Starting phenix.real_space_refine on Wed Nov 19 14:19:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ef0_9042/11_2025/6ef0_9042.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ef0_9042/11_2025/6ef0_9042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ef0_9042/11_2025/6ef0_9042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ef0_9042/11_2025/6ef0_9042.map" model { file = "/net/cci-nas-00/data/ceres_data/6ef0_9042/11_2025/6ef0_9042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ef0_9042/11_2025/6ef0_9042.cif" } resolution = 4.43 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 88 5.16 5 C 15565 2.51 5 N 4292 2.21 5 O 4788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 24748 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1864 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1859 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 12, 'TRANS': 237} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 1834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1834 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 238} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1856 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 231} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1885 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 244} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1783 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 227} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1868 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 236} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1831 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 243} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 12, 'PHE:plan': 3, 'ASP:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 122 Chain: "I" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1913 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 11, 'TRANS': 259} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 7, 'TYR:plan': 2, 'ARG:plan': 9, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 108 Chain: "J" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2005 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 258} Chain breaks: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'HIS:plan': 1, 'PHE:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "K" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2016 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 259} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 4, 'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 78 Chain: "L" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2057 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 257} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 4, 'ASP:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 55 Chain: "M" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1737 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 9, 'TRANS': 248} Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 11, 'PHE:plan': 4, 'TYR:plan': 2, 'ARG:plan': 6, 'GLN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 175 Chain: "s" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 66 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.67, per 1000 atoms: 0.23 Number of scatterers: 24748 At special positions: 0 Unit cell: (136.99, 139.05, 129.78, 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 88 16.00 P 15 15.00 O 4788 8.00 N 4292 7.00 C 15565 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6118 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 23 sheets defined 39.6% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 removed outlier: 4.125A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 109 removed outlier: 4.125A pdb=" N ASN A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.535A pdb=" N LEU A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 128 removed outlier: 3.526A pdb=" N ILE A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.545A pdb=" N LYS A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 215 removed outlier: 3.653A pdb=" N GLU A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.557A pdb=" N ILE A 241 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 243 " --> pdb=" O ASN A 240 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 244 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 removed outlier: 3.881A pdb=" N THR B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 27 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 96 removed outlier: 4.111A pdb=" N ASP B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 88 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 109 through 120 removed outlier: 3.731A pdb=" N MET B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 4.202A pdb=" N GLU B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 178 " --> pdb=" O PHE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 198 removed outlier: 4.255A pdb=" N HIS B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'C' and resid 20 through 29 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 81 through 84 removed outlier: 3.674A pdb=" N ALA C 84 " --> pdb=" O THR C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 81 through 84' Processing helix chain 'C' and resid 86 through 103 removed outlier: 4.195A pdb=" N ILE C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS C 94 " --> pdb=" O THR C 90 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 123 removed outlier: 5.052A pdb=" N ASP C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE C 118 " --> pdb=" O ARG C 114 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 177 removed outlier: 3.774A pdb=" N THR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 198 Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 231 through 242 removed outlier: 4.118A pdb=" N ILE C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 27 removed outlier: 3.780A pdb=" N GLU D 21 " --> pdb=" O ILE D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 81 through 100 removed outlier: 3.843A pdb=" N LEU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG D 90 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 removed outlier: 3.700A pdb=" N TYR D 112 " --> pdb=" O TYR D 108 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLN D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 179 removed outlier: 3.523A pdb=" N LYS D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 200 removed outlier: 3.713A pdb=" N LEU D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 203 No H-bonds generated for 'chain 'D' and resid 201 through 203' Processing helix chain 'D' and resid 216 through 220 removed outlier: 3.509A pdb=" N ASP D 220 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 239 removed outlier: 3.690A pdb=" N TYR D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN D 235 