Starting phenix.real_space_refine on Wed Nov 19 13:56:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ef2_9044/11_2025/6ef2_9044.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ef2_9044/11_2025/6ef2_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ef2_9044/11_2025/6ef2_9044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ef2_9044/11_2025/6ef2_9044.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ef2_9044/11_2025/6ef2_9044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ef2_9044/11_2025/6ef2_9044.map" } resolution = 4.27 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'GLU:plan': 3, 'ARG: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: {'GLU:plan': 11, 'PHE:plan': 1, '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: {'ARG:plan': 2, 'GLU:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 1} 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: {'ASP:plan': 4, 'GLU:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 2} 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, 'ASP:plan': 3, 'ASN:plan1': 1} 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: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2, 'PHE: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: {'GLU:plan': 5, 'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2} 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, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} 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: {'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 2, '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: {'ASP:plan': 5, 'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1, 'PHE: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: {'GLU:plan': 11, 'ARG:plan': 10, 'PHE:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 5, 'HIS:plan': 1} 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: {'GLU:plan': 1, 'GLN:plan1': 2, '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: 6.51, per 1000 atoms: 0.26 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 - 3.00 Amino acid : True - 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 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... Secondary structure from input PDB file: 133 helices and 27 sheets defined 42.3% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 Processing helix chain 'A' and resid 86 through 109 removed outlier: 3.632A pdb=" N ALA A 90 " --> pdb=" O PRO A 86 " (cutoff:3.500A) 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 113 through 128 removed outlier: 3.539A pdb=" N TYR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 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 198 through 215 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 242 through 247 Processing helix chain 'B' and resid 20 through 31 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 84 through 97 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) removed outlier: 3.689A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 107 through 119 removed outlier: 4.475A pdb=" N GLU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 178 Processing helix chain 'B' and resid 185 through 197 removed outlier: 3.518A pdb=" N ILE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 245 removed outlier: 3.738A pdb=" N ASP B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 249 Processing helix chain 'C' and resid 19 through 27 removed outlier: 3.844A pdb=" N GLU C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 81 through 103 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 107 through 117 removed outlier: 3.727A pdb=" N LEU C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.737A pdb=" N THR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N MET C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 207 through 211 removed outlier: 3.583A pdb=" N LEU C 211 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 234 Processing helix chain 'C' and resid 235 through 241 removed outlier: 3.637A pdb=" N LEU C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL C 240 " --> pdb=" O LYS C 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 28 Processing helix chain 'D' and resid 79 through 101 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 105 through 118 Processing helix chain 'D' and resid 118 through 123 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.608A pdb=" N VAL D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) 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 187 through 196 removed outlier: 3.505A pdb=" N CYS D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 4.144A pdb=" N GLN D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 removed outlier: 3.615A pdb=" N ASN D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 239 removed outlier: 3.688A pdb=" N ILE D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 32 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) removed outlier: 4.091A pdb=" N LYS E 32 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 removed outlier: 3.600A pdb=" N ILE E 64 " --> pdb=" O SER E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 removed outlier: 3.770A pdb=" N ALA E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) 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 94 through 103 removed outlier: 3.620A pdb=" N THR E 98 " --> pdb=" O THR E 94 " (cutoff:3.500A) 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 108 through 121 removed outlier: 3.546A pdb=" N LEU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) 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) Processing helix chain 'E' and resid 122 through 124 No H-bonds generated for 'chain 'E' and resid 122 through 124' Processing helix chain 'E' and resid 178 through 183 removed outlier: 3.598A pdb=" N GLU E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 186 No H-bonds generated for 'chain 'E' and resid 184 through 186' Processing helix chain 'E' and resid 196 through 207 removed outlier: 3.535A pdb=" N LEU E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 248 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 19 through 26 Processing helix chain 'F' and resid 27 through 32 removed outlier: 3.761A pdb=" N LYS F 30 " --> pdb=" O GLU F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 92 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 104 through 122 removed outlier: 3.613A pdb=" N ALA F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) 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) removed outlier: 4.582A pdb=" N SER F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 176 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 185 through 198 removed outlier: 3.979A pdb=" N LEU F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) 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 207 through 211 removed outlier: 3.744A pdb=" N LEU F 211 " --> pdb=" O VAL F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 230 removed outlier: 4.145A pdb=" N ALA F 229 " --> pdb=" O ASP F 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.573A pdb=" N GLU G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) 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) Processing helix chain 'G' and resid 83 through 97 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) removed outlier: 4.151A pdb=" N ALA G 97 " --> pdb=" O ARG G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 104 Processing helix chain 'G' and resid 108 through 123 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 168 through 176 removed outlier: 3.679A pdb=" N ALA G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 183 removed outlier: 3.785A pdb=" N VAL G 180 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 205 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) Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'G' and resid 235 through 240 Processing helix chain 'G' and resid 240 through 248 removed outlier: 4.409A pdb=" N GLU G 246 " --> pdb=" O PHE G 242 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN G 248 " --> pdb=" O GLN G 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 199 Processing helix chain 'H' and resid 216 through 225 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 225 through 231 removed outlier: 3.545A pdb=" N LEU H 229 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 239 removed outlier: 3.775A pdb=" N LEU H 238 " --> pdb=" O ARG H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 268 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) removed