p0) cc_final: 0.6565 (p0) REVERT: H 333 MET cc_start: 0.8680 (ttt) cc_final: 0.8418 (ttt) REVERT: H 373 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7817 (mtp85) REVERT: I 211 MET cc_start: 0.8465 (mmm) cc_final: 0.7993 (mtp) REVERT: I 259 ASP cc_start: 0.7540 (p0) cc_final: 0.7175 (p0) REVERT: I 301 GLU cc_start: 0.8098 (mp0) cc_final: 0.7632 (mp0) REVERT: I 306 MET cc_start: 0.8660 (ttp) cc_final: 0.8398 (ttt) REVERT: J 243 SER cc_start: 0.9545 (t) cc_final: 0.8988 (m) REVERT: J 269 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8011 (tm-30) REVERT: J 351 ASN cc_start: 0.5677 (p0) cc_final: 0.5455 (p0) REVERT: J 367 MET cc_start: 0.8797 (mmp) cc_final: 0.8531 (mmp) REVERT: K 183 GLU cc_start: 0.7873 (mp0) cc_final: 0.6993 (mp0) REVERT: K 224 LYS cc_start: 0.9290 (mtmt) cc_final: 0.8526 (tptt) REVERT: K 389 GLU cc_start: 0.8745 (pp20) cc_final: 0.8273 (pp20) REVERT: L 269 TYR cc_start: 0.7924 (t80) cc_final: 0.7644 (t80) REVERT: M 307 GLU cc_start: 0.8295 (tt0) cc_final: 0.7951 (tp30) REVERT: M 390 GLN cc_start: 0.8765 (mp10) cc_final: 0.8346 (mp10) REVERT: M 421 GLU cc_start: 0.8558 (tt0) cc_final: 0.8313 (tt0) REVERT: s 127 VAL cc_start: 0.9011 (p) cc_final: 0.8660 (m) outliers start: 1 outliers final: 0 residues processed: 468 average time/residue: 0.3636 time to fit residues: 262.1852 Evaluate side-chains 361 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 290 optimal weight: 0.6980 chunk 220 optimal weight: 0.1980 chunk 152 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 197 optimal weight: 0.5980 chunk 294 optimal weight: 0.0670 chunk 312 optimal weight: 0.0050 chunk 154 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.2332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN D 117 GLN D 162 GLN ** F 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN G 118 GLN G 195 GLN H 356 ASN I 311 ASN J 287 ASN J 295 ASN L 175 GLN L 364 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25059 Z= 0.148 Angle : 0.610 10.937 34025 Z= 0.302 Chirality : 0.044 0.240 3977 Planarity : 0.004 0.041 4395 Dihedral : 8.438 83.430 3716 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.12 % Allowed : 3.56 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.14), residues: 3260 helix: -1.56 (0.14), residues: 1218 sheet: -2.15 (0.22), residues: 488 loop : -2.02 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 158 HIS 0.009 0.001 HIS F 110 PHE 0.017 0.001 PHE I 268 TYR 0.019 0.001 TYR B 5 ARG 0.017 0.001 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 491 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8092 (p0) cc_final: 0.7735 (p0) REVERT: A 81 MET cc_start: 0.8765 (ttp) cc_final: 0.8476 (ttp) REVERT: A 209 HIS cc_start: 0.7754 (t70) cc_final: 0.7524 (t-90) REVERT: B 57 MET cc_start: 0.8066 (mpp) cc_final: 0.7485 (mtm) REVERT: B 119 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7684 (tm-30) REVERT: B 123 GLN cc_start: 0.7023 (pt0) cc_final: 0.6543 (pt0) REVERT: B 180 ASN cc_start: 0.8639 (t0) cc_final: 0.7896 (t0) REVERT: B 186 GLU cc_start: 0.8372 (tp30) cc_final: 0.7726 (tp30) REVERT: C 18 ARG cc_start: 0.8703 (ptp-110) cc_final: 0.8248 (mtp-110) REVERT: C 49 GLU cc_start: 0.8142 (tt0) cc_final: 0.7840 (tt0) REVERT: C 50 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8188 (mtm-85) REVERT: C 173 GLN cc_start: 0.8416 (mm110) cc_final: 0.7969 (tp40) REVERT: D 5 ASP cc_start: 0.7303 (p0) cc_final: 0.6776 (p0) REVERT: D 139 ASP cc_start: 0.8442 (t0) cc_final: 0.8064 (t0) REVERT: D 175 LEU cc_start: 0.8182 (mp) cc_final: 0.7962 (mt) REVERT: D 202 VAL cc_start: 0.8020 (m) cc_final: 0.7709 (t) REVERT: E 134 MET cc_start: 0.8503 (mtp) cc_final: 0.7768 (mtm) REVERT: E 213 ASP cc_start: 0.8175 (t70) cc_final: 0.7191 (t70) REVERT: E 221 CYS cc_start: 0.7164 (p) cc_final: 0.6913 (p) REVERT: F 31 GLN cc_start: 0.8745 (pt0) cc_final: 0.8502 (pt0) REVERT: F 122 SER cc_start: 0.9156 (m) cc_final: 0.8935 (t) REVERT: F 152 ASN