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 30 removed outlier: 4.359A pdb=" N GLU E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA E 30 " --> pdb=" O TYR E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 103 removed outlier: 4.419A pdb=" N THR E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 95 " --> pdb=" O HIS E 91 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 118 removed outlier: 4.104A pdb=" N GLN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 122 removed outlier: 3.603A pdb=" N ARG E 122 " --> pdb=" O LEU E 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 119 through 122' Processing helix chain 'E' and resid 176 through 185 removed outlier: 3.639A pdb=" N ALA E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLU E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 208 removed outlier: 3.928A pdb=" N LEU E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS E 202 " --> pdb=" O LEU E 198 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE E 203 " --> pdb=" O LEU E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 232 through 240 Processing helix chain 'E' and resid 241 through 248 removed outlier: 3.567A pdb=" N LYS E 244 " --> pdb=" O LYS E 241 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU E 245 " --> pdb=" O GLU E 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 32 removed outlier: 3.684A pdb=" N GLU F 23 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA F 28 " --> pdb=" O TYR F 24 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 95 removed outlier: 3.573A pdb=" N ARG F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN F 91 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS F 92 " --> pdb=" O LEU F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 119 removed outlier: 3.574A pdb=" N GLY F 109 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASP F 114 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 175 Processing helix chain 'F' and resid 185 through 196 removed outlier: 4.045A pdb=" N LEU F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE F 190 " --> pdb=" O PRO F 186 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.356A pdb=" N ALA F 229 " --> pdb=" O ASP F 226 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS F 232 " --> pdb=" O ALA F 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 33 Processing helix chain 'G' and resid 82 through 104 removed outlier: 3.688A pdb=" N LEU G 88 " --> pdb=" O ASP G 84 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA G 97 " --> pdb=" O ARG G 93 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 120 removed outlier: 4.582A pdb=" N GLN G 118 " --> pdb=" O ASP G 114 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 124 Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 168 through 181 removed outlier: 3.575A pdb=" N ALA G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU G 175 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 204 removed outlier: 3.833A pdb=" N ALA G 192 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE G 199 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE G 200 " --> pdb=" O ALA G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 208 removed outlier: 4.135A pdb=" N LYS G 208 " --> pdb=" O GLU G 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 221 through 225 Processing helix chain 'G' and resid 233 through 246 removed outlier: 3.629A pdb=" N GLN G 237 " --> pdb=" O GLY G 233 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP G 241 " --> pdb=" O GLN G 237 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE G 242 " --> pdb=" O GLU G 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 221 removed outlier: 4.390A pdb=" N GLU H 219 " --> pdb=" O LYS H 215 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS H 220 " --> pdb=" O ASP H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 237 removed outlier: 4.513A pdb=" N THR H 237 " --> pdb=" O GLU H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 removed outlier: 4.054A pdb=" N ALA H 260 " --> pdb=" O LYS H 256 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL H 263 " --> pdb=" O CYS H 259 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 269 Processing helix chain 'H' and resid 275 through 280 removed outlier: 4.069A pdb=" N LEU H 279 " --> pdb=" O ILE H 275 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL H 280 " --> pdb=" O GLY H 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 275 through 280' Processing helix chain 'H' and resid 286 through 299 Processing helix chain 'H' and resid 311 through 316 Processing helix chain 'H' and resid 318 through 322 removed outlier: 4.022A pdb=" N ASP H 321 " --> pdb=" O ARG H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 341 removed outlier: 4.401A pdb=" N ASP H 341 " --> pdb=" O ILE H 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 387 Processing helix chain 'H' and resid 405 through 410 Processing helix chain 'H' and resid 418 through 427 Processing helix chain 'H' and resid 428 through 434 Processing helix chain 'H' and resid 440 through 451 removed outlier: 3.509A pdb=" N LEU H 444 " --> pdb=" O GLU H 440 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS H 449 " --> pdb=" O LYS H 445 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 450 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE H 451 " --> pdb=" O VAL H 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 198 removed outlier: 3.974A pdb=" N ILE I 194 " --> pdb=" O GLN I 190 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS I 195 " --> pdb=" O ILE I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 204 Processing helix chain 'I' and resid 205 through 212 removed outlier: 3.700A pdb=" N GLU I 209 " --> pdb=" O PRO I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 240 removed outlier: 3.637A pdb=" N ALA I 237 " --> pdb=" O ALA I 233 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ASN I 238 " --> pdb=" O LYS I 234 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN I 239 " --> pdb=" O ALA I 235 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 253 removed outlier: 3.710A pdb=" N ILE I 253 " --> pdb=" O SER I 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 250 through 253' Processing helix chain 'I' and resid 260 through 274 removed outlier: 3.980A pdb=" N CYS I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG I 265 " --> pdb=" O PRO I 261 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE I 268 " --> pdb=" O CYS I 264 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS I 269 " --> pdb=" O ARG I 265 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL I 270 " --> pdb=" O GLN I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 Processing helix chain 'I' and resid 298 through 316 removed outlier: 3.542A pdb=" N ILE I 302 " --> pdb=" O GLY I 298 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU I 308 " --> pdb=" O ARG I 304 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU I 309 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP I 314 " --> pdb=" O LEU I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 360 removed outlier: 3.509A pdb=" N LYS I 360 " --> pdb=" O SER I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 367 Processing helix chain 'I' and resid 376 through 380 Processing helix chain 'I' and resid 391 through 405 removed outlier: 4.248A pdb=" N GLY I 400 " --> pdb=" O CYS I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 412 through 427 removed outlier: 3.901A pdb=" N PHE I 416 " --> pdb=" O THR I 412 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN I 426 " --> pdb=" O ARG I 422 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 139 removed outlier: 3.969A pdb=" N LEU J 136 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET J 138 " --> pdb=" O SER J 135 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL J 139 " --> pdb=" O LEU J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 161 Processing helix chain 'J' and resid 161 through 166 removed outlier: 4.117A pdb=" N LEU J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 205 removed outlier: 4.339A pdb=" N ALA J 203 " --> pdb=" O ALA J 199 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS J 204 " --> pdb=" O ARG J 200 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS J 205 " --> pdb=" O ALA J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 241 removed outlier: 4.249A pdb=" N SER J 227 " --> pdb=" O ILE J 223 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE J 234 " --> pdb=" O VAL J 230 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL J 235 " --> pdb=" O ARG J 231 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA J 237 " --> pdb=" O LEU J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 276 removed outlier: 3.541A pdb=" N MET J 272 " --> pdb=" O VAL J 268 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU J 274 " --> pdb=" O ARG J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 306 removed outlier: 4.532A pdb=" N LEU J 305 " --> pdb=" O ASP J 301 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG J 306 " --> pdb=" O PRO J 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 301 through 306' Processing helix chain 'J' and resid 320 through 331 removed outlier: 3.569A pdb=" N ALA J 325 " --> pdb=" O VAL J 321 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU J 326 " --> pdb=" O ALA J 322 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N HIS J 331 " --> pdb=" O ILE J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 344 through 350 Processing helix chain 'J' and resid 357 through 371 removed outlier: 3.707A pdb=" N ALA J 365 " --> pdb=" O VAL J 361 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY J 366 " --> pdb=" O CYS J 362 " (cutoff:3.500A) Processing helix chain 'J' and resid 378 through 391 removed outlier: 4.215A pdb=" N PHE J 382 " --> pdb=" O THR J 378 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY J 387 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL J 389 " --> pdb=" O ALA J 385 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET J 390 " --> pdb=" O VAL J 386 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN J 391 " --> pdb=" O GLY J 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 189 removed outlier: 3.546A pdb=" N ILE K 184 " --> pdb=" O GLN K 180 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ARG K 185 " --> pdb=" O LYS K 181 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA K 187 " --> pdb=" O GLU K 183 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL K 188 " --> pdb=" O ILE K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 194 Processing helix chain 'K' and resid 195 through 200 Processing helix chain 'K' and resid 221 through 229 removed outlier: 4.069A pdb=" N ALA K 225 " --> pdb=" O MET K 221 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL K 226 " --> pdb=" O LEU K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 265 removed outlier: 4.347A pdb=" N ASP K 256 " --> pdb=" O ARG K 252 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL K 257 " --> pdb=" O MET K 253 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE K 258 " --> pdb=" O VAL K 254 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG K 259 " --> pdb=" O ARG K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 274 through 278 removed outlier: 3.657A pdb=" N ALA K 278 " --> pdb=" O ASP K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 305 removed outlier: 3.771A pdb=" N ILE K 295 " --> pdb=" O GLU K 291 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU K 299 " --> pdb=" O ILE K 295 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP K 304 " --> pdb=" O LEU K 300 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 359 removed outlier: 3.723A pdb=" N ARG K 349 " --> pdb=" O ASP K 345 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG K 350 " --> pdb=" O ARG K 346 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU K 351 " --> pdb=" O ARG K 347 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY K 354 " --> pdb=" O ARG K 350 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS K 359 " --> pdb=" O THR K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 381 through 396 removed outlier: 4.004A pdb=" N ALA K 385 " --> pdb=" O ALA K 381 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLY K 391 " --> pdb=" O MET K 387 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU K 392 " --> pdb=" O GLN K 388 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA K 394 " --> pdb=" O ALA K 390 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG K 396 " --> pdb=" O LEU K 392 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 415 removed outlier: 3.946A pdb=" N GLU K 408 " --> pdb=" O GLN K 404 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA K 412 " --> pdb=" O GLU K 408 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR K 413 " --> pdb=" O GLU K 409 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN K 414 " --> pdb=" O ALA K 410 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL K 415 " --> pdb=" O TYR K 411 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 171 removed outlier: 4.574A pdb=" N THR L 171 " --> pdb=" O VAL L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 183 removed outlier: 3.554A pdb=" N GLY L 182 " --> pdb=" O THR L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 211 removed outlier: 3.822A pdb=" N GLN L 208 " --> pdb=" O PRO L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 240 removed outlier: 3.550A pdb=" N VAL L 235 " --> pdb=" O LEU L 231 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ALA L 236 " --> pdb=" O ALA L 232 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA L 237 " --> pdb=" O LYS L 233 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR L 238 " --> pdb=" O ALA L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 272 removed outlier: 3.826A pdb=" N ILE L 262 " --> pdb=" O GLU L 258 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG L 264 " --> pdb=" O ALA L 260 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA L 268 " --> pdb=" O ARG L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 287 Processing helix chain 'L' and resid 298 through 312 removed outlier: 3.802A pdb=" N GLN L 302 " --> pdb=" O ASP L 298 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU L 307 " --> pdb=" O ARG L 303 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU L 308 " --> pdb=" O THR L 304 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET L 312 " --> pdb=" O LEU L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 339 removed outlier: 3.772A pdb=" N LEU L 338 " --> pdb=" O ASP L 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 366 removed outlier: 4.356A pdb=" N ILE L 360 " --> pdb=" O GLY L 356 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE L 361 " --> pdb=" O ARG L 357 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS L 364 " --> pdb=" O ILE L 360 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR L 365 " --> pdb=" O PHE L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 385 removed outlier: 4.204A pdb=" N ASP L 384 " --> pdb=" O LYS L 381 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY L 385 " --> pdb=" O MET L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 389 through 403 removed outlier: 4.449A pdb=" N ASN L 393 " --> pdb=" O ALA L 389 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY L 399 " --> pdb=" O ALA L 395 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE L 403 " --> pdb=" O GLY L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 428 removed outlier: 3.558A pdb=" N ALA L 418 " --> pdb=" O ASP L 414 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA L 423 " --> pdb=" O VAL L 419 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU L 424 " --> pdb=" O ARG L 420 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL L 425 " --> pdb=" O LYS L 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 194 removed outlier: 3.588A pdb=" N ILE M 190 " --> pdb=" O LEU M 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 202 removed outlier: 4.624A pdb=" N LEU M 199 " --> pdb=" O GLU M 195 " (cutoff:3.500A) Proline residue: M 200 - end of helix Processing helix chain 'M' and resid 206 through 211 Processing helix chain 'M' and resid 227 through 236 removed outlier: 3.588A pdb=" N ALA M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 251 Processing helix chain 'M' and resid 257 through 271 removed outlier: 3.746A pdb=" N ARG M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE M 267 " --> pdb=" O VAL M 263 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA M 268 " --> pdb=" O ARG M 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 311 removed outlier: 3.510A pdb=" N ARG M 303 " --> pdb=" O ARG M 299 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU M 306 " --> pdb=" O GLN M 302 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU M 307 " --> pdb=" O ARG M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 364 removed outlier: 3.619A pdb=" N ALA M 358 " --> pdb=" O GLU M 354 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLN M 359 " --> pdb=" O ASP M 355 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE M 360 " --> pdb=" O SER M 356 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE M 363 " --> pdb=" O GLN M 359 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 380 Processing helix chain 'M' and resid 387 through 404 removed outlier: 3.765A pdb=" N LYS M 392 " --> pdb=" O GLY M 388 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA M 393 " --> pdb=" O ALA M 389 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL M 394 " --> pdb=" O GLN M 390 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR M 395 " --> pdb=" O LEU M 391 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL M 396 " --> pdb=" O LYS M 392 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLU M 397 " --> pdb=" O ALA M 393 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET M 400 " --> pdb=" O VAL M 396 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA M 402 " --> pdb=" O ALA M 398 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU M 403 " --> pdb=" O GLY M 399 " (cutoff:3.500A) Processing helix chain 'M' and resid 415 through 420 removed outlier: 4.251A pdb=" N SER M 420 " --> pdb=" O VAL M 416 " (cutoff:3.500A) Processing helix chain 'M' and resid 421 through 423 No H-bonds generated for 'chain 'M' and resid 421 through 423' Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.535A pdb=" N LEU A 43 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 52 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.711A pdb=" N TYR A 155 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A 154 " --> pdb=" O TYR A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.711A pdb=" N PHE A 234 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.525A pdb=" N VAL B 44 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 47 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 210 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 213 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 236 " --> pdb=" O ILE B 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.745A pdb=" N LEU B 67 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 163 through 164 removed outlier: 3.947A pdb=" N ILE C 38 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 45 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU C 46 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA C 214 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 74 through 75 removed outlier: 4.093A pdb=" N GLY C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA9, first strand: chain 'C' and resid 149 through 150 Processing sheet with id=AB1, first strand: chain 'D' and resid 161 through 164 removed outlier: 3.549A pdb=" N GLN D 162 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 164 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 44 " --> pdb=" O THR D 213 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR D 213 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL D 222 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 72 through 74 removed outlier: 3.648A pdb=" N ALA D 136 " --> pdb=" O VAL D 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 169 through 171 removed outlier: 3.605A pdb=" N GLY E 39 " --> pdb=" O LYS E 170 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL E 47 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL E 46 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN E 218 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS E 229 " --> pdb=" O CYS E 