outlier: 3.725A pdb=" N ASP H 268 " --> pdb=" O ALA H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 301 removed outlier: 4.289A pdb=" N VAL H 291 " --> pdb=" O GLY H 287 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG H 292 " --> pdb=" O ALA H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 341 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 357 through 361 removed outlier: 3.880A pdb=" N THR H 360 " --> pdb=" O ARG H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 386 Processing helix chain 'H' and resid 388 through 393 removed outlier: 3.759A pdb=" N HIS H 392 " --> pdb=" O ILE H 388 " (cutoff:3.500A) Processing helix chain 'H' and resid 403 through 411 removed outlier: 3.904A pdb=" N ILE H 407 " --> pdb=" O ARG H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 433 removed outlier: 3.523A pdb=" N SER H 421 " --> pdb=" O ALA H 417 " (cutoff:3.500A) 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 440 through 452 removed outlier: 3.543A pdb=" N LEU H 444 " --> pdb=" O GLU H 440 " (cutoff:3.500A) 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) removed outlier: 3.645A pdb=" N SER H 452 " --> pdb=" O ASP H 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 198 removed outlier: 3.513A pdb=" N LYS I 195 " --> pdb=" O ILE I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 212 removed outlier: 3.604A pdb=" N MET I 211 " --> pdb=" O LEU I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 239 removed outlier: 3.560A pdb=" N ASN I 238 " --> pdb=" O LYS I 234 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN I 239 " --> pdb=" O ALA I 235 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 274 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 283 through 287 Processing helix chain 'I' and resid 299 through 314 removed outlier: 3.907A pdb=" N GLN I 303 " --> pdb=" O GLU I 299 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR I 305 " --> pdb=" O GLU I 301 " (cutoff:3.500A) 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 354 through 366 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 376 through 381 removed outlier: 3.538A pdb=" N LEU I 380 " --> pdb=" O ASN I 376 " (cutoff:3.500A) Processing helix chain 'I' and resid 390 through 405 removed outlier: 3.958A pdb=" N ALA I 394 " --> pdb=" O ALA I 390 " (cutoff:3.500A) 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 412 through 424 removed outlier: 4.260A pdb=" N PHE I 416 " --> pdb=" O THR I 412 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA I 419 " --> pdb=" O ASP I 415 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET I 424 " --> pdb=" O LYS I 420 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 161 removed outlier: 3.814A pdb=" N LYS J 161 " --> pdb=" O ILE J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 170 removed outlier: 3.781A pdb=" N VAL J 168 " --> pdb=" O ILE J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 177 Processing helix chain 'J' and resid 194 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 225 through 239 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) removed outlier: 3.680A pdb=" N GLU J 239 " --> pdb=" O VAL J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 276 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 278 through 285 removed outlier: 3.664A pdb=" N GLU J 283 " --> pdb=" O LEU J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 306 removed outlier: 4.547A pdb=" N LEU J 305 " --> pdb=" O ASP J 301 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 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 343 through 348 Processing helix chain 'J' and resid 355 through 371 removed outlier: 3.681A pdb=" N LYS J 359 " --> pdb=" O GLY J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 390 removed outlier: 3.789A pdb=" N GLU J 383 " --> pdb=" O GLN J 379 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET J 390 " --> pdb=" O VAL J 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 395 Processing helix chain 'K' and resid 179 through 188 removed outlier: 4.111A pdb=" N GLU K 183 " --> pdb=" O MET K 179 " (cutoff:3.500A) 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 188 through 194 removed outlier: 4.389A pdb=" N LEU K 192 " --> pdb=" O VAL K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 202 Processing helix chain 'K' and resid 219 through 229 removed outlier: 3.997A pdb=" N VAL K 223 " --> pdb=" O LYS K 219 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS K 224 " --> pdb=" O THR K 220 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 242 Processing helix chain 'K' and resid 248 through 264 removed outlier: 3.857A pdb=" N ARG K 252 " --> pdb=" O GLY K 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 304 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 345 through 359 removed outlier: 3.762A pdb=" N ARG K 349 " --> pdb=" O ASP K 345 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY K 354 " --> pdb=" O ARG K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 396 removed outlier: 3.860A pdb=" N ALA K 384 " --> pdb=" O GLY K 380 " (cutoff:3.500A) 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) Processing helix chain 'K' and resid 407 through 414 removed outlier: 3.553A pdb=" N TYR K 411 " --> pdb=" O LEU K 407 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA K 412 " --> pdb=" O GLU K 408 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 424 Processing helix chain 'L' and resid 171 through 175 removed outlier: 3.714A pdb=" N GLU L 174 " --> pdb=" O THR L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 197 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 197 through 203 removed outlier: 3.521A pdb=" N LEU L 201 " --> pdb=" O ILE L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 211 Processing helix chain 'L' and resid 229 through 240 removed outlier: 3.555A pdb=" N LYS L 233 " --> pdb=" O THR L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 251 Processing helix chain 'L' and resid 259 through 273 removed outlier: 3.889A pdb=" N ILE L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 286 Processing helix chain 'L' and resid 294 through 313 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) removed outlier: 4.029A pdb=" N ASP L 313 " --> pdb=" O LEU L 309 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 365 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 378 through 383 Processing helix chain 'L' and resid 387 through 403 removed outlier: 3.717A pdb=" N ILE L 391 " --> pdb=" O ASN L 387 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA L 402 " --> pdb=" O ALA L 398 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE L 403 " --> pdb=" O GLY L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 423 removed outlier: 4.048A pdb=" N LEU L 415 " --> pdb=" O ASN L 411 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG L 420 " --> pdb=" O MET L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 424 through 429 Processing helix chain 'M' and resid 186 through 198 removed outlier: 4.190A pdb=" N ILE M 190 " --> pdb=" O LEU M 186 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU M 191 " --> pdb=" O ASP M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 198 through 203 Processing helix chain 'M' and resid 205 through 210 Processing helix chain 'M' and resid 227 through 240 removed outlier: 3.676A pdb=" N LEU M 231 " --> pdb=" O GLY M 227 " (cutoff:3.500A) 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 247 through 253 Processing helix chain 'M' and resid 258 through 272 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 298 through 311 removed outlier: 3.612A pdb=" N GLN M 302 " --> pdb=" O ASP M 298 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR M 304 " --> pdb=" O GLU M 300 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 364 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) removed outlier: 3.631A pdb=" N HIS M 364 " --> pdb=" O ILE M 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 382 removed outlier: 4.622A pdb=" N LEU M 379 " --> pdb=" O ASN M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 387 through 406 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 411 through 423 removed outlier: 3.588A pdb=" N PHE M 415 " --> pdb=" O LYS M 411 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN M 423 " --> pdb=" O ILE M 419 " (cutoff:3.500A) Processing sheet with id=AA1, 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=AA2, 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=AA3, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.538A