cc_start: 0.8638 (m110) cc_final: 0.8349 (m-40) REVERT: F 203 ASP cc_start: 0.7591 (m-30) cc_final: 0.7294 (t70) REVERT: G 9 ASP cc_start: 0.8381 (m-30) cc_final: 0.8053 (m-30) REVERT: G 26 TYR cc_start: 0.8443 (m-80) cc_final: 0.8077 (m-80) REVERT: G 125 LEU cc_start: 0.8650 (tp) cc_final: 0.8361 (tt) REVERT: G 177 GLU cc_start: 0.7269 (tp30) cc_final: 0.6979 (tp30) REVERT: G 218 TRP cc_start: 0.8225 (p-90) cc_final: 0.7699 (p-90) REVERT: G 238 GLU cc_start: 0.8200 (pp20) cc_final: 0.7889 (pp20) REVERT: H 333 MET cc_start: 0.8365 (ttt) cc_final: 0.8138 (ttt) REVERT: H 373 ARG cc_start: 0.8074 (ttm110) cc_final: 0.7646 (mtp85) REVERT: I 211 MET cc_start: 0.8313 (mmm) cc_final: 0.7953 (mtm) REVERT: I 259 ASP cc_start: 0.7533 (p0) cc_final: 0.7145 (p0) REVERT: I 301 GLU cc_start: 0.8000 (mp0) cc_final: 0.7496 (mp0) REVERT: I 306 MET cc_start: 0.8494 (ttp) cc_final: 0.8213 (ttt) REVERT: I 329 ASN cc_start: 0.8415 (m-40) cc_final: 0.8156 (m-40) REVERT: J 243 SER cc_start: 0.9417 (t) cc_final: 0.8911 (m) REVERT: J 269 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8075 (tm-30) REVERT: J 367 MET cc_start: 0.8669 (mmp) cc_final: 0.8341 (mmp) REVERT: K 246 TYR cc_start: 0.8011 (m-80) cc_final: 0.7793 (m-80) REVERT: K 389 GLU cc_start: 0.8723 (pp20) cc_final: 0.8182 (pp20) REVERT: M 221 TYR cc_start: 0.7861 (p90) cc_final: 0.7143 (p90) REVERT: M 307 GLU cc_start: 0.8241 (tt0) cc_final: 0.7910 (tp30) REVERT: M 421 GLU cc_start: 0.8482 (tt0) cc_final: 0.8265 (tt0) REVERT: s 127 VAL cc_start: 0.8942 (p) cc_final: 0.8478 (m) outliers start: 3 outliers final: 1 residues processed: 492 average time/residue: 0.3752 time to fit residues: 283.9063 Evaluate side-chains 356 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 355 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 260 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 232 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 266 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN D 149 GLN ** F 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 GLN J 295 ASN K 285 GLN L 175 GLN L 208 GLN L 364 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25059 Z= 0.251 Angle : 0.640 9.367 34025 Z= 0.321 Chirality : 0.045 0.193 3977 Planarity : 0.004 0.042 4395 Dihedral : 8.450 89.080 3716 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.14), residues: 3260 helix: -1.35 (0.14), residues: 1214 sheet: -1.93 (0.22), residues: 501 loop : -1.92 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 158 HIS 0.006 0.001 HIS B 190 PHE 0.025 0.002 PHE H 389 TYR 0.024 0.001 TYR F 24 ARG 0.006 0.001 ARG J 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 470 time to evaluate : 2.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.7579 (t0) cc_final: 0.7364 (t0) REVERT: A 49 ASP cc_start: 0.8121 (p0) cc_final: 0.7798 (p0) REVERT: A 81 MET cc_start: 0.8853 (ttp) cc_final: 0.8556 (ttp) REVERT: B 21 ILE cc_start: 0.8376 (pt) cc_final: 0.8044 (mt) REVERT: B 57 MET cc_start: 0.8069 (mpp) cc_final: 0.7492 (mtm) REVERT: B 82 TYR cc_start: 0.8366 (t80) cc_final: 0.8072 (t80) REVERT: B 119 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7888 (tm-30) REVERT: B 123 GLN cc_start: 0.7235 (pt0) cc_final: 0.6961 (pt0) REVERT: B 180 ASN cc_start: 0.8985 (t0) cc_final: 0.8754 (t0) REVERT: B 186 GLU cc_start: 0.8444 (tp30) cc_final: 0.7818 (tp30) REVERT: C 18 ARG cc_start: 0.8645 (ptp-110) cc_final: 0.8247 (mtp-110) REVERT: C 114 ARG cc_start: 0.8043 (tmt-80) cc_final: 0.7153 (tpt170) REVERT: D 5 ASP cc_start: 0.7319 (p0) cc_final: 0.6885 (p0) REVERT: D 139 ASP cc_start: 0.8546 (t0) cc_final: 0.8208 (t0) REVERT: D 202 VAL cc_start: 0.8265 (m) cc_final: 0.7989 (t) REVERT: E 28 LEU cc_start: 0.9173 (mm) cc_final: 0.8821 (mp) REVERT: E 134 MET cc_start: 0.8682 (mtp) cc_final: 0.7894 (mtm) REVERT: E 151 ASP cc_start: 0.7417 (p0) cc_final: 0.6992 (t0) REVERT: E 213 ASP cc_start: 0.7882 (t70) cc_final: 0.7574 (t70) REVERT: F 