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.785A pdb=" N LEU E 143 " --> pdb=" O ALA E 77 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 35 through 39 removed outlier: 3.739A pdb=" N LEU F 38 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA F 214 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 48 " --> pdb=" O SER F 212 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR F 223 " --> pdb=" O ILE F 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 63 through 67 removed outlier: 3.937A pdb=" N CYS F 66 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY F 71 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU F 133 " --> pdb=" O SER F 73 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY F 136 " --> pdb=" O HIS F 143 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS F 143 " --> pdb=" O GLY F 136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR F 154 " --> pdb=" O GLU F 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 37 through 41 removed outlier: 3.520A pdb=" N ILE G 38 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA G 49 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL G 50 " --> pdb=" O GLU G 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 37 through 41 removed outlier: 3.520A pdb=" N ILE G 38 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA G 49 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS G 219 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.589A pdb=" N GLN G 68 " --> pdb=" O CYS G 76 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS G 76 " --> pdb=" O GLN G 68 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY G 75 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE G 137 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AC2, first strand: chain 'H' and resid 246 through 248 removed outlier: 7.120A pdb=" N LEU H 247 " --> pdb=" O VAL H 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'I' and resid 246 through 248 removed outlier: 3.844A pdb=" N ASP I 282 " --> pdb=" O ILE I 247 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 291 through 293 removed outlier: 3.693A pdb=" N ILE J 314 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR J 188 " --> pdb=" O ILE J 314 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 218 through 219 removed outlier: 6.884A pdb=" N VAL L 218 " --> pdb=" O MET L 325 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 1935 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: 3.68 Time building geometry restraints manager: 3.02 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: 8160 1.34 - 1.45: 4299 1.45 - 1.57: 12509 1.57 - 1.69: 26 1.69 - 1.81: 147 Bond restraints: 25141 Sorted by residual: bond pdb=" C4 ATP I 501 " pdb=" C5 ATP I 501 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C4 ATP J 501 " pdb=" C5 ATP J 501 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.72e+01 bond pdb=" C4 ATP K 501 " pdb=" C5 ATP K 501 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.59e+01 bond pdb=" C5 ATP K 501 " pdb=" C6 ATP K 501 " ideal model delta sigma weight residual 1.409 1.466 -0.057 1.00e-02 1.00e+04 3.29e+01 bond pdb=" C5 ATP I 501 " pdb=" N7 ATP I 501 " ideal model delta sigma weight residual 1.387 1.331 0.056 1.00e-02 1.00e+04 3.12e+01 ... (remaining 25136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.75: 33932 4.75 - 9.51: 173 9.51 - 14.26: 1 14.26 - 19.01: 1 19.01 - 23.76: 5 Bond angle restraints: 34112 Sorted by residual: angle pdb=" PB ATP J 501 " pdb=" O3B ATP J 501 " pdb=" PG ATP J 501 " ideal model delta sigma weight residual 139.87 116.11 23.76 1.00e+00 1.00e+00 5.65e+02 angle pdb=" PB ATP K 501 " pdb=" O3B ATP K 501 " pdb=" PG ATP K 501 " ideal model delta sigma weight residual 139.87 118.79 21.08 1.00e+00 1.00e+00 4.44e+02 angle pdb=" PB ATP I 501 " pdb=" O3B ATP I 501 " pdb=" PG ATP I 501 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PA ATP I 501 " pdb=" O3A ATP I 501 " pdb=" PB ATP I 501 " ideal model delta sigma weight residual 136.83 117.43 19.40 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PA ATP J 501 " pdb=" O3A ATP J 501 " pdb=" PB ATP J 501 " ideal model delta sigma weight residual 136.83 117.48 19.35 1.00e+00 1.00e+00 3.74e+02 ... (remaining 34107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 15139 35.73 - 71.45: 153 71.45 - 107.18: 11 107.18 - 142.90: 2 142.90 - 178.63: 2 Dihedral angle restraints: 15307 sinusoidal: 5786 harmonic: 9521 Sorted by residual: dihedral pdb=" C5' ADP L 501 " pdb=" O5' ADP L 501 " pdb=" PA ADP L 501 " pdb=" O2A ADP L 501 " ideal model delta sinusoidal sigma weight residual 300.00 121.38 178.63 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP L 501 " pdb=" O3A ADP L 501 " pdb=" PA ADP L 501 " pdb=" PB ADP L 501 " ideal model delta sinusoidal sigma weight residual -60.00 115.03 -175.03 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CA ILE I 361 " pdb=" C ILE I 361 " pdb=" N LEU I 362 " pdb=" CA LEU I 362 " ideal model delta harmonic sigma weight residual -180.00 -145.56 -34.44 0 5.00e+00 4.00e-02 4.75e+01 ... (remaining 15304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3389 0.081 - 0.161: 556 0.161 - 0.242: 30 0.242 - 0.322: 0 0.322 - 0.403: 1 Chirality restraints: 3976 Sorted by residual: chirality pdb=" CB ILE H 431 " pdb=" CA ILE H 431 " pdb=" CG1 ILE H 431 " pdb=" CG2 ILE H 431 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CB VAL D 116 " pdb=" CA VAL D 116 " pdb=" CG1 VAL D 116 " pdb=" CG2 VAL D 116 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL C 75 " pdb=" CA VAL C 75 " pdb=" CG1 VAL C 75 " pdb=" CG2 VAL C 75 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 3973 not shown) Planarity restraints: 4421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU J 173 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C LEU J 173 " -0.061 2.00e-02 2.50e+03 pdb=" O LEU J 173 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE J 174 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP H 362 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO H 363 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 363 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 363 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 130 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO G 131 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO G 131 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 131 " -0.032 5.00e-02 4.00e+02 ... (remaining 4418 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 735 2.65 - 3.21: 27179 3.21 - 3.78: 37074 3.78 - 4.34: 50102 4.34 - 4.90: 76401 Nonbonded interactions: 191491 Sorted by model distance: nonbonded pdb=" OG1 THR K 220 " pdb=" O3B ATP K 501 " model vdw 2.089 3.040 nonbonded pdb=" OG1 THR I 230 " pdb=" O1B ATP I 501 " model vdw 2.099 3.040 nonbonded pdb=" OG1 THR M 370 " pdb=" O VAL M 410 " model vdw 2.147 3.040 nonbonded pdb=" O ALA H 