pdb=" N SER B 65 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 73 " --> pdb=" O SER B 65 " (cutoff:3.500A) 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=AA5, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.577A pdb=" N ALA C 214 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AA6, 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=AA7, first strand: chain 'D' and resid 161 through 162 removed outlier: 3.703A pdb=" N GLN D 162 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL D 42 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 222 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing sheet with id=AA8, 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=AA9, first strand: chain 'E' and resid 169 through 171 removed outlier: 3.506A pdb=" N VAL E 46 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER E 220 " --> pdb=" O LEU E 48 " (cutoff:3.500A) 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=AB1, first strand: chain 'E' and resid 74 through 75 Processing sheet with id=AB2, first strand: chain 'E' and resid 157 through 158 Processing sheet with id=AB3, 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) removed outlier: 5.246A pdb=" N GLY F 217 " --> pdb=" O PRO F 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.837A pdb=" N ILE F 63 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU F 74 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LYS F 65 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU F 72 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET F 70 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY F 71 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE F 135 " --> pdb=" O GLY F 71 " (cutoff:3.500A) 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=AB5, 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=AB6, 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) Processing sheet with id=AB7, 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=AB8, 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=AB9, 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) removed outlier: 3.650A pdb=" N PHE G 138 " --> pdb=" O TYR G 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 247 through 249 Processing sheet with id=AC2, first strand: chain 'H' and resid 270 through 274 Processing sheet with id=AC3, first strand: chain 'I' and resid 326 through 327 removed outlier: 6.523A pdb=" N VAL I 219 " --> pdb=" O MET I 326 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE I 220 " --> pdb=" O ILE I 348 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'I' and resid 277 through 279 Processing sheet with id=AC5, first strand: chain 'J' and resid 209 through 213 removed outlier: 5.818A pdb=" N LYS J 209 " --> pdb=" O ILE J 244 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N PHE J 246 " --> pdb=" O LYS J 209 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE J 211 " --> pdb=" O PHE J 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 269 through 270 removed outlier: 6.541A pdb=" N ILE K 269 " --> pdb=" O ILE K 315 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY K 208 " --> pdb=" O ARG K 336 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE K 338 " --> pdb=" O GLY K 208 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU K 210 " --> pdb=" O ILE K 338 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 325 through 326 removed outlier: 7.185A pdb=" N LEU L 219 " --> pdb=" O VAL L 347 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 276 through 277 removed outlier: 6.583A pdb=" N CYS L 276 " --> pdb=" O LYS L 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'M' and resid 276 through 280 removed outlier: 3.849A pdb=" N ALA M 326 " --> pdb=" O ILE M 280 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA M 325 " --> pdb=" O ALA M 218 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR M 327 " --> pdb=" O MET M 220 " (cutoff:3.500A) 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) 814 hydrogen bonds defined for protein. 2271 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: 4.40 Time building geometry restraints manager: 2.90 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: 0.00 - 4.98: 33888 4.98 - 9.96: 129 9.96 - 14.94: 0 14.94 - 19.93: 1 19.93 - 24.91: 7 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: 1025 2.69 - 3.24: 27127 3.24 - 3.80: 36325 3.80 - 4.35: 47267 4.35 - 4.90: 75630 Nonbonded interactions: 187374 Sorted by model distance: nonbonded pdb=" OD2 ASP K 304 " pdb=" NH2 ARG K 330 " model vdw 2.139 3.120 nonbonded pdb=" OG SER D 153 " pdb=" OE1 GLN H 465 " model vdw 2.141 3.040 nonbonded pdb=" O ASP C 42 " pdb=" OH TYR C 146 " model vdw 2.150 3.040 nonbonded pdb=" O ILE J 330 " pdb=" NH1 ARG J 333 " model vdw 2.150 3.120 nonbonded pdb=" NH1 ARG H 385 " pdb=" O CYS H 411 " model vdw 2.153 3.120 ... (remaining 187369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.490 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.880 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.000 ------------------------------------------------------------------------------- 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= 0.483 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.015 0.002 ARG F 126 TYR 0.034 0.003 TYR E 26 PHE 0.031 0.003 PHE J 382 TRP 0.017 0.003 TRP H 404 HIS 0.013 0.003 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.01108 (25059) covalent geometry : angle 1.02423 (34025) hydrogen bonds : bond 0.32090 ( 807) hydrogen bonds : angle 11.41555 ( 2271) *********************** 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 to be fit. rotamer outliers: 0 poor density : 633 time to evaluate : 0.957 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: 0.2107 time to fit residues: 195.9626 Evaluate side-chains 390 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0170 chunk 298 optimal weight: 0.0020 overall best weight: 0.5428 ------------------------------------------------------------------------------- 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 D 118 GLN F 21 GLN F 119 ASN G 33 ASN G 68 GLN G 118 GLN G 182 HIS H 356 ASN I 238 ASN J 295 ASN J 391 ASN ** K 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.086843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.076306 restraints weight = 68521.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.077699 restraints weight = 43697.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.078434 restraints weight = 29659.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.079085 restraints weight = 21530.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.079155 restraints weight = 19769.766| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25059 Z= 0.144 Angle : 0.711 10.255 34025 Z= 0.364 Chirality : 0.047 0.186 3977 Planarity : 0.005 0.049 4395 Dihedral : 9.317 77.993 3716 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.04 % Allowed : 4.17 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.15 (0.13), residues: 3260 helix: -2.60 (0.12), residues: 1237 sheet: -3.02 (0.20), residues: 481 loop : -2.71 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 10 TYR 0.021 0.001 TYR B 82 PHE 0.018 0.002 PHE B 204 TRP 0.028 0.002 TRP M 376 HIS 0.011 0.001 HIS F 110 Details of bonding type rmsd covalent geometry : bond 0.00309 (25059) covalent geometry : angle 0.71139 (34025) hydrogen bonds : bond 0.05484 ( 807) hydrogen bonds : angle 6.39401 ( 2271) *********************** 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 544 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 543 time to evaluate : 1.008 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: 0.8094 (p0) cc_final: 0.7745 (p0) REVERT: A 210 MET cc_start: 0.7968 (ptm) cc_final: 0.7700 (ptm) REVERT: B 4 ARG cc_start: 0.7681 (ttt90) cc_final: 0.6782 (ttm110) REVERT: C 26 LEU cc_start: 0.8992 (mp) cc_final: 0.8778 (mp) REVERT: C 68 LYS cc_start: 0.8897 (tttt) cc_final: 0.8539 (tttm) REVERT: C 160 TRP cc_start: 0.8021 (m100) cc_final: 0.7546 (m100) REVERT: C 173 GLN cc_start: 0.8347 (mm110) cc_final: 0.8002 (mm-40) REVERT: D 5 ASP cc_start: 0.7495 (p0) cc_final: 0.7060 (p0) REVERT: D 22 TYR cc_start: 0.7896 (m-10) cc_final: 0.7565 (m-80) REVERT: D 102 ASP cc_start: 0.8414 (t0) cc_final: 0.8105 (t0) REVERT: D 175 LEU cc_start: 0.8142 (mp) cc_final: 0.7857 (mt) REVERT: E 59 LEU cc_start: 0.8167 (tt) cc_final: 0.7966 (tt) REVERT: E 122 ARG cc_start: 0.8868 (tpp80) cc_final: 0.8531 (tpt170) REVERT: E 151 ASP cc_start: 0.7309 (p0) cc_final: 0.6690 (t0) REVERT: E 221 CYS cc_start: 0.7390 (p) cc_final: 0.7165 (p) REVERT: F 27 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7305 (mt-10) REVERT: F 31 GLN cc_start: 0.8962 (pt0) cc_final: 0.8491 (tt0) REVERT: F 42 THR cc_start: 0.8401 (p) cc_final: 0.8137 (p) REVERT: F 114 ASP cc_start: 0.7856 (m-30) cc_final: 0.7635 (m-30) REVERT: F 138 ASP cc_start: 0.8371 (p0) cc_final: 0.7960 (p0) REVERT: F 145 LEU cc_start: 0.8427 (mp) cc_final: 0.8189 (mt) REVERT: F 152 ASN cc_start: 0.8607 (m110) cc_final: 0.8325 (m-40) REVERT: G 9 ASP cc_start: 0.8227 (m-30) cc_final: 0.7548 (m-30) REVERT: G 26 TYR cc_start: 0.7986 (m-80) cc_final: 0.7754 (m-80) REVERT: G 238 GLU cc_start: 0.8235 (pp20) cc_final: 0.7954 (pp20) REVERT: I 246 ARG cc_start: 0.4569 (pmt-80) cc_final: 0.3020 (mtt90) REVERT: I 259 ASP cc_start: 0.7523 (p0) cc_final: 0.7082 (p0) REVERT: I 306 MET cc_start: 0.8616 (ttp) cc_final: 0.8311 (ttt) REVERT: I 329 ASN cc_start: 0.7976 (m-40) cc_final: 0.7732 (m-40) REVERT: I 406 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6929 (tm-30) REVERT: I 421 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7388 (tp30) REVERT: J 148 ASP cc_start: 0.8314 (p0) cc_final: 0.8055 (p0) REVERT: J 243 SER cc_start: 0.9265 (t) cc_final: 0.8828 (m) REVERT: J 274 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8091 (tm-30) REVERT: J 370 LEU cc_start: 0.9024 (tt) cc_final: 0.8492 (tt) REVERT: K 224 LYS cc_start: 0.9021 (mtmt) cc_final: 0.8078 (tptt) REVERT: L 189 GLN cc_start: 0.7601 (mp10) cc_final: 0.7155 (mm-40) REVERT: L 269 TYR cc_start: 0.7937 (t80) cc_final: 0.7682 (t80) REVERT: L 271 LYS cc_start: 0.8795 (mtpp) cc_final: 0.8543 (mtpp) REVERT: L 394 CYS cc_start: 0.6473 (p) cc_final: 0.6254 (p) REVERT: M 280 ILE cc_start: 0.8385 (pt) cc_final: 0.7960 (mt) REVERT: M 307 GLU cc_start: 0.8151 (tt0) cc_final: 0.7774 (tp30) REVERT: s 127 VAL cc_start: 0.9004 (p) cc_final: 0.8710 (m) outliers start: 1 outliers final: 0 residues processed: 543 average time/residue: 0.1777 time to fit residues: 149.5365 Evaluate side-chains 367 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 268 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 221 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 254 optimal weight: 0.0370 chunk 37 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 234 optimal weight: 0.0770 overall best weight: 1.4222 ------------------------------------------------------------------------------- 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** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS G 121 GLN G 127 ASN G 182 HIS J 269 GLN J 295 ASN J 331 HIS K 285 GLN ** K 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 364 HIS M 412 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.083946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.073087 restraints weight = 68742.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.074649 restraints weight = 43632.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.075315 restraints weight = 28365.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.075504 restraints weight = 21607.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.075602 restraints weight = 21235.694| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25059 Z= 0.140 Angle : 0.655 9.947 34025 Z= 0.334 Chirality : 0.046 0.175 3977 Planarity : 0.005 0.054 4395 Dihedral : 8.685 73.544 3716 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.04 % Allowed : 4.70 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.13), residues: 3260 helix: -1.96 (0.13), residues: 1240 sheet: -2.45 (0.22), residues: 479 loop : -2.43 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 333 TYR 0.029 0.001 TYR E 26 PHE 0.016 0.002 PHE L 173 TRP 0.041 0.003 TRP M 376 HIS 0.008 0.001 HIS F 143 Details of bonding type rmsd covalent geometry : bond 0.00316 (25059) covalent geometry : angle 0.65472 (34025) hydrogen bonds : bond 0.03981 ( 807) hydrogen bonds : angle 5.35608 ( 2271) *********************** 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 501 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 500 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8074 (p0) cc_final: 0.7786 (p0) REVERT: A 81 MET cc_start: 0.8650 (ttp) cc_final: 0.8419 (ttp) REVERT: A 210 MET cc_start: 0.7912 (ptm) cc_final: 0.7703 (ttm) REVERT: B 57 MET cc_start: 0.7887 (mpp) cc_final: 0.7245 (mtm) REVERT: C 68 LYS cc_start: 0.8879 (tttt) cc_final: 0.8582 (tttm) REVERT: C 160 TRP cc_start: 0.7985 (m100) cc_final: 0.7595 (m100) REVERT: C 173 GLN cc_start: 0.8533 (mm110) cc_final: 0.8139 (mm-40) REVERT: D 5 ASP cc_start: 0.7460 (p0) cc_final: 0.7026 (p0) REVERT: D 22 TYR cc_start: 0.8221 (m-10) cc_final: 0.7964 (m-10) REVERT: D 102 ASP cc_start: 0.8605 (t0) cc_final: 0.8266 (t0) REVERT: D 139 ASP cc_start: 0.8344 (t0) cc_final: 0.8047 (t0) REVERT: D 175 LEU cc_start: 0.8264 (mp) cc_final: 0.7973 (mt) REVERT: E 134 MET cc_start: 0.8452 (mtp) cc_final: 0.7747 (mtm) REVERT: E 151 ASP cc_start: 0.7384 (p0) cc_final: 0.6593 (t0) REVERT: E 182 GLU cc_start: 0.8606 (pp20) cc_final: 0.8313 (pp20) REVERT: F 31 GLN cc_start: 0.9036 (pt0) cc_final: 0.8763 (pt0) REVERT: F 145 LEU cc_start: 0.8512 (mp) cc_final: 0.8308 (mt) REVERT: F 152 ASN cc_start: 0.8666 (m110) cc_final: 0.8430 (m-40) REVERT: F 226 ASP cc_start: 0.7457 (p0) cc_final: 0.7142 (p0) REVERT: G 9 ASP cc_start: 0.8389 (m-30) cc_final: 0.8148 (m-30) REVERT: G 26 TYR cc_start: 0.8209 (m-80) cc_final: 0.7925 (m-80) REVERT: G 238 GLU cc_start: 0.8313 (pp20) cc_final: 0.8067 (pp20) REVERT: I 211 MET cc_start: 0.7868 (mmm) cc_final: 0.7510 (mtp) REVERT: I 259 ASP cc_start: 0.7461 (p0) cc_final: 0.7012 (p0) REVERT: I 306 MET cc_start: 0.8622 (ttp) cc_final: 0.8267 (ttt) REVERT: I 329 ASN cc_start: 0.8050 (m-40) cc_final: 0.7818 (m-40) REVERT: J 148 ASP cc_start: 0.8380 (p0) cc_final: 0.8161 (p0) REVERT: J 243 SER cc_start: 0.9317 (t) cc_final: 0.8834 (m) REVERT: J 269 GLN cc_start: 0.8162 (tm130) cc_final: 0.7514 (tm-30) REVERT: J 274 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8164 (tm-30) REVERT: J 367 MET cc_start: 0.8311 (mmp) cc_final: 0.7777 (mmp) REVERT: K 221 MET cc_start: 0.7400 (ptp) cc_final: 0.7071 (ptp) REVERT: L 271 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8523 (mtpp) REVERT: L 394 CYS cc_start: 0.6344 (p) cc_final: 0.6132 (p) REVERT: M 265 ASP cc_start: 0.8297 (t0) cc_final: 0.8026 (t0) REVERT: M 280 ILE cc_start: 0.8422 (pt) cc_final: 0.8068 (mt) REVERT: M 307 GLU cc_start: 0.8188 (tt0) cc_final: 0.7951 (tp30) REVERT: s 127 VAL cc_start: 0.8938 (p) cc_final: 0.8613 (m) outliers start: 1 outliers final: 0 residues processed: 500 average time/residue: 0.1745 time to fit residues: 136.6539 Evaluate side-chains 362 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 254 optimal weight: 3.9990 chunk 117 optimal weight: 0.0570 chunk 207 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 185 optimal weight: 0.0870 chunk 29 optimal weight: 8.9990 chunk 23 optimal weight: 0.0170 chunk 282 optimal weight: 10.0000 chunk 124 optimal weight: 0.0770 chunk 238 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 overall best weight: 0.2472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 GLN D 118 GLN D 149 GLN D 162 GLN F 4 ASN F 31 GLN ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 GLN H 356 ASN I 311 ASN J 220 GLN J 287 ASN J 295 ASN J 331 HIS K 285 GLN L 175 GLN L 203 ASN L 364 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.086221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.075483 restraints weight = 68543.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.077067 restraints weight = 43729.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.077782 restraints weight = 29469.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.078174 restraints weight = 20836.