24 TYR cc_start: 0.9031 (m-80) cc_final: 0.8698 (m-80) REVERT: F 31 GLN cc_start: 0.8917 (pt0) cc_final: 0.8580 (pt0) REVERT: F 203 ASP cc_start: 0.7633 (m-30) cc_final: 0.7295 (t70) REVERT: G 177 GLU cc_start: 0.7481 (tp30) cc_final: 0.7197 (tp30) REVERT: G 218 TRP cc_start: 0.8357 (p-90) cc_final: 0.7940 (p-90) REVERT: G 238 GLU cc_start: 0.8210 (pp20) cc_final: 0.7942 (pp20) REVERT: H 333 MET cc_start: 0.8550 (ttt) cc_final: 0.8259 (ttt) REVERT: H 373 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7667 (mtp85) REVERT: I 211 MET cc_start: 0.8508 (mmm) cc_final: 0.8062 (mtp) REVERT: I 259 ASP cc_start: 0.7647 (p0) cc_final: 0.7229 (p0) REVERT: I 301 GLU cc_start: 0.8058 (mp0) cc_final: 0.7569 (mp0) REVERT: I 306 MET cc_start: 0.8602 (ttp) cc_final: 0.8380 (ttt) REVERT: I 329 ASN cc_start: 0.8573 (m-40) cc_final: 0.8270 (m-40) REVERT: J 217 GLU cc_start: 0.8133 (tt0) cc_final: 0.7914 (tt0) REVERT: J 243 SER cc_start: 0.9423 (t) cc_final: 0.8889 (m) REVERT: J 269 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8199 (tm-30) REVERT: J 367 MET cc_start: 0.8716 (mmp) cc_final: 0.8470 (mmp) REVERT: K 212 TYR cc_start: 0.8846 (p90) cc_final: 0.8207 (p90) REVERT: K 389 GLU cc_start: 0.8817 (pp20) cc_final: 0.8444 (pp20) REVERT: M 221 TYR cc_start: 0.7925 (p90) cc_final: 0.7292 (p90) REVERT: M 280 ILE cc_start: 0.8412 (pt) cc_final: 0.7976 (mt) REVERT: M 307 GLU cc_start: 0.8243 (tt0) cc_final: 0.7844 (tp30) REVERT: s 127 VAL cc_start: 0.8887 (p) cc_final: 0.8555 (m) outliers start: 0 outliers final: 0 residues processed: 470 average time/residue: 0.3521 time to fit residues: 262.8250 Evaluate side-chains 355 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 105 optimal weight: 4.9990 chunk 281 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 183 optimal weight: 0.3980 chunk 77 optimal weight: 10.0000 chunk 312 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 HIS C 124 GLN ** F 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 GLN H 356 ASN ** I 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 393 GLN J 295 ASN K 285 GLN L 175 GLN L 208 GLN L 364 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25059 Z= 0.205 Angle : 0.622 10.003 34025 Z= 0.309 Chirality : 0.045 0.177 3977 Planarity : 0.004 0.043 4395 Dihedral : 8.296 83.381 3716 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.04 % Allowed : 2.59 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.14), residues: 3260 helix: -1.21 (0.14), residues: 1230 sheet: -1.80 (0.23), residues: 487 loop : -1.83 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 158 HIS 0.008 0.001 HIS F 110 PHE 0.015 0.001 PHE I 268 TYR 0.023 0.001 TYR F 24 ARG 0.006 0.000 ARG J 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 463 time to evaluate : 2.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8089 (p0) cc_final: 0.7773 (p0) REVERT: A 81 MET cc_start: 0.8842 (ttp) cc_final: 0.8589 (ttp) REVERT: B 21 ILE cc_start: 0.8361 (pt) cc_final: 0.8107 (mt) REVERT: B 57 MET cc_start: 0.8013 (mpp) cc_final: 0.7547 (mtm) REVERT: B 119 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7969 (tm-30) REVERT: B 186 GLU cc_start: 0.8404 (tp30) cc_final: 0.7836 (tp30) REVERT: C 18 ARG cc_start: 0.8813 (ptp-110) cc_final: 0.8288 (mtp-110) REVERT: C 23 GLU cc_start: 0.8483 (pm20) cc_final: 0.8202 (pm20) REVERT: C 27 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8152 (mm-30) REVERT: C 50 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.8115 (mtm-85) REVERT: C 88 ILE cc_start: 0.8670 (pt) cc_final: 0.8192 (mt) REVERT: C 114 ARG cc_start: 0.8034 (tmt-80) cc_final: 0.6955 (tpt90) REVERT: D 5 ASP cc_start: 0.7291 (p0) cc_final: 0.6847 (p0) REVERT: D 139 ASP cc_start: 0.8498 (t0) cc_final: 0.8190 (t0) REVERT: D 202 VAL cc_start: 0.8279 (m) cc_final: 0.7981 (t) REVERT: E 28 LEU cc_start: 0.9125 (mm) cc_final: 0.8785 (mp) REVERT: E 72 ARG cc_start: 0.8136 (tpt170) cc_final: 0.7468 (tpt170) REVERT: E 