430 " pdb=" N ARG H 435 " model vdw 2.172 3.120 nonbonded pdb=" O GLN F 166 " pdb=" OG1 THR F 170 " model vdw 2.184 3.040 ... (remaining 191486 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: 4.290 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.710 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 0.117 25141 Z= 0.486 Angle : 1.074 23.763 34112 Z= 0.630 Chirality : 0.057 0.403 3976 Planarity : 0.006 0.060 4421 Dihedral : 13.016 178.628 9189 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.76 % Favored : 83.24 % Rotamer: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.06 % 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: -5.24 (0.12), residues: 3288 helix: -3.88 (0.10), residues: 979 sheet: -4.35 (0.18), residues: 363 loop : -3.19 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG D 97 TYR 0.027 0.003 TYR A 162 PHE 0.032 0.003 PHE D 11 TRP 0.023 0.003 TRP B 159 HIS 0.018 0.003 HIS L 273 Details of bonding type rmsd covalent geometry : bond 0.01074 (25141) covalent geometry : angle 1.07384 (34112) hydrogen bonds : bond 0.32858 ( 698) hydrogen bonds : angle 11.32578 ( 1935) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 641 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.7442 (m-10) cc_final: 0.7174 (m-10) REVERT: A 49 ASP cc_start: 0.8616 (t70) cc_final: 0.8163 (t0) REVERT: A 89 ASP cc_start: 0.8463 (p0) cc_final: 0.7453 (t0) REVERT: A 106 TYR cc_start: 0.7791 (t80) cc_final: 0.6624 (m-10) REVERT: B 97 TYR cc_start: 0.6933 (t80) cc_final: 0.6508 (t80) REVERT: B 99 ARG cc_start: 0.8282 (mtt90) cc_final: 0.7897 (mtt90) REVERT: B 111 VAL cc_start: 0.9021 (p) cc_final: 0.8761 (t) REVERT: B 241 GLN cc_start: 0.7637 (pm20) cc_final: 0.7279 (pm20) REVERT: C 1 MET cc_start: 0.5345 (ptm) cc_final: 0.4811 (ptt) REVERT: C 27 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7874 (tm-30) REVERT: C 129 ARG cc_start: 0.8664 (ptt-90) cc_final: 0.8446 (ptt90) REVERT: C 213 PHE cc_start: 0.8274 (p90) cc_final: 0.7761 (p90) REVERT: C 235 ILE cc_start: 0.8816 (mt) cc_final: 0.8563 (mt) REVERT: D 149 GLN cc_start: 0.7091 (tm130) cc_final: 0.6544 (tm-30) REVERT: E 90 GLU cc_start: 0.8517 (tt0) cc_final: 0.7850 (tp30) REVERT: E 182 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7581 (tm-30) REVERT: F 24 TYR cc_start: 0.8846 (m-80) cc_final: 0.8412 (m-80) REVERT: F 173 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8185 (mt-10) REVERT: G 86 ARG cc_start: 0.7723 (tpp-160) cc_final: 0.7322 (tpt170) REVERT: G 132 PHE cc_start: 0.7681 (m-10) cc_final: 0.7475 (m-10) REVERT: G 212 PHE cc_start: 0.8622 (p90) cc_final: 0.8216 (p90) REVERT: G 225 ASN cc_start: 0.7292 (t0) cc_final: 0.7089 (t0) REVERT: G 242 PHE cc_start: 0.7279 (t80) cc_final: 0.6937 (t80) REVERT: H 376 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6605 (tm-30) REVERT: H 392 HIS cc_start: 0.8050 (m-70) cc_final: 0.7539 (m90) REVERT: I 222 TYR cc_start: 0.6680 (m-80) cc_final: 0.6414 (m-80) REVERT: I 306 MET cc_start: 0.8760 (tmm) cc_final: 0.8513 (tmm) REVERT: I 348 ILE cc_start: 0.8812 (mp) cc_final: 0.8521 (mp) REVERT: I 398 GLU cc_start: 0.8492 (tp30) cc_final: 0.8260 (tp30) REVERT: J 137 MET cc_start: 0.8779 (pmm) cc_final: 0.8492 (pmm) REVERT: J 156 GLN cc_start: 0.8940 (mp10) cc_final: 0.8275 (mp10) REVERT: J 227 SER cc_start: 0.9206 (m) cc_final: 0.8697 (t) REVERT: J 247 MET cc_start: 0.8762 (mtt) cc_final: 0.8276 (mtt) REVERT: J 292 MET cc_start: 0.8458 (ttm) cc_final: 0.8223 (mtm) REVERT: J 327 ILE cc_start: 0.9415 (mm) cc_final: 0.9185 (mm) REVERT: J 368 TYR cc_start: 0.7698 (t80) cc_final: 0.6931 (t80) REVERT: K 164 ASN cc_start: 0.8762 (p0) cc_final: 0.8549 (p0) REVERT: K 196 ASP cc_start: 0.9037 (p0) cc_final: 0.8778 (p0) REVERT: K 238 ASN cc_start: 0.9102 (p0) cc_final: 0.8893 (p0) REVERT: K 289 ASP cc_start: 0.8695 (p0) cc_final: 0.8384 (p0) REVERT: K 322 ASP cc_start: 0.8251 (p0) cc_final: 0.8042 (p0) REVERT: K 346 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.7594 (ppt170) REVERT: L 221 TYR cc_start: 0.8390 (p90) cc_final: 0.8136 (p90) REVERT: L 279 PHE cc_start: 0.8592 (t80) cc_final: 0.7744 (t80) REVERT: L 328 ASN cc_start: 0.8898 (m110) cc_final: 0.8471 (m-40) REVERT: L 359 GLU cc_start: 0.9302 (mp0) cc_final: 0.8994 (mp0) outliers start: 0 outliers final: 0 residues processed: 641 average time/residue: 0.1797 time to fit residues: 172.1492 Evaluate side-chains 422 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN A 181 ASN B 218 ASN C 21 GLN C 103 ASN C 177 GLN D 19 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN F 210 ASN I 418 GLN K 244 HIS L 311 GLN L 328 ASN ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.087079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.074102 restraints weight = 88960.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.075758 restraints weight = 57703.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.076940 restraints weight = 41043.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.077773 restraints weight = 31490.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.078376 restraints weight = 25744.152| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25141 Z= 0.182 Angle : 0.795 7.845 34112 Z= 0.409 Chirality : 0.049 0.176 3976 Planarity : 0.005 0.065 4421 Dihedral : 9.953 155.151 3694 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 0.20 % Allowed : 5.16 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -4.26 (0.13), residues: 3288 helix: -2.63 (0.12), residues: 1143 sheet: -3.43 (0.22), residues: 385 loop : -2.84 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 409 TYR 0.020 0.002 TYR H 249 PHE 0.021 0.002 PHE A 205 TRP 0.011 0.002 TRP G 218 HIS 0.008 0.001 HIS M 364 Details of bonding type rmsd covalent geometry : bond 0.00401 (25141) covalent geometry : angle 0.79454 (34112) hydrogen bonds : bond 0.05426 ( 698) hydrogen bonds : angle 6.92795 ( 1935) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 595 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8496 (t70) cc_final: 0.8189 (t0) REVERT: A 89 ASP cc_start: 0.8307 (p0) cc_final: 0.7702 (t0) REVERT: A 162 TYR cc_start: 0.6912 (p90) cc_final: 0.6632 (p90) REVERT: A 175 GLN cc_start: 0.8191 (pm20) cc_final: 0.7629 (pm20) REVERT: B 75 TYR cc_start: 0.8157 (p90) cc_final: 0.7823 (p90) REVERT: B 99 ARG cc_start: 0.8294 (mtt90) cc_final: 0.8061 (mtt90) REVERT: B 117 ILE cc_start: 0.8978 (mm) cc_final: 0.8636 (mm) REVERT: B 241 GLN cc_start: 0.7751 (pm20) cc_final: 0.7319 (pm20) REVERT: C 1 MET cc_start: 0.5515 (ptm) cc_final: 0.4951 (ptt) REVERT: C 114 ARG cc_start: 0.8835 (tpm170) cc_final: 0.8507 (tpp-160) REVERT: C 120 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8331 (tm-30) REVERT: C 213 PHE cc_start: 0.8314 (p90) cc_final: 0.8029 (p90) REVERT: D 56 ASP cc_start: 0.7526 (t70) cc_final: 0.6880 (m-30) REVERT: D 120 TYR cc_start: 0.8144 (m-80) cc_final: 0.7505 (m-80) REVERT: D 149 