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.078926 restraints weight = 19767.243| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25059 Z= 0.109 Angle : 0.624 10.565 34025 Z= 0.312 Chirality : 0.044 0.213 3977 Planarity : 0.004 0.050 4395 Dihedral : 8.223 77.161 3716 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.12 % Allowed : 3.89 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.14), residues: 3260 helix: -1.56 (0.13), residues: 1256 sheet: -2.01 (0.22), residues: 479 loop : -2.16 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 50 TYR 0.035 0.001 TYR E 26 PHE 0.029 0.001 PHE A 32 TRP 0.046 0.002 TRP M 376 HIS 0.010 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00231 (25059) covalent geometry : angle 0.62396 (34025) hydrogen bonds : bond 0.03247 ( 807) hydrogen bonds : angle 4.93672 ( 2271) *********************** 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 527 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 524 time to evaluate : 1.085 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: 0.8038 (p0) cc_final: 0.7728 (p0) REVERT: A 62 LYS cc_start: 0.7052 (mtmt) cc_final: 0.6620 (ptpt) REVERT: A 81 MET cc_start: 0.8562 (ttp) cc_final: 0.8288 (ttp) REVERT: B 4 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7689 (ttp80) REVERT: B 21 ILE cc_start: 0.8338 (pt) cc_final: 0.8034 (mt) REVERT: B 57 MET cc_start: 0.7958 (mpp) cc_final: 0.7228 (mtm) REVERT: C 27 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7912 (mm-30) REVERT: C 68 LYS cc_start: 0.8869 (tttt) cc_final: 0.8593 (tttm) REVERT: C 160 TRP cc_start: 0.8062 (m100) cc_final: 0.7640 (m100) REVERT: C 173 GLN cc_start: 0.8471 (mm110) cc_final: 0.8151 (mm110) REVERT: D 5 ASP cc_start: 0.7202 (p0) cc_final: 0.6712 (p0) REVERT: D 102 ASP cc_start: 0.8646 (t0) cc_final: 0.8293 (t0) REVERT: D 139 ASP cc_start: 0.8387 (t0) cc_final: 0.8039 (t0) REVERT: D 175 LEU cc_start: 0.8328 (mp) cc_final: 0.8055 (mt) REVERT: E 47 VAL cc_start: 0.9177 (p) cc_final: 0.8908 (p) REVERT: E 134 MET cc_start: 0.8281 (mtp) cc_final: 0.7651 (mtm) REVERT: E 151 ASP cc_start: 0.7344 (p0) cc_final: 0.6954 (m-30) REVERT: E 221 CYS cc_start: 0.7277 (p) cc_final: 0.6602 (p) REVERT: F 42 THR cc_start: 0.8586 (p) cc_final: 0.8265 (p) REVERT: F 60 GLN cc_start: 0.7474 (mt0) cc_final: 0.7265 (mt0) REVERT: F 152 ASN cc_start: 0.8598 (m110) cc_final: 0.8302 (m-40) REVERT: G 9 ASP cc_start: 0.8349 (m-30) cc_final: 0.8067 (m-30) REVERT: G 26 TYR cc_start: 0.8175 (m-80) cc_final: 0.7880 (m-80) REVERT: G 125 LEU cc_start: 0.8672 (tp) cc_final: 0.8269 (tp) REVERT: G 218 TRP cc_start: 0.8271 (p-90) cc_final: 0.7541 (p-90) REVERT: G 238 GLU cc_start: 0.8209 (pp20) cc_final: 0.7932 (pp20) REVERT: H 310 GLU cc_start: 0.7972 (tp30) cc_final: 0.7731 (mm-30) REVERT: H 333 MET cc_start: 0.8252 (ttt) cc_final: 0.7813 (ttt) REVERT: I 259 ASP cc_start: 0.7463 (p0) cc_final: 0.6894 (p0) REVERT: I 306 MET cc_start: 0.8548 (ttp) cc_final: 0.8231 (ttt) REVERT: I 329 ASN cc_start: 0.7907 (m-40) cc_final: 0.7705 (m-40) REVERT: J 243 SER cc_start: 0.9232 (t) cc_final: 0.8759 (m) REVERT: J 269 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7762 (tm-30) REVERT: J 274 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8101 (tm-30) REVERT: J 367 MET cc_start: 0.8269 (mmp) cc_final: 0.7538 (mmp) REVERT: K 179 MET cc_start: 0.7077 (tmm) cc_final: 0.6865 (tmm) REVERT: K 224 LYS cc_start: 0.8936 (mtmt) cc_final: 0.8132 (tptt) REVERT: K 291 GLU cc_start: 0.8158 (tp30) cc_final: 0.7726 (tp30) REVERT: L 271 LYS cc_start: 0.8780 (mtpp) cc_final: 0.8511 (mtpp) REVERT: L 307 GLU cc_start: 0.7751 (tp30) cc_final: 0.7337 (tm-30) REVERT: L 394 CYS cc_start: 0.6426 (p) cc_final: 0.6199 (p) REVERT: M 265 ASP cc_start: 0.8436 (t0) cc_final: 0.8103 (t0) REVERT: M 271 LYS cc_start: 0.8795 (pttt) cc_final: 0.8519 (tptp) REVERT: M 307 GLU cc_start: 0.8203 (tt0) cc_final: 0.7999 (tp30) REVERT: s 127 VAL cc_start: 0.8944 (p) cc_final: 0.8589 (m) outliers start: 3 outliers final: 1 residues processed: 526 average time/residue: 0.1752 time to fit residues: 143.3504 Evaluate side-chains 366 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 132 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 278 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 291 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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** D 55 GLN D 122 GLN E 216 ASN F 4 ASN F 31 GLN G 195 GLN J 220 GLN J 287 ASN J 295 ASN K 285 GLN L 175 GLN L 364 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.082192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.071230 restraints weight = 68866.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.072392 restraints weight = 45531.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.073072 restraints weight = 31699.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.073675 restraints weight = 23995.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.073674 restraints weight = 20697.561| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25059 Z= 0.144 Angle : 0.644 10.286 34025 Z= 0.325 Chirality : 0.045 0.161 3977 Planarity : 0.004 0.053 4395 Dihedral : 8.212 76.456 3716 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.14), residues: 3260 helix: -1.34 (0.14), residues: 1263 sheet: -1.82 (0.23), residues: 491 loop : -2.01 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 131 TYR 0.027 0.001 TYR E 26 PHE 0.013 0.001 PHE L 173 TRP 0.057 0.002 TRP M 376 HIS 0.005 0.001 HIS D 16 Details of bonding type rmsd covalent geometry : bond 0.00335 (25059) covalent geometry : angle 0.64373 (34025) hydrogen bonds : bond 0.03427 ( 807) hydrogen bonds : angle 4.82884 ( 2271) *********************** 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 497 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 495 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8104 (p0) cc_final: 0.7810 (p0) REVERT: A 81 MET cc_start: 0.8698 (ttp) cc_final: 0.8412 (ttp) REVERT: A 209 HIS cc_start: 0.7869 (t-90) cc_final: 0.7595 (t-90) REVERT: B 21 ILE cc_start: 0.8546 (pt) cc_final: 0.8265 (mt) REVERT: B 57 MET cc_start: 0.7936 (mpp) cc_final: 0.7456 (mtp) REVERT: B 123 GLN cc_start: 0.6768 (pt0) cc_final: 0.6349 (pt0) REVERT: C 68 LYS cc_start: 0.8958 (tttt) cc_final: 0.8653 (tttm) REVERT: C 114 ARG cc_start: 0.8061 (tmt-80) cc_final: 0.6997 (tpt170) REVERT: C 173 GLN cc_start: 0.8585 (mm110) cc_final: 0.8221 (tp40) REVERT: C 212 GLU cc_start: 0.8290 (pm20) cc_final: 0.8059 (pm20) REVERT: D 5 ASP cc_start: 0.7389 (p0) cc_final: 0.7065 (p0) REVERT: D 139 ASP cc_start: 0.8454 (t0) cc_final: 0.8095 (t0) REVERT: D 175 LEU cc_start: 0.8387 (mp) cc_final: 0.8147 (mt) REVERT: E 134 MET cc_start: 0.8456 (mtp) cc_final: 0.7857 (mtm) REVERT: E 151 ASP cc_start: 0.7596 (p0) cc_final: 0.6662 (t0) REVERT: E 233 ASN cc_start: 0.8243 (m110) cc_final: 0.7871 (p0) REVERT: F 60 GLN cc_start: 0.7609 (mt0) cc_final: 0.7337 (mt0) REVERT: F 65 LYS cc_start: 0.8512 (tttm) cc_final: 0.8132 (tttp) REVERT: G 9 ASP cc_start: 0.8450 (m-30) cc_final: 0.8081 (m-30) REVERT: G 177 GLU cc_start: 0.7228 (tp30) cc_final: 0.6891 (tp30) REVERT: G 218 TRP cc_start: 0.8222 (p-90) cc_final: 0.7512 (p-90) REVERT: G 238 GLU cc_start: 0.8309 (pp20) cc_final: 0.8104 (pp20) REVERT: H 310 GLU cc_start: 0.8004 (tp30) cc_final: 0.7722 (mm-30) REVERT: I 259 ASP cc_start: 0.7489 (p0) cc_final: 0.7135 (p0) REVERT: I 306 MET cc_start: 0.8617 (ttp) cc_final: 0.8242 (ttt) REVERT: I 329 ASN cc_start: 0.8087 (m-40) cc_final: 0.7841 (m-40) REVERT: J 148 ASP cc_start: 0.8444 (p0) cc_final: 0.8240 (p0) REVERT: J 243 SER cc_start: 0.9303 (t) cc_final: 0.8758 (m) REVERT: J 269 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7654 (tm-30) REVERT: J 274 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8122 (tm-30) REVERT: J 357 ASP cc_start: 0.8635 (p0) cc_final: 0.8335 (p0) REVERT: J 367 MET cc_start: 0.8488 (mmp) cc_final: 0.7583 (mmp) REVERT: K 291 GLU cc_start: 0.8196 (tp30) cc_final: 0.7936 (tp30) REVERT: K 320 ARG cc_start: 0.7132 (tmm160) cc_final: 0.6926 (ttp80) REVERT: L 271 LYS cc_start: 0.8716 (mtpp) cc_final: 0.8311 (ttmt) REVERT: L 307 GLU cc_start: 0.7899 (tp30) cc_final: 0.7576 (tm-30) REVERT: L 322 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7850 (mmmt) REVERT: M 265 ASP cc_start: 0.8485 (t0) cc_final: 0.8131 (t0) REVERT: M 307 GLU cc_start: 0.8313 (tt0) cc_final: 0.7961 (tp30) REVERT: s 127 VAL cc_start: 0.8717 (p) cc_final: 0.8487 (m) outliers start: 2 outliers final: 0 residues processed: 496 average time/residue: 0.1649 time to fit residues: 129.8917 Evaluate side-chains 358 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 24 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 310 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 249 optimal weight: 0.8980 chunk 316 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 295 optimal weight: 0.4980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 GLN H 356 ASN J 287 ASN J 295 ASN K 285 GLN L 175 GLN L 208 GLN L 364 HIS M 362 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.082124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.071003 restraints weight = 68593.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.072459 restraints weight = 46683.