134 MET cc_start: 0.8641 (mtp) cc_final: 0.7919 (mtm) REVERT: E 151 ASP cc_start: 0.7417 (p0) cc_final: 0.6997 (t0) REVERT: E 197 GLU cc_start: 0.8647 (mp0) cc_final: 0.8329 (mp0) REVERT: E 221 CYS cc_start: 0.7093 (p) cc_final: 0.6777 (p) REVERT: F 31 GLN cc_start: 0.8869 (pt0) cc_final: 0.8544 (pt0) REVERT: F 60 GLN cc_start: 0.7696 (mt0) cc_final: 0.7226 (mt0) REVERT: F 203 ASP cc_start: 0.7650 (m-30) cc_final: 0.7326 (t70) REVERT: G 167 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7825 (mmtm) REVERT: G 177 GLU cc_start: 0.7468 (tp30) cc_final: 0.6780 (tp30) REVERT: G 218 TRP cc_start: 0.8387 (p-90) cc_final: 0.7991 (p-90) REVERT: G 238 GLU cc_start: 0.8169 (pp20) cc_final: 0.7918 (pp20) REVERT: H 310 GLU cc_start: 0.8182 (tp30) cc_final: 0.7726 (mm-30) REVERT: H 333 MET cc_start: 0.8513 (ttt) cc_final: 0.8239 (ttt) REVERT: H 373 ARG cc_start: 0.8323 (ttm110) cc_final: 0.7652 (ptp-110) REVERT: I 259 ASP cc_start: 0.7656 (p0) cc_final: 0.7215 (p0) REVERT: I 306 MET cc_start: 0.8666 (ttp) cc_final: 0.8395 (ttt) REVERT: I 329 ASN cc_start: 0.8598 (m-40) cc_final: 0.8203 (m-40) REVERT: J 243 SER cc_start: 0.9438 (t) cc_final: 0.8844 (m) REVERT: J 256 THR cc_start: 0.8555 (m) cc_final: 0.8336 (m) REVERT: J 269 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8202 (tm-30) REVERT: J 367 MET cc_start: 0.8697 (mmp) cc_final: 0.8489 (mmp) REVERT: K 212 TYR cc_start: 0.8948 (p90) cc_final: 0.8350 (p90) REVERT: K 339 GLU cc_start: 0.8072 (tp30) cc_final: 0.7858 (tp30) REVERT: K 389 GLU cc_start: 0.8832 (pp20) cc_final: 0.8411 (pp20) REVERT: M 221 TYR cc_start: 0.7857 (p90) cc_final: 0.7185 (p90) REVERT: M 280 ILE cc_start: 0.8396 (pt) cc_final: 0.7963 (mt) REVERT: M 307 GLU cc_start: 0.8227 (tt0) cc_final: 0.7712 (tp30) REVERT: M 401 ILE cc_start: 0.8865 (pt) cc_final: 0.8228 (pt) REVERT: s 127 VAL cc_start: 0.8833 (p) cc_final: 0.8516 (m) outliers start: 1 outliers final: 1 residues processed: 463 average time/residue: 0.3514 time to fit residues: 258.0079 Evaluate side-chains 359 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 358 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 178 optimal weight: 30.0000 chunk 228 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 263 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 311 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS C 124 GLN D 122 GLN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 GLN H 392 HIS ** I 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 GLN ** K 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 GLN L 208 GLN L 364 HIS M 310 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25059 Z= 0.318 Angle : 0.691 10.275 34025 Z= 0.347 Chirality : 0.047 0.174 3977 Planarity : 0.004 0.049 4395 Dihedral : 8.529 86.803 3716 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.14), residues: 3260 helix: -1.16 (0.14), residues: 1222 sheet: -1.77 (0.23), residues: 497 loop : -1.87 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 158 HIS 0.008 0.001 HIS F 110 PHE 0.030 0.002 PHE A 32 TYR 0.014 0.002 TYR A 133 ARG 0.007 0.001 ARG M 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 436 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8127 (p0) cc_final: 0.7804 (p0) REVERT: B 21 ILE cc_start: 0.8456 (pt) cc_final: 0.8116 (mt) REVERT: B 57 MET cc_start: 0.8034 (mpp) cc_final: 0.7686 (mtm) REVERT: B 113 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7081 (mm-30) REVERT: B 120 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7216 (mm-30) REVERT: B 186 GLU cc_start: 0.8526 (tp30) cc_final: 0.7957 (tp30) REVERT: C 18 ARG cc_start: 0.8784 (ptp-110) cc_final: 0.8343 (mtp-110) REVERT: C 23 GLU cc_start: 0.8482 (pm20) cc_final: 0.8154 (pm20) REVERT: C 88 ILE cc_start: 0.8684 (pt) cc_final: 0.8213 (mt) REVERT: C 114 ARG cc_start: 0.8073 (tmt-80) cc_final: 0.6873 (tpt90) REVERT: D 5 ASP cc_start: 0.7529 (p0) cc_final: 0.7074 (p0) REVERT: D 139 ASP cc_start: 