GLN cc_start: 0.7412 (tm-30) cc_final: 0.7034 (tm-30) REVERT: D 163 THR cc_start: 0.9485 (p) cc_final: 0.9162 (t) REVERT: E 84 ASP cc_start: 0.8737 (p0) cc_final: 0.8415 (p0) REVERT: E 90 GLU cc_start: 0.8388 (tt0) cc_final: 0.7648 (tp30) REVERT: E 206 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7872 (tm-30) REVERT: F 19 LEU cc_start: 0.8812 (mp) cc_final: 0.8186 (mp) REVERT: F 23 GLU cc_start: 0.8502 (mp0) cc_final: 0.7936 (mp0) REVERT: F 24 TYR cc_start: 0.8810 (m-80) cc_final: 0.8487 (m-10) REVERT: F 144 LEU cc_start: 0.9073 (tp) cc_final: 0.8870 (tp) REVERT: F 145 LEU cc_start: 0.8860 (mt) cc_final: 0.8655 (mt) REVERT: F 147 PHE cc_start: 0.8592 (t80) cc_final: 0.7941 (t80) REVERT: F 228 GLU cc_start: 0.8480 (mp0) cc_final: 0.8241 (mm-30) REVERT: G 18 ASP cc_start: 0.9008 (p0) cc_final: 0.8677 (p0) REVERT: G 53 LEU cc_start: 0.8607 (tt) cc_final: 0.8037 (pp) REVERT: G 212 PHE cc_start: 0.8726 (p90) cc_final: 0.8398 (p90) REVERT: G 225 ASN cc_start: 0.7206 (t0) cc_final: 0.6905 (t0) REVERT: H 392 HIS cc_start: 0.7508 (m-70) cc_final: 0.7059 (m90) REVERT: H 448 ASP cc_start: 0.8791 (t0) cc_final: 0.8554 (t0) REVERT: I 191 ILE cc_start: 0.7630 (pt) cc_final: 0.7346 (tp) REVERT: I 194 ILE cc_start: 0.8317 (mp) cc_final: 0.7610 (mm) REVERT: I 326 MET cc_start: 0.8494 (pmm) cc_final: 0.8249 (pmm) REVERT: I 395 MET cc_start: 0.8854 (tpp) cc_final: 0.8618 (tpp) REVERT: I 417 LYS cc_start: 0.9214 (tttm) cc_final: 0.8917 (tptt) REVERT: J 327 ILE cc_start: 0.9372 (mm) cc_final: 0.9131 (mm) REVERT: J 359 LYS cc_start: 0.9160 (ptmt) cc_final: 0.8797 (tttt) REVERT: J 368 TYR cc_start: 0.7713 (t80) cc_final: 0.7092 (t80) REVERT: K 161 MET cc_start: 0.7451 (ppp) cc_final: 0.7102 (ppp) REVERT: K 179 MET cc_start: 0.8078 (ppp) cc_final: 0.7860 (ppp) REVERT: K 285 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8915 (mm-40) REVERT: K 289 ASP cc_start: 0.8626 (p0) cc_final: 0.8400 (p0) REVERT: K 322 ASP cc_start: 0.7896 (p0) cc_final: 0.7671 (p0) REVERT: K 387 MET cc_start: 0.8896 (mtp) cc_final: 0.8526 (mtp) REVERT: L 167 VAL cc_start: 0.8865 (t) cc_final: 0.8472 (p) REVERT: L 306 MET cc_start: 0.8316 (mtt) cc_final: 0.7829 (mtt) REVERT: L 311 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7685 (mm-40) REVERT: L 328 ASN cc_start: 0.8646 (m-40) cc_final: 0.8245 (m-40) REVERT: M 303 ARG cc_start: 0.8540 (mtt90) cc_final: 0.8110 (mtm-85) REVERT: M 368 MET cc_start: 0.6632 (ptp) cc_final: 0.6255 (ptt) outliers start: 5 outliers final: 3 residues processed: 598 average time/residue: 0.1685 time to fit residues: 154.6928 Evaluate side-chains 453 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 449 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 59 optimal weight: 0.6980 chunk 172 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 chunk 211 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 320 optimal weight: 0.0000 chunk 146 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 chunk 210 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 84 ASN A 209 HIS B 218 ASN D 117 GLN D 204 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN J 269 GLN M 310 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.087632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.074954 restraints weight = 88442.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.076816 restraints weight = 57314.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.078259 restraints weight = 37426.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.078754 restraints weight = 28557.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.079744 restraints weight = 22345.028| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25141 Z= 0.142 Angle : 0.714 8.845 34112 Z= 0.363 Chirality : 0.046 0.170 3976 Planarity : 0.004 0.049 4421 Dihedral : 8.906 127.612 3694 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -3.57 (0.14), residues: 3288 helix: -2.05 (0.13), residues: 1166 sheet: -2.86 (0.22), residues: 422 loop : -2.45 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 169 TYR 0.017 0.001 TYR A 162 PHE 0.021 0.001 PHE A 205 TRP 0.008 0.001 TRP G 218 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00320 (25141) covalent geometry : angle 0.71375 (34112) hydrogen bonds : bond 0.04537 ( 698) hydrogen bonds : angle 6.20524 ( 1935) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 557 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8349 (t70) cc_final: 0.7885 (t0) REVERT: A 89 ASP cc_start: 0.8382 (p0) cc_final: 0.7544 (t0) REVERT: A 175 GLN cc_start: 0.7806 (pm20) cc_final: 0.7591 (pm20) REVERT: B 75 TYR cc_start: 0.8176 (p90) cc_final: 0.7944 (p90) REVERT: B 99 ARG cc_start: 0.8215 (mtt90) cc_final: 0.7979 (mtt90) REVERT: B 117 ILE cc_start: 0.8945 (mm) cc_final: 0.8663 (mm) REVERT: B 119 GLN cc_start: 0.7947 (tp-100) cc_final: 0.7662 (tp-100) REVERT: B 241 GLN cc_start: 0.7715 (pm20) cc_final: 0.7373 (pm20) REVERT: C 1 MET cc_start: 0.5262 (ptm) cc_final: 0.4992 (ptt) REVERT: C 114 ARG cc_start: 0.8876 (tpm170) cc_final: 0.8524 (tpp-160) REVERT: C 120 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8425 (tm-30) REVERT: D 16 HIS cc_start: 0.8567 (m90) cc_final: 0.8242 (m90) REVERT: D 56 ASP cc_start: 0.7486 (t70) cc_final: 0.7071 (m-30) REVERT: D 120 TYR cc_start: 0.8078 (m-80) cc_final: 0.7629 (m-80) REVERT: D 149 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7012 (tm-30) REVERT: D 153 SER cc_start: 0.9147 (p) cc_final: 0.8881 (p) REVERT: E 84 ASP cc_start: 0.8804 (p0) cc_final: 0.8565 (p0) REVERT: E 90 GLU cc_start: 0.8262 (tt0) cc_final: 0.8038 (tt0) REVERT: E 121 LEU cc_start: 0.7520 (mt) cc_final: 0.7228 (tp) REVERT: F 24 TYR cc_start: 0.8844 (m-80) cc_final: 0.8574 (m-10) REVERT: F 147 PHE cc_start: 0.8266 (t80) cc_final: 0.8064 (t80) REVERT: G 18 ASP cc_start: 0.9074 (p0) cc_final: 0.8709 (p0) REVERT: G 53 LEU cc_start: 0.8699 (tt) cc_final: 0.8265 (pp) REVERT: G 84 ASP cc_start: 0.8391 (p0) cc_final: 0.8131 (p0) REVERT: G 86 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7404 (ttm-80) REVERT: G 104 LYS cc_start: 0.3160 (mttt) cc_final: 0.2877 (mttp) REVERT: G 110 PRO cc_start: 0.9165 (Cg_exo) cc_final: 0.8893 (Cg_endo) REVERT: G 206 ASP cc_start: 0.8982 (p0) cc_final: 0.8741 (p0) REVERT: G 212 PHE cc_start: 0.8696 (p90) cc_final: 0.8483 (p90) REVERT: G 225 ASN cc_start: 0.7167 (t0) cc_final: 0.6874 (t0) REVERT: H 387 ASN cc_start: 0.8650 (m-40) cc_final: 0.8431 (m110) REVERT: H 392 HIS cc_start: 0.7300 (m-70) cc_final: 0.6855 (m90) REVERT: H 448 ASP cc_start: 0.8913 (t0) cc_final: 0.8610 (t0) REVERT: I 180 SER cc_start: 0.5031 (t) cc_final: 0.4827 (m) REVERT: I 253 ILE cc_start: 0.8777 (mp) cc_final: 0.8441 (mm) REVERT: I 326 MET cc_start: 0.8341 (pmm) cc_final: 0.8121 (pmm) REVERT: I 395 MET cc_start: 0.8938 (tpp) cc_final: 0.8520 (tpp) REVERT: I 417 LYS cc_start: 0.9152 (tttm) cc_final: 0.8818 (tptt) REVERT: J 240 HIS cc_start: 