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.073027 restraints weight = 31620.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.073286 restraints weight = 23853.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.073318 restraints weight = 21727.417| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25059 Z= 0.128 Angle : 0.633 9.825 34025 Z= 0.318 Chirality : 0.045 0.203 3977 Planarity : 0.004 0.050 4395 Dihedral : 8.050 76.397 3716 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.04 % Allowed : 2.47 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.14), residues: 3260 helix: -1.08 (0.14), residues: 1258 sheet: -1.68 (0.23), residues: 496 loop : -1.89 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 342 TYR 0.018 0.001 TYR E 26 PHE 0.019 0.001 PHE L 180 TRP 0.070 0.003 TRP M 376 HIS 0.006 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00296 (25059) covalent geometry : angle 0.63318 (34025) hydrogen bonds : bond 0.03236 ( 807) hydrogen bonds : angle 4.70268 ( 2271) *********************** 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 486 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 485 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8110 (p0) cc_final: 0.7826 (p0) REVERT: B 21 ILE cc_start: 0.8563 (pt) cc_final: 0.8289 (mt) REVERT: B 57 MET cc_start: 0.8030 (mpp) cc_final: 0.7497 (mtp) REVERT: B 123 GLN cc_start: 0.6915 (pt0) cc_final: 0.6518 (pt0) REVERT: C 27 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8010 (mm-30) REVERT: C 68 LYS cc_start: 0.8984 (tttt) cc_final: 0.8677 (tttm) REVERT: C 114 ARG cc_start: 0.8027 (tmt-80) cc_final: 0.6909 (tpt90) REVERT: C 173 GLN cc_start: 0.8552 (mm110) cc_final: 0.8150 (tp40) REVERT: C 212 GLU cc_start: 0.8244 (pm20) cc_final: 0.8043 (pm20) REVERT: D 5 ASP cc_start: 0.7343 (p0) cc_final: 0.6963 (p0) REVERT: D 102 ASP cc_start: 0.8644 (t0) cc_final: 0.8405 (t0) REVERT: D 139 ASP cc_start: 0.8473 (t0) cc_final: 0.8156 (t0) REVERT: D 146 LYS cc_start: 0.8960 (mtmm) cc_final: 0.8629 (mtmt) REVERT: E 134 MET cc_start: 0.8293 (mtp) cc_final: 0.7800 (mtm) REVERT: E 151 ASP cc_start: 0.7675 (p0) cc_final: 0.6721 (t0) REVERT: E 233 ASN cc_start: 0.8236 (m110) cc_final: 0.7757 (p0) REVERT: F 60 GLN cc_start: 0.7665 (mt0) cc_final: 0.7366 (mt0) REVERT: G 9 ASP cc_start: 0.8319 (m-30) cc_final: 0.8106 (m-30) REVERT: G 125 LEU cc_start: 0.8706 (tp) cc_final: 0.8430 (tt) REVERT: G 167 LYS cc_start: 0.7737 (mmmt) cc_final: 0.7502 (mmtt) REVERT: G 177 GLU cc_start: 0.7198 (tp30) cc_final: 0.6438 (tp30) REVERT: G 218 TRP cc_start: 0.8250 (p-90) cc_final: 0.7689 (p-90) REVERT: H 310 GLU cc_start: 0.8058 (tp30) cc_final: 0.7708 (mm-30) REVERT: H 333 MET cc_start: 0.8334 (tpp) cc_final: 0.8083 (tpp) REVERT: H 352 MET cc_start: 0.8532 (ptp) cc_final: 0.8331 (ptp) REVERT: H 428 MET cc_start: 0.7871 (ttm) cc_final: 0.7510 (ttm) REVERT: I 196 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7893 (mt-10) REVERT: I 259 ASP cc_start: 0.7495 (p0) cc_final: 0.7163 (p0) REVERT: I 306 MET cc_start: 0.8576 (ttp) cc_final: 0.8204 (ttt) REVERT: I 329 ASN cc_start: 0.8010 (m-40) cc_final: 0.7798 (m-40) REVERT: J 229 MET cc_start: 0.6803 (mtt) cc_final: 0.6591 (mtt) REVERT: J 243 SER cc_start: 0.9337 (t) cc_final: 0.8790 (m) REVERT: J 256 THR cc_start: 0.8440 (m) cc_final: 0.8159 (m) REVERT: J 265 ASP cc_start: 0.7970 (t70) cc_final: 0.7766 (t70) REVERT: J 269 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7740 (tm-30) REVERT: J 274 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8133 (tm-30) REVERT: J 357 ASP cc_start: 0.8654 (p0) cc_final: 0.8349 (p0) REVERT: J 367 MET cc_start: 0.8346 (mmp) cc_final: 0.7616 (mmm) REVERT: K 212 TYR cc_start: 0.8837 (p90) cc_final: 0.8496 (p90) REVERT: K 221 MET cc_start: 0.7044 (ptp) cc_final: 0.6567 (ptp) REVERT: K 291 GLU cc_start: 0.8163 (tp30) cc_final: 0.7927 (tp30) REVERT: K 319 ASN cc_start: 0.8058 (m110) cc_final: 0.7612 (m-40) REVERT: K 320 ARG cc_start: 0.7084 (tmm160) cc_final: 0.6745 (ttp80) REVERT: L 271 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8417 (ttmt) REVERT: L 307 GLU cc_start: 0.8055 (tp30) cc_final: 0.7470 (tm-30) REVERT: L 312 MET cc_start: 0.8031 (ptp) cc_final: 0.7691 (ptm) REVERT: L 322 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7892 (mmmt) REVERT: M 221 TYR cc_start: 0.7947 (p90) cc_final: 0.7123 (p90) REVERT: M 265 ASP cc_start: 0.8433 (t0) cc_final: 0.7935 (t0) REVERT: M 271 LYS cc_start: 0.8906 (pptt) cc_final: 0.8525 (tptt) REVERT: M 307 GLU cc_start: 0.8152 (tt0) cc_final: 0.7845 (tp30) REVERT: M 401 ILE cc_start: 0.8602 (pt) cc_final: 0.7992 (pt) REVERT: s 127 VAL cc_start: 0.8766 (p) cc_final: 0.8482 (m) outliers start: 1 outliers final: 1 residues processed: 486 average time/residue: 0.1720 time to fit residues: 131.7485 Evaluate side-chains 367 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 366 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 304 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 285 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 243 optimal weight: 0.0770 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 HIS E 73 HIS E 216 ASN ** F 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN J 220 GLN J 295 ASN K 285 GLN L 175 GLN L 208 GLN L 364 HIS M 253 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.079296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.068115 restraints weight = 69467.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.069394 restraints weight = 46968.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.070032 restraints weight = 31308.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.070432 restraints weight = 25460.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.070499 restraints weight = 21436.310| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25059 Z= 0.165 Angle : 0.679 10.151 34025 Z= 0.342 Chirality : 0.046 0.163 3977 Planarity : 0.004 0.057 4395 Dihedral : 8.137 76.870 3716 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.14), residues: 3260 helix: -0.98 (0.14), residues: 1264 sheet: -1.67 (0.23), residues: 498 loop : -1.89 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 191 TYR 0.019 0.001 TYR G 26 PHE 0.021 0.002 PHE J 382 TRP 0.053 0.003 TRP M 376 HIS 0.006 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00390 (25059) covalent geometry : angle 0.67867 (34025) hydrogen bonds : bond 0.03521 ( 807) hydrogen bonds : angle 4.78527 ( 2271) *********************** 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 468 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8125 (p0) cc_final: 0.7845 (p0) REVERT: B 4 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7518 (ttp80) REVERT: B 21 ILE cc_start: 0.8611 (pt) cc_final: 0.8400 (mt) REVERT: C 68 LYS cc_start: 0.9001 (tttt) cc_final: 0.8701 (tttm) REVERT: C 88 ILE cc_start: 0.8539 (pt) cc_final: 0.8116 (mt) REVERT: C 114 ARG cc_start: 0.8036 (tmt-80) cc_final: 0.6926 (tpt90) REVERT: C 173 GLN cc_start: 0.8566 (mm110) cc_final: 0.8222 (tp40) REVERT: C 212 GLU cc_start: 0.8262 (pm20) cc_final: 0.8052 (pm20) REVERT: D 5 ASP cc_start: 0.7397 (p0) cc_final: 0.7175 (p0) REVERT: D 139 ASP cc_start: 0.8493 (t0) cc_final: 0.8143 (t0) REVERT: D 162 GLN cc_start: 0.8805 (tp-100) cc_final: 0.8540 (tp40) REVERT: E 28 LEU cc_start: 0.9038 (mm) cc_final: 0.8682 (mp) REVERT: E 134 MET cc_start: 0.8595 (mtp) cc_final: 0.7873 (mtm) REVERT: E 151 ASP cc_start: 0.7827 (p0) cc_final: 0.7029 (t0) REVERT: E 233 ASN cc_start: 0.8414 (m110) cc_final: 0.8147 (m-40) REVERT: F 60 GLN cc_start: 0.7779 (mt0) cc_final: 0.7502 (mt0) REVERT: G 9 ASP cc_start: 0.8475 (m-30) cc_final: 0.8197 (m-30) REVERT: G 218 TRP cc_start: 0.8294 (p-90) cc_final: 0.7670 (p-90) REVERT: H 310 GLU cc_start: 0.8125 (tp30) cc_final: 0.7704 (mm-30) REVERT: I 259 ASP cc_start: 0.7565 (p0) cc_final: 0.7100 (p0) REVERT: I 306 MET cc_start: 0.8557 (ttp) cc_final: 0.8132 (ttt) REVERT: I 329 ASN cc_start: 0.8189 (m-40) cc_final: 0.7907 (m-40) REVERT: J 229 MET cc_start: 0.6930 (mtt) cc_final: 0.6705 (mtt) REVERT: J 243 SER cc_start: 0.9349 (t) cc_final: 0.8813 (m) REVERT: J 269 GLN cc_start: 0.8499 (tm-30) cc_final: 0.7888 (tm-30) REVERT: J 357 ASP cc_start: 0.8735 (p0) cc_final: 0.8406 (p0) REVERT: J 367 MET cc_start: 0.8327 (mmp) cc_final: 0.7595 (mmm) REVERT: K 183 GLU cc_start: 0.7837 (mp0) cc_final: 0.7504 (mp0) REVERT: K 221 MET cc_start: 0.7299 (ptp) cc_final: 0.7088 (ptp) REVERT: K 319 ASN cc_start: 0.8068 (m110) cc_final: 0.7641 (m-40) REVERT: K 320 ARG cc_start: 0.7127 (tmm160) cc_final: 0.6796 (ttp80) REVERT: K 388 GLN