0.8554 (t0) cc_final: 0.8228 (t0) REVERT: D 202 VAL cc_start: 0.8336 (m) cc_final: 0.8062 (t) REVERT: E 28 LEU cc_start: 0.9178 (mm) cc_final: 0.8857 (mp) REVERT: E 134 MET cc_start: 0.8814 (mtp) cc_final: 0.8060 (mtm) REVERT: E 197 GLU cc_start: 0.8666 (mp0) cc_final: 0.8368 (mp0) REVERT: E 221 CYS cc_start: 0.7144 (p) cc_final: 0.6888 (p) REVERT: F 31 GLN cc_start: 0.8997 (pt0) cc_final: 0.8630 (pt0) REVERT: F 60 GLN cc_start: 0.7748 (mt0) cc_final: 0.7369 (mt0) REVERT: F 203 ASP cc_start: 0.7679 (m-30) cc_final: 0.7391 (t70) REVERT: G 218 TRP cc_start: 0.8454 (p-90) cc_final: 0.7856 (p-90) REVERT: G 238 GLU cc_start: 0.8201 (pp20) cc_final: 0.7951 (pp20) REVERT: H 310 GLU cc_start: 0.8254 (tp30) cc_final: 0.7802 (mm-30) REVERT: H 333 MET cc_start: 0.8635 (ttt) cc_final: 0.8400 (ttt) REVERT: I 211 MET cc_start: 0.8566 (mmm) cc_final: 0.8106 (mtp) REVERT: I 259 ASP cc_start: 0.7575 (p0) cc_final: 0.7186 (p0) REVERT: I 306 MET cc_start: 0.8714 (ttp) cc_final: 0.8428 (ttt) REVERT: I 329 ASN cc_start: 0.8672 (m-40) cc_final: 0.8269 (m-40) REVERT: I 421 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8279 (tm-30) REVERT: J 243 SER cc_start: 0.9457 (t) cc_final: 0.8909 (m) REVERT: J 269 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8261 (tm-30) REVERT: K 246 TYR cc_start: 0.8167 (m-80) cc_final: 0.7863 (m-10) REVERT: K 389 GLU cc_start: 0.8821 (pp20) cc_final: 0.8441 (pp20) REVERT: M 221 TYR cc_start: 0.7902 (p90) cc_final: 0.7238 (p90) REVERT: M 280 ILE cc_start: 0.8538 (pt) cc_final: 0.8147 (mt) REVERT: M 307 GLU cc_start: 0.8263 (tt0) cc_final: 0.7756 (tp30) REVERT: M 421 GLU cc_start: 0.8682 (tt0) cc_final: 0.8451 (tt0) outliers start: 0 outliers final: 0 residues processed: 436 average time/residue: 0.3609 time to fit residues: 246.9273 Evaluate side-chains 340 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 192 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS C 124 GLN D 55 GLN E 215 ASN H 356 ASN ** I 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 GLN L 175 GLN L 208 GLN L 364 HIS M 412 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25059 Z= 0.281 Angle : 0.677 10.001 34025 Z= 0.337 Chirality : 0.046 0.168 3977 Planarity : 0.004 0.048 4395 Dihedral : 8.528 88.326 3716 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.04 % Allowed : 1.94 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.14), residues: 3260 helix: -1.11 (0.14), residues: 1221 sheet: -1.72 (0.23), residues: 487 loop : -1.81 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 158 HIS 0.008 0.001 HIS F 110 PHE 0.023 0.002 PHE H 389 TYR 0.016 0.001 TYR E 26 ARG 0.008 0.000 ARG I 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 432 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8130 (p0) cc_final: 0.7807 (p0) REVERT: A 81 MET cc_start: 0.8908 (ttp) cc_final: 0.8624 (ttp) REVERT: B 57 MET cc_start: 0.8002 (mpp) cc_final: 0.7562 (mtm) REVERT: B 113 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7125 (mm-30) REVERT: B 119 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 186 GLU cc_start: 0.8462 (tp30) cc_final: 0.7920 (tp30) REVERT: C 18 ARG cc_start: 0.8792 (ptp-110) cc_final: 0.8384 (mtp-110) REVERT: C 23 GLU cc_start: 0.8469 (pm20) cc_final: 0.8062 (pm20) REVERT: C 53 THR cc_start: 0.7860 (m) cc_final: 0.7375 (p) REVERT: C 88 ILE cc_start: 0.8679 (pt) cc_final: 0.8221 (mt) REVERT: C 114 ARG cc_start: 0.8038 (tmt-80) cc_final: 0.6729 (tpt90) REVERT: D 5 ASP cc_start: 0.7640 (p0) cc_final: 0.7182 (p0) REVERT: D 139 ASP cc_start: 0.8640 (t0) cc_final: 0.8342 (t0) REVERT: D 202 VAL cc_start: 0.8476 (m) cc_final: 0.8167 (t) REVERT: E 28 LEU cc_start: 0.9164 (mm) cc_final: 0.8828 (mp) REVERT: E 134 MET cc_start: 0.8674 (mtp) cc_final: 0.8061 (mtm) REVERT: E 197 GLU cc_start: 0.8610 (mp0) cc_final: 0.8323 (mp0) REVERT: E 221 CYS cc_start: 0.7228 (p) cc_final: 0.7008 (p) REVERT: F 31 GLN cc_start: 0.8839 (pt0) cc_final: 0.8473 (pt0) REVERT: F 203 ASP cc_start: 0.7518 (m-30) cc_final: 0.7235 (t70) REVERT: G 218 TRP cc_start: 0.8479 (p-90) cc_final: 0.7922 (p-90) REVERT: G 238 GLU cc_start: 0.8171 (pp20) cc_final: 0.7970 (pp20) REVERT: H 310 GLU cc_start: 0.8262 (tp30) cc_final: 0.7748 (mm-30) REVERT: H 373 ARG cc_start: 0.8335 (ttm110) cc_final: 0.7760 (ptm160) REVERT: I 259 ASP cc_start: 0.7555 (p0) cc_final: 0.7152 (p0) REVERT: I 306 MET cc_start: 0.8685 (ttp) cc_final: 0.8407 (ttt) REVERT: I 329 ASN cc_start: 0.8646 (m-40) cc_final: 0.8235 (m-40) REVERT: I 421 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8260 (tm-30) REVERT: J 243 SER cc_start: 0.9477 (t) cc_final: 0.8877 (m) REVERT: J 269 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8278 (tm-30) REVERT: J 272 MET cc_start: 0.8589 (tmm) cc_final: 0.8373 (tmm) REVERT: J 367 MET cc_start: 0.8974 (mmm) cc_final: 0.8383 (mmm) REVERT: K 246 TYR cc_start: 0.8154 (m-80) cc_final: 0.7937 (m-10) REVERT: K 389 GLU cc_start: 0.8831 (pp20) cc_final: 0.8433 (pp20) REVERT: L 191 ARG cc_start: 0.6752 (ptm-80) cc_final: 0.6548 (ptm-80) REVERT: L 219 LEU cc_start: 0.8442 (tp) cc_final: 0.8220 (tt) REVERT: M 221 TYR cc_start: 0.7839 (p90) cc_final: 0.7219 (p90) REVERT: M 280 ILE cc_start: 0.8528 (pt) cc_final: 0.8131 (mt) REVERT: M 307 GLU cc_start: 0.8229 (tt0) cc_final: 0.7778 (tp30) outliers start: 1 outliers final: 1 residues processed: 432 average time/residue: 0.3591 time to fit residues: 241.0142 Evaluate side-chains 345 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 344 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 283 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 chunk 272 optimal weight: 20.0000 chunk 290 optimal weight: 0.0270 chunk 174 optimal weight: 20.0000 chunk 126 optimal weight: 0.8980 chunk 227 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 262 optimal weight: 3.9990 chunk 274 optimal weight: 0.6980 chunk 289 optimal weight: 7.9990 overall best weight: 1.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 HIS C 124 GLN D 209 ASN E 215 ASN F 60 GLN ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 GLN L 175 GLN L 208 GLN L 364 HIS ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25059 Z= 0.232 Angle : 0.659 11.434 34025 Z= 0.326 Chirality : 0.046 0.321 3977 Planarity : 0.004 0.049 4395 Dihedral : 8.395 88.296 3716 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.14), residues: 3260 helix: -0.99 (0.14), residues: 1236 sheet: -1.60 (0.23), residues: 483 loop : -1.72 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 218 HIS 0.009 0.001 HIS F 110 PHE 0.021 0.002 PHE L 180 TYR 0.016 0.001 TYR L 269 ARG 0.013 0.000 ARG H 299 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 436 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8108 (p0) cc_final: 0.7828 (p0) REVERT: B 57 MET cc_start: 0.8397 (mpp) cc_final: 0.8074 (mtm) REVERT: B 113 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7224 (mm-30) REVERT: B 120 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7322 (mm-30) REVERT: B 186 GLU cc_start: 0.8480 (tp30) cc_final: 0.7930 (tp30) REVERT: C 18 ARG cc_start: 0.8809 (ptp-110) cc_final: 0.8413 (mtp-110) REVERT: C 23 GLU cc_start: 0.8341 (pm20) cc_final: 0.8070 (pm20) REVERT: C 27 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8169 (mm-30) REVERT: C 88 ILE cc_start: 0.8661 (pt) cc_final: 0.8248 (mt) REVERT: C 114 ARG cc_start: 0.8040 (tmt-80) cc_final: 0.6870 (tpt90) REVERT: C 237 ASP cc_start: 0.6675 (m-30) cc_final: 0.6473 (p0) REVERT: D 5 ASP cc_start: 0.7650 (p0) cc_final: 0.7222 (p0) REVERT: D 139 ASP cc_start: 0.8573 (t0) cc_final: 0.8332 (t0) REVERT: D 202 VAL cc_start: 0.8427 (m) cc_final: 0.8140 (t) REVERT: E 28 LEU cc_start: 0.9170 (mm) cc_final: 0.8810 (mp) REVERT: E 134 MET cc_start: 0.8691 (mtp) cc_final: 0.8145 (mtm) REVERT: E 197 GLU cc_start: 0.8577 (mp0) cc_final: 0.8288 (mp0) REVERT: E 221 CYS cc_start: 0.7245 (p) cc_final: 0.7002 (p) REVERT: F 