cc_start: 0.8270 (tp40) cc_final: 0.8069 (tp40) REVERT: K 389 GLU cc_start: 0.8541 (pp20) cc_final: 0.8228 (pp20) REVERT: L 191 ARG cc_start: 0.6978 (ptm-80) cc_final: 0.6682 (tmm160) REVERT: L 271 LYS cc_start: 0.8786 (mtpp) cc_final: 0.8444 (ttmt) REVERT: L 307 GLU cc_start: 0.8055 (tp30) cc_final: 0.7486 (tm-30) REVERT: L 322 LYS cc_start: 0.8188 (mmmt) cc_final: 0.7914 (mmmt) REVERT: M 307 GLU cc_start: 0.8235 (tt0) cc_final: 0.7845 (tp30) REVERT: M 311 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8571 (tm-30) REVERT: M 401 ILE cc_start: 0.8745 (pt) cc_final: 0.8177 (pt) REVERT: M 417 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7488 (pp20) outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.1657 time to fit residues: 124.6984 Evaluate side-chains 353 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 103 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 0.1980 chunk 169 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 296 optimal weight: 0.0470 chunk 83 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 HIS ** F 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN H 356 ASN J 295 ASN K 285 GLN L 175 GLN L 208 GLN L 364 HIS M 253 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.081824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.070821 restraints weight = 68730.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.072203 restraints weight = 44976.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.072872 restraints weight = 30660.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.073163 restraints weight = 23706.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.073251 restraints weight = 22890.068| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25059 Z= 0.111 Angle : 0.642 11.253 34025 Z= 0.318 Chirality : 0.044 0.189 3977 Planarity : 0.004 0.050 4395 Dihedral : 7.852 73.451 3716 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.04 % Allowed : 1.50 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.14), residues: 3260 helix: -0.75 (0.14), residues: 1266 sheet: -1.39 (0.24), residues: 476 loop : -1.75 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 296 TYR 0.030 0.001 TYR F 24 PHE 0.021 0.001 PHE L 180 TRP 0.039 0.002 TRP M 376 HIS 0.006 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00251 (25059) covalent geometry : angle 0.64242 (34025) hydrogen bonds : bond 0.03097 ( 807) hydrogen bonds : angle 4.61066 ( 2271) *********************** 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 475 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 474 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8110 (p0) cc_final: 0.7836 (p0) REVERT: A 218 PHE cc_start: 0.8126 (m-10) cc_final: 0.7849 (m-10) REVERT: B 4 ARG cc_start: 0.7791 (ttp80) cc_final: 0.7503 (ttp80) REVERT: B 21 ILE cc_start: 0.8474 (pt) cc_final: 0.8239 (mt) REVERT: C 53 THR cc_start: 0.7967 (m) cc_final: 0.7560 (p) REVERT: C 68 LYS cc_start: 0.8971 (tttt) cc_final: 0.8682 (tttm) REVERT: C 88 ILE cc_start: 0.8567 (pt) cc_final: 0.8117 (mt) REVERT: C 114 ARG cc_start: 0.7990 (tmt-80) cc_final: 0.6754 (tpt90) REVERT: C 173 GLN cc_start: 0.8537 (mm110) cc_final: 0.8171 (tp40) REVERT: C 212 GLU cc_start: 0.8230 (pm20) cc_final: 0.7648 (pm20) REVERT: D 5 ASP cc_start: 0.7381 (p0) cc_final: 0.7104 (p0) REVERT: D 139 ASP cc_start: 0.8454 (t0) cc_final: 0.8188 (t0) REVERT: E 28 LEU cc_start: 0.9023 (mm) cc_final: 0.8640 (mp) REVERT: E 134 MET cc_start: 0.8442 (mtp) cc_final: 0.7793 (mtm) REVERT: E 151 ASP cc_start: 0.7729 (p0) cc_final: 0.6767 (t0) REVERT: E 216 ASN cc_start: 0.7808 (t0) cc_final: 0.7591 (t0) REVERT: E 221 CYS cc_start: 0.7411 (p) cc_final: 0.7091 (p) REVERT: F 27 GLU cc_start: 0.8225 (pp20) cc_final: 0.7673 (pp20) REVERT: F 60 GLN cc_start: 0.7723 (mt0) cc_final: 0.7329 (mt0) REVERT: G 125 LEU cc_start: 0.8687 (tp) cc_final: 0.8449 (tt) REVERT: G 218 TRP cc_start: 0.8280 (p-90) cc_final: 0.7742 (p-90) REVERT: H 310 GLU cc_start: 0.8181 (tp30) cc_final: 0.7682 (mm-30) REVERT: H 333 MET cc_start: 0.8349 (tpp) cc_final: 0.8040 (tpt) REVERT: H 352 MET cc_start: 0.8551 (ptp) cc_final: 0.8319 (ptp) REVERT: I 259 ASP cc_start: 0.7554 (p0) cc_final: 0.7304 (p0) REVERT: I 306 MET cc_start: 0.8498 (ttp) cc_final: 0.8124 (ttt) REVERT: J 229 MET cc_start: 0.6809 (mtt) cc_final: 0.6591 (mtt) REVERT: J 243 SER cc_start: 0.9284 (t) cc_final: 0.8808 (m) REVERT: J 256 THR cc_start: 0.8446 (m) cc_final: 0.8105 (m) REVERT: J 269 GLN cc_start: 0.8478 (tm-30) cc_final: 0.7924 (tm-30) REVERT: J 357 ASP cc_start: 0.8620 (p0) cc_final: 0.8216 (p0) REVERT: J 367 MET cc_start: 0.8454 (mmp) cc_final: 0.7832 (mmm) REVERT: K 221 MET cc_start: 0.7092 (ptp) cc_final: 0.6690 (ptp) REVERT: K 319 ASN cc_start: 0.8010 (m110) cc_final: 0.7550 (m-40) REVERT: K 320 ARG cc_start: 0.6987 (tmm160) cc_final: 0.6685 (ttp80) REVERT: K 388 GLN cc_start: 0.8276 (tp40) cc_final: 0.8026 (tp40) REVERT: K 389 GLU cc_start: 0.8486 (pp20) cc_final: 0.8199 (pp20) REVERT: L 191 ARG cc_start: 0.7195 (ptm-80) cc_final: 0.6634 (tmm160) REVERT: L 271 LYS cc_start: 0.8882 (mtpp) cc_final: 0.8576 (ttmt) REVERT: L 307 GLU cc_start: 0.8082 (tp30) cc_final: 0.7542 (tm-30) REVERT: L 322 LYS cc_start: 0.8096 (mmmt) cc_final: 0.7870 (mmmt) REVERT: M 180 TYR cc_start: 0.7426 (t80) cc_final: 0.7180 (t80) REVERT: M 221 TYR cc_start: 0.7866 (p90) cc_final: 0.7099 (p90) REVERT: M 265 ASP cc_start: 0.8599 (t0) cc_final: 0.8043 (t0) REVERT: M 307 GLU cc_start: 0.8253 (tt0) cc_final: 0.7854 (tp30) outliers start: 1 outliers final: 0 residues processed: 475 average time/residue: 0.1774 time to fit residues: 131.9466 Evaluate side-chains 341 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 77 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 91 optimal weight: 0.3980 chunk 116 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 290 optimal weight: 0.0570 chunk 230 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 HIS ** F 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 356 ASN J 220 GLN J 295 ASN K 285 GLN L 208 GLN L 364 HIS M 253 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.080075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.068778 restraints weight = 69360.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.070249 restraints weight = 45678.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.070685 restraints weight = 30553.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.071132 restraints weight = 25318.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.071147 restraints weight = 21908.549| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25059 Z= 0.133 Angle : 0.656 10.510 34025 Z= 0.326 Chirality : 0.045 0.195 3977 Planarity : 0.004 0.054 4395 Dihedral : 7.824 75.224 3716 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.04 % Allowed : 0.97 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.15), residues: 3260 helix: -0.62 (0.15), residues: 1270 sheet: -1.37 (0.24), residues: 489 loop : -1.70 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 342 TYR 0.019 0.001 TYR F 24 PHE 0.020 0.001 PHE M 279 TRP 0.036 0.002 TRP M 376 HIS 0.012 0.001 HIS F 110 Details of bonding type rmsd covalent geometry : bond 0.00310 (25059) covalent geometry : angle 0.65630 (34025) hydrogen bonds : bond 0.03168 ( 807) hydrogen bonds : angle 4.60926 ( 2271) *********************** 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 464 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 463 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8166 (p0) cc_final: 0.7878 (p0) REVERT: B 4 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7581 (ttp80) REVERT: B 21 ILE cc_start: 0.8542 (pt) cc_final: 0.8339 (mt) REVERT: C 68 LYS cc_start: 0.9059 (tttt) cc_final: 0.8793 (tttm) REVERT: C 88 ILE cc_start: 0.8550 (pt) cc_final: 0.8127 (mt) REVERT: C 114 ARG cc_start: 0.8021 (tmt-80) cc_final: 0.6867 (tpt90) REVERT: C 173 GLN cc_start: 0.8547 (mm110) cc_final: 0.8212 (tp40) REVERT: C 212 GLU cc_start: 0.8009 (pm20) cc_final: 0.7795 (pm20) REVERT: D 139 ASP cc_start: 0.8464 (t0) cc_final: 0.8191 (t0) REVERT: D 142 ASP cc_start: 0.8064 (t0) cc_final: 0.7825 (t0) REVERT: D 162 GLN cc_start: 0.8790 (tp-100) cc_final: 0.8428 (tp40) REVERT: E 28 LEU cc_start: 0.9016 (mm) cc_final: 0.8656 (mp) REVERT: E 134 MET cc_start: 0.8494 (mtp) cc_final: 0.7890 (mtm) REVERT: E 151 ASP cc_start: 0.7856 (p0) cc_final: 0.6922 (t0) REVERT: F 60 GLN cc_start: 0.7758 (mt0) cc_final: 0.7394 (mt0) REVERT: G 9 ASP cc_start: 0.8266 (m-30) cc_final: 0.8038 (m-30) REVERT: G 125 LEU cc_start: 0.8750 (tp) cc_final: 0.8528 (tt) REVERT: G 218 TRP cc_start: 0.8430 (p-90) cc_final: 0.7977 (p-90) REVERT: H 310 GLU cc_start: 0.8208 (tp30) cc_final: 0.7698 (mm-30) REVERT: H 333 MET cc_start: 0.8409 (tpp) cc_final: 0.8029 (tpp) REVERT: H 425 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7931 (mm-30) REVERT: I 259 ASP cc_start: 0.7608 (p0) cc_final: 0.7270 (p0) REVERT: I 306 MET cc_start: 0.8542 (ttp) cc_final: 0.8139 (ttt) REVERT: I 376 ASN cc_start: 0.7856 (t0) cc_final: 0.7605 (t0) REVERT: I 421 GLU cc_start: 0.8232 (pp20) cc_final: 0.7966 (tm-30) REVERT: J 243 SER cc_start: 0.9359 (t) cc_final: 0.8834 (m) REVERT: J 269 GLN cc_start: 0.8399 (tm-30) cc_final: 0.7933 (tm-30) REVERT: J 357 ASP cc_start: 0.8674 (p0) cc_final: 0.8261 (p0) REVERT: J 367 MET cc_start: 0.8265 (mmp) cc_final: 0.7641 (mmm) REVERT: K 183 GLU cc_start: 0.7708 (mp0) cc_final: 0.7414 (mp0) REVERT: K 189 GLU cc_start: 0.7733 (pm20) cc_final: 0.7513 (pm20) REVERT: K 319 ASN cc_start: 0.8107 (m110) cc_final: 0.7663 (m-40) REVERT: K 320 ARG cc_start: 0.7014 (tmm160) cc_final: 0.6741 (ttp80) REVERT: K 388 GLN cc_start: 0.8296 (tp40) cc_final: 0.8064 (tp40) REVERT: K 389 GLU cc_start: 0.8520 (pp20) cc_final: 0.8237 (pp20) REVERT: L 191 ARG cc_start: 0.7260 (ptm-80) cc_final: 0.6695 (tmm160) REVERT: L 194 ARG cc_start: 0.8281 (mmt90) cc_final: 0.7963 (mmt90) REVERT: L 271 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8592 (ttmt) REVERT: L 307 GLU cc_start: 0.8179 (tp30) cc_final: 0.7572 (tm-30) REVERT: L 322 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7862 (mmmt) REVERT: M 180 TYR cc_start: 0.7384 (t80) cc_final: 0.7148 (t80) REVERT: M 265 ASP cc_start: 0.8625 (t0) cc_final: 0.8073 (t0) REVERT: M 307 GLU cc_start: 0.8201 (tt0) cc_final: 0.7805 (tp30) REVERT: M 311 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8511 (tm-30) outliers start: 1 outliers final: 1 residues processed: 464 average time/residue: 0.1764 time to fit residues: 129.1565 Evaluate side-chains 358 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 39 optimal weight: 0.5980 chunk 293 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 85 optimal weight: 0.0980 chunk 95 optimal weight: 9.9990 chunk 187 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 183 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN B 190 HIS D 209 ASN ** F 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 311 ASN I 352 ASN J 295 ASN K 285 GLN L 364 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.081955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.070850 restraints weight = 68863.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.072347 restraints weight = 43201.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.073500 restraints weight = 28921.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.073850 restraints weight = 20149.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.073884 restraints weight = 18472.360| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25059 Z= 0.108 Angle : 0.641 11.396 34025 Z= 0.316 Chirality : 0.044 0.185 3977 Planarity : 0.004 0.046 4395 Dihedral : 7.605 73.693 3716 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.15), residues: 3260 helix: -0.56 (0.15), residues: 1285 sheet: -1.32 (0.24), residues: 500 loop : -1.60 (0.16), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 296 TYR 0.016 0.001 TYR F 24 PHE 0.021 0.001 PHE L 180 TRP 0.034 0.002 TRP M 376 HIS 0.010 0.001 HIS F 110 Details of bonding type rmsd covalent geometry : bond 0.00242 (25059) covalent geometry : angle 0.64052 (34025) hydrogen bonds : bond 0.02938 ( 807) hydrogen bonds : angle 4.50222 ( 2271) ********************** 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 470 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 469 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8040 (p0) cc_final: 0.7777 (p0) REVERT: B 4 ARG cc_start: 0.7811 (ttp80) cc_final: 0.7527 (ttp80) REVERT: C 23 GLU cc_start: 0.7904 (mp0) cc_final: 0.7680 (mp0) REVERT: C 53 THR cc_start: 0.7975 (m) cc_final: 0.7586 (p) REVERT: C 68 LYS cc_start: 0.9042 (tttt) cc_final: 0.8784 (tttm) REVERT: C 88 ILE cc_start: 0.8538 (pt) cc_final: 0.8111 (mt) REVERT: C 114 ARG cc_start: 0.7988 (tmt-80) cc_final: 0.6980 (tpt90) REVERT: C 173 GLN cc_start: 0.8439 (mm110) cc_final: 0.8129 (tp40) REVERT: D 5 ASP cc_start: 0.7309 (p0) cc_final: 0.7021 (p0) REVERT: D 139 ASP cc_start: 0.8461 (t0) cc_final: 0.8212 (t0) REVERT: D 142 ASP cc_start: 0.7919 (t0) cc_final: 0.7679 (t0) REVERT: E 28 LEU cc_start: 0.9000 (mm) cc_final: 0.8591 (mp) REVERT: E 134 MET cc_start: 0.8405 (mtp) cc_final: 0.7806 (mtm) REVERT: E 151 ASP cc_start: 0.7798 (p0) cc_final: 0.6757 (t0) REVERT: E 221 CYS cc_start: 0.7345 (p) cc_final: 0.6578 (p) REVERT: F 60 GLN cc_start: 0.7694 (mt0) cc_final: 0.7216 (mt0) REVERT: G 125 LEU cc_start: 0.8709 (tp) cc_final: 0.8313 (tt) REVERT: G 218 TRP cc_start: 0.8408 (p-90) cc_final: 0.7951 (p-90) REVERT: H 310 GLU cc_start: 0.8144 (tp30) cc_final: 0.7626 (mm-30) REVERT: H 352 MET cc_start: 0.8512 (ptp) cc_final: 0.8246 (ptp) REVERT: H 425 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7884 (mm-30) REVERT: I 259 ASP cc_start: 0.7488 (p0) cc_final: 0.7172 (p0) REVERT: I 306 MET cc_start: 0.8520 (ttp) cc_final: 0.8081 (ttt) REVERT: I 329 ASN cc_start: 0.8225 (m-40) cc_final: 0.7989 (m-40) REVERT: I 376 ASN cc_start: 0.7680 (t0) cc_final: 0.7475 (t0) REVERT: I 421 GLU cc_start: 0.8223 (pp20) cc_final: 0.7917 (tm-30) REVERT: J 229 MET cc_start: 0.6737 (mtt) cc_final: 0.6402 (mtt) REVERT: J 243 SER cc_start: 0.9344 (t) cc_final: 0.9087 (p) REVERT: J 269 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8104 (tm-30) REVERT: J 357 ASP cc_start: 0.8601 (p0) cc_final: 0.8153 (p0) REVERT: J 367 MET cc_start: 0.8156 (mmp) cc_final: 0.7513 (mmm) REVERT: K 189 GLU cc_start: 0.7519 (pm20) cc_final: 0.7264 (pm20) REVERT: K 319 ASN cc_start: 0.8125 (m110) cc_final: 0.7430 (m-40) REVERT: K 320 ARG cc_start: 0.6900 (tmm160) cc_final: 0.6539 (ttp80) REVERT: K 389 GLU cc_start: 0.8448 (pp20) cc_final: 0.8159 (pp20) REVERT: L 191 ARG cc_start: 0.6951 (ptm-80) cc_final: 0.6616 (tmm160) REVERT: L 194 ARG cc_start: 0.8298 (mmt90) cc_final: 0.8020 (mmt90) REVERT: L 271 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8553 (ttmt) REVERT: L 307 GLU cc_start: 0.8126 (tp30) cc_final: 0.7687 (tm-30) REVERT: L 322 LYS cc_start: 0.7989 (mmmt) cc_final: 0.7784 (mmmt) REVERT: M 180 TYR cc_start: 0.7210 (t80) cc_final: 0.6995 (t80) REVERT: M 221 TYR cc_start: 0.7835 (p90) cc_final: 0.7009 (p90) REVERT: M 265 ASP cc_start: 0.8576 (t0) cc_final: 0.7993 (t0) REVERT: M 307 GLU cc_start: 0.8109 (tt0) cc_final: 0.7743 (tp30) REVERT: M 400 MET cc_start: 0.7370 (mmm) cc_final: 0.7120 (mmm) outliers start: 1 outliers final: 0 residues processed: 469 average time/residue: 0.1792 time to fit residues: 132.1084 Evaluate side-chains 352 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 200 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 173 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN B 190 HIS ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 ASN ** F 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 311 ASN J 295 ASN K 285 GLN L 208 GLN L 364 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.081880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.070651 restraints weight = 69095.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.072086 restraints weight = 42547.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.073028 restraints weight = 29619.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.073720 restraints weight = 22681.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.074150 restraints weight = 18606.592| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25059 Z= 0.111 Angle : 0.638 10.998 34025 Z= 0.315 Chirality : 0.044 0.173 3977 Planarity : 0.004 0.052 4395 Dihedral : 7.513 74.460 3716 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.15), residues: 3260 helix: -0.48 (0.15), residues: 1286 sheet: -1.30 (0.23), residues: 507 loop : -1.52 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 296 TYR 0.020 0.001 TYR F 171 PHE 0.020 0.001 PHE M 279 TRP 0.044 0.002 TRP M 376 HIS 0.009 0.001 HIS F 110 Details of bonding type rmsd covalent geometry : bond 0.00253 (25059) covalent geometry : angle 0.63763 (34025) hydrogen bonds : bond 0.02914 ( 807) hydrogen bonds : angle 4.48394 ( 2271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3828.09 seconds wall clock time: 67 minutes 10.83 seconds (4030.83 seconds total)