31 GLN cc_start: 0.8791 (pt0) cc_final: 0.8438 (pt0) REVERT: F 203 ASP cc_start: 0.7634 (m-30) cc_final: 0.7335 (t70) REVERT: G 218 TRP cc_start: 0.8464 (p-90) cc_final: 0.7931 (p-90) REVERT: H 310 GLU cc_start: 0.8312 (tp30) cc_final: 0.7761 (mm-30) REVERT: H 333 MET cc_start: 0.8695 (ttt) cc_final: 0.8435 (ttt) REVERT: I 259 ASP cc_start: 0.7549 (p0) cc_final: 0.7145 (p0) REVERT: I 301 GLU cc_start: 0.8092 (mp0) cc_final: 0.7593 (mp0) REVERT: I 306 MET cc_start: 0.8663 (ttp) cc_final: 0.8387 (ttt) REVERT: I 329 ASN cc_start: 0.8654 (m-40) cc_final: 0.8264 (m-40) REVERT: I 421 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8248 (tm-30) REVERT: I 424 MET cc_start: 0.7429 (mmm) cc_final: 0.6993 (tpt) REVERT: J 243 SER cc_start: 0.9465 (t) cc_final: 0.8918 (m) REVERT: J 269 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8322 (tm-30) REVERT: J 272 MET cc_start: 0.8586 (tmm) cc_final: 0.8317 (tmm) REVERT: J 273 LEU cc_start: 0.8768 (tp) cc_final: 0.8404 (tt) REVERT: J 357 ASP cc_start: 0.8717 (p0) cc_final: 0.8442 (p0) REVERT: K 212 TYR cc_start: 0.8887 (p90) cc_final: 0.8235 (p90) REVERT: K 246 TYR cc_start: 0.8170 (m-80) cc_final: 0.7916 (m-10) REVERT: K 339 GLU cc_start: 0.8118 (tp30) cc_final: 0.7753 (tp30) REVERT: L 189 GLN cc_start: 0.7167 (mp10) cc_final: 0.6943 (pm20) REVERT: L 191 ARG cc_start: 0.6780 (ptm-80) cc_final: 0.6530 (ptm-80) REVERT: M 221 TYR cc_start: 0.7791 (p90) cc_final: 0.7172 (p90) REVERT: M 280 ILE cc_start: 0.8500 (pt) cc_final: 0.8134 (mt) REVERT: M 307 GLU cc_start: 0.8165 (tt0) cc_final: 0.7699 (tp30) REVERT: M 416 VAL cc_start: 0.9475 (m) cc_final: 0.9244 (p) outliers start: 0 outliers final: 0 residues processed: 436 average time/residue: 0.3531 time to fit residues: 242.2828 Evaluate side-chains 338 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 190 optimal weight: 1.9990 chunk 306 optimal weight: 6.9990 chunk 187 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 321 optimal weight: 8.9990 chunk 296 optimal weight: 0.0060 chunk 256 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 197 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN E 215 ASN F 60 GLN ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 356 ASN I 393 GLN L 175 GLN L 208 GLN L 364 HIS L 393 ASN ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25059 Z= 0.180 Angle : 0.644 13.327 34025 Z= 0.316 Chirality : 0.045 0.309 3977 Planarity : 0.004 0.045 4395 Dihedral : 8.135 87.283 3716 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.04 % Allowed : 0.45 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.14), residues: 3260 helix: -0.95 (0.14), residues: 1245 sheet: -1.40 (0.23), residues: 479 loop : -1.62 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 376 HIS 0.009 0.001 HIS F 110 PHE 0.022 0.001 PHE H 389 TYR 0.020 0.001 TYR F 171 ARG 0.009 0.000 ARG H 299 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 459 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8088 (p0) cc_final: 0.7792 (p0) REVERT: A 183 GLU cc_start: 0.8232 (pp20) cc_final: 0.7962 (pp20) REVERT: B 57 MET cc_start: 0.8357 (mpp) cc_final: 0.8146 (mtm) REVERT: B 113 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7208 (mm-30) REVERT: B 186 GLU cc_start: 0.8431 (tp30) cc_final: 0.7928 (tp30) REVERT: B 211 LEU cc_start: 0.8451 (pp) cc_final: 0.8245 (pp) REVERT: C 18 ARG cc_start: 0.8821 (ptp-110) cc_final: 0.8427 (mtp-110) REVERT: C 23 GLU cc_start: 0.8324 (pm20) cc_final: 0.7910 (pm20) REVERT: C 27 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8151 (mm-30) REVERT: C 53 THR cc_start: 0.7909 (m) cc_final: 0.7408 (p) REVERT: C 88 ILE cc_start: 0.8633 (pt) cc_final: 0.8223 (mt) REVERT: C 114 ARG cc_start: 0.7967 (tmt-80) cc_final: 0.6938 (tpt90) REVERT: C 160 TRP cc_start: 0.7813 (m100) cc_final: 0.7103 (m100) REVERT: D 5 ASP cc_start: 0.7590 (p0) cc_final: 0.7121 (p0) REVERT: D 202 VAL cc_start: 0.8413 (m) cc_final: 0.8098 (t) REVERT: E 28 LEU cc_start: 0.9125 (mm) cc_final: 0.8808 (mp) REVERT: E 134 MET cc_start: 0.8606 (mtp) cc_final: 0.7999 (mtm) REVERT: E 151 ASP cc_start: 0.7338 (p0) cc_final: 0.6733 (t0) REVERT: E 197 GLU cc_start: 0.8564 (mp0) cc_final: 0.8285 (mp0) REVERT: E 221 CYS cc_start: 0.7294 (p) cc_final: 0.6585 (p) REVERT: E 231 TYR cc_start: 0.8537 (m-10) cc_final: 0.8301 (m-10) REVERT: F 31 GLN cc_start: 0.8651 (pt0) cc_final: 0.8385 (pt0) REVERT: F 203 ASP cc_start: 0.7660 (m-30) cc_final: 0.7331 (t70) REVERT: G 95 GLU cc_start: 0.8315 (tp30) cc_final: 0.8105 (tp30) REVERT: G 218 TRP cc_start: 0.8393 (p-90) cc_final: 0.7984 (p-90) REVERT: H 310 GLU cc_start: 0.8305 (tp30) cc_final: 0.7738 (mm-30) REVERT: H 333 MET cc_start: 0.8593 (ttt) cc_final: 0.8357 (tpp) REVERT: H 373 ARG cc_start: 0.8236 (ttm110) cc_final: 0.7755 (ptm160) REVERT: I 211 MET cc_start: 0.8631 (mmm) cc_final: 0.8421 (mtp) REVERT: I 259 ASP cc_start: 0.7539 (p0) cc_final: 0.7120 (p0) REVERT: I 306 MET cc_start: 0.8644 (ttp) cc_final: 0.8344 (ttt) REVERT: I 329 ASN cc_start: 0.8731 (m-40) cc_final: 0.8414 (m-40) REVERT: I 351 GLU cc_start: 0.8246 (pm20) cc_final: 0.7978 (pm20) REVERT: I 421 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8213 (tm-30) REVERT: J 243 SER cc_start: 0.9437 (t) cc_final: 0.8869 (m) REVERT: J 269 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8358 (tm-30) REVERT: J 272 MET cc_start: 0.8626 (tmm) cc_final: 0.8345 (tmm) REVERT: J 273 LEU cc_start: 0.8719 (tp) cc_final: 0.8355 (tt) REVERT: J 357 ASP cc_start: 0.8766 (p0) cc_final: 0.8371 (p0) REVERT: K 179 MET cc_start: 0.7886 (tmm) cc_final: 0.7179 (tmm) REVERT: K 212 TYR cc_start: 0.8861 (p90) cc_final: 0.8007 (p90) REVERT: K 241 GLU cc_start: 0.8362 (pp20) cc_final: 0.8041 (tm-30) REVERT: K 339 GLU cc_start: 0.7978 (tp30) cc_final: 0.7635 (tp30) REVERT: K 389 GLU cc_start: 0.8916 (pp20) cc_final: 0.8559 (pp20) REVERT: L 271 LYS cc_start: 0.8722 (mmmm) cc_final: 0.7998 (ttmt) REVERT: M 221 TYR cc_start: 0.7750 (p90) cc_final: 0.7099 (p90) REVERT: M 307 GLU cc_start: 0.8155 (tt0) cc_final: 0.7676 (tp30) REVERT: M 416 VAL cc_start: 0.9464 (m) cc_final: 0.9222 (p) outliers start: 1 outliers final: 0 residues processed: 459 average time/residue: 0.3756 time to fit residues: 273.6697 Evaluate side-chains 354 residues out of total 2761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 203 optimal weight: 2.9990 chunk 272 optimal weight: 20.0000 chunk 78 optimal weight: 0.0980 chunk 236 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 256 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 chunk 263 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 HIS C 124 GLN D 209 ASN ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS H 356 ASN I 204 HIS ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 393 GLN ** I 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 GLN L 208 GLN L 364 HIS ** M 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.079049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.067919 restraints weight = 69967.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.069175 restraints weight = 43224.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.070486 restraints weight = 31663.224| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25059 Z= 0.169 Angle : 0.638 12.579 34025 Z= 0.310 Chirality : 0.044 0.288 3977 Planarity : 0.004 0.044 4395 Dihedral : 7.952 88.194 3716 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.04 % Allowed : 0.36 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.15), residues: 3260 helix: -0.80 (0.15), residues: 1250 sheet: -1.43 (0.23), residues: 475 loop : -1.51 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 159 HIS 0.009 0.001 HIS F 110 PHE 0.021 0.001 PHE L 180 TYR 0.016 0.001 TYR L 269 ARG 0.008 0.000 ARG H 299 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5377.29 seconds wall clock time: 98 minutes 13.31 seconds (5893.31 seconds total)