0.7510 (m90) cc_final: 0.6747 (m90) REVERT: J 327 ILE cc_start: 0.9310 (mm) cc_final: 0.9080 (mm) REVERT: J 359 LYS cc_start: 0.9152 (ptmt) cc_final: 0.8807 (tttt) REVERT: J 368 TYR cc_start: 0.7625 (t80) cc_final: 0.7252 (t80) REVERT: K 161 MET cc_start: 0.7642 (ppp) cc_final: 0.7265 (ppp) REVERT: K 221 MET cc_start: 0.7878 (ppp) cc_final: 0.7572 (ppp) REVERT: K 222 LEU cc_start: 0.8937 (tt) cc_final: 0.8716 (tt) REVERT: K 285 GLN cc_start: 0.9251 (mm-40) cc_final: 0.9033 (mm-40) REVERT: K 292 VAL cc_start: 0.8857 (m) cc_final: 0.8483 (p) REVERT: K 322 ASP cc_start: 0.7964 (p0) cc_final: 0.7685 (p0) REVERT: L 213 LYS cc_start: 0.8801 (tptt) cc_final: 0.8426 (ttmt) REVERT: L 281 ASP cc_start: 0.8273 (p0) cc_final: 0.6458 (p0) REVERT: L 328 ASN cc_start: 0.8554 (m-40) cc_final: 0.8150 (m-40) REVERT: L 359 GLU cc_start: 0.8939 (mp0) cc_final: 0.8685 (mp0) outliers start: 2 outliers final: 0 residues processed: 558 average time/residue: 0.1657 time to fit residues: 143.3425 Evaluate side-chains 434 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 216 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 229 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 309 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 84 ASN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS M 390 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.081206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.067683 restraints weight = 88957.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.069331 restraints weight = 57402.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.070506 restraints weight = 40879.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.071333 restraints weight = 31514.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.071928 restraints weight = 25826.739| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 25141 Z= 0.287 Angle : 0.836 9.681 34112 Z= 0.436 Chirality : 0.050 0.199 3976 Planarity : 0.005 0.075 4421 Dihedral : 8.925 100.237 3694 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 0.08 % Allowed : 6.86 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -3.42 (0.14), residues: 3288 helix: -1.99 (0.13), residues: 1195 sheet: -2.46 (0.23), residues: 429 loop : -2.39 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 238 TYR 0.024 0.002 TYR D 232 PHE 0.028 0.002 PHE D 174 TRP 0.013 0.002 TRP B 179 HIS 0.010 0.002 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00644 (25141) covalent geometry : angle 0.83596 (34112) hydrogen bonds : bond 0.04823 ( 698) hydrogen bonds : angle 6.41079 ( 1935) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 504 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8689 (t70) cc_final: 0.8177 (t0) REVERT: A 89 ASP cc_start: 0.8298 (p0) cc_final: 0.7909 (t0) REVERT: B 75 TYR cc_start: 0.8648 (p90) cc_final: 0.8405 (p90) REVERT: B 99 ARG cc_start: 0.8337 (mtt90) cc_final: 0.8033 (mtt90) REVERT: B 103 GLU cc_start: 0.8192 (pm20) cc_final: 0.7937 (pm20) REVERT: B 117 ILE cc_start: 0.8919 (mm) cc_final: 0.8598 (mm) REVERT: B 241 GLN cc_start: 0.7750 (pm20) cc_final: 0.7464 (pm20) REVERT: C 1 MET cc_start: 0.5547 (ptm) cc_final: 0.5185 (ptt) REVERT: C 93 ILE cc_start: 0.8551 (pt) cc_final: 0.8335 (mp) REVERT: C 114 ARG cc_start: 0.9039 (tpm170) cc_final: 0.8805 (tpp-160) REVERT: C 173 GLN cc_start: 0.9246 (mm-40) cc_final: 0.9044 (mm-40) REVERT: C 212 GLU cc_start: 0.8055 (pm20) cc_final: 0.7842 (pm20) REVERT: D 16 HIS cc_start: 0.8697 (m90) cc_final: 0.7997 (m90) REVERT: D 56 ASP cc_start: 0.8031 (t70) cc_final: 0.7386 (m-30) REVERT: E 84 ASP cc_start: 0.8717 (p0) cc_final: 0.8406 (p0) REVERT: E 121 LEU cc_start: 0.7760 (mt) cc_final: 0.7447 (tp) REVERT: F 19 LEU cc_start: 0.8900 (mp) cc_final: 0.8572 (mp) REVERT: F 147 PHE cc_start: 0.8357 (t80) cc_final: 0.8144 (t80) REVERT: F 228 GLU cc_start: 0.8385 (mp0) cc_final: 0.8172 (mm-30) REVERT: G 9 ASP cc_start: 0.7250 (p0) cc_final: 0.6930 (p0) REVERT: G 18 ASP cc_start: 0.9073 (p0) cc_final: 0.8811 (p0) REVERT: G 53 LEU cc_start: 0.8559 (tt) cc_final: 0.8239 (pp) REVERT: G 86 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7738 (ttm-80) REVERT: G 104 LYS cc_start: 0.2945 (mttt) cc_final: 0.2651 (mttt) REVERT: G 110 PRO cc_start: 0.9263 (Cg_exo) cc_final: 0.9002 (Cg_endo) REVERT: G 150 MET cc_start: 0.7990 (ttm) cc_final: 0.7399 (tpp) REVERT: G 206 ASP cc_start: 0.9013 (p0) cc_final: 0.8784 (p0) REVERT: G 212 PHE cc_start: 0.9059 (p90) cc_final: 0.8588 (p90) REVERT: G 225 ASN cc_start: 0.7476 (t0) cc_final: 0.7235 (t0) REVERT: G 237 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8698 (tp40) REVERT: I 194 ILE cc_start: 0.8397 (mm) cc_final: 0.7658 (mm) REVERT: I 326 MET cc_start: 0.8447 (pmm) cc_final: 0.7950 (mpp) REVERT: I 343 ARG cc_start: 0.7365 (mtt90) cc_final: 0.7141 (mtt90) REVERT: I 395 MET cc_start: 0.8754 (tpp) cc_final: 0.8305 (tpp) REVERT: J 249 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7538 (mm-30) REVERT: J 269 GLN cc_start: 0.9234 (tt0) cc_final: 0.8504 (tm-30) REVERT: J 327 ILE cc_start: 0.9359 (mm) cc_final: 0.9147 (mm) REVERT: K 161 MET cc_start: 0.8121 (ppp) cc_final: 0.7803 (ppp) REVERT: K 253 MET cc_start: 0.8267 (ppp) cc_final: 0.7939 (tmm) REVERT: K 292 VAL cc_start: 0.9255 (m) cc_final: 0.8969 (p) REVERT: L 203 ASN cc_start: 0.8824 (p0) cc_final: 0.8600 (p0) REVERT: L 255 TYR cc_start: 0.8584 (m-10) cc_final: 0.8332 (m-10) REVERT: L 328 ASN cc_start: 0.8741 (m-40) cc_final: 0.8278 (m-40) REVERT: L 349 ILE cc_start: 0.9158 (pt) cc_final: 0.8555 (pt) REVERT: L 359 GLU cc_start: 0.9116 (mp0) cc_final: 0.8805 (mp0) REVERT: M 303 ARG cc_start: 0.8577 (mtt90) cc_final: 0.8219 (ptp-170) REVERT: M 342 ARG cc_start: 0.5636 (ptm-80) cc_final: 0.5436 (ptt180) REVERT: M 397 GLU cc_start: 0.9028 (mp0) cc_final: 0.8629 (mp0) outliers start: 2 outliers final: 0 residues processed: 504 average time/residue: 0.1632 time to fit residues: 127.1500 Evaluate side-chains 419 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 69 optimal weight: 8.9990 chunk 258 optimal weight: 4.9990 chunk 179 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 275 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 84 ASN B 119 GLN B 218 ASN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN I 238 ASN I 254 GLN J 204 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.082010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.068636 restraints weight = 88108.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.070314 restraints weight = 56148.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.071503 restraints weight = 39722.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.072346 restraints weight = 30509.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.072934 restraints weight = 24885.211| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25141 Z= 0.203 Angle : 0.748 10.521 34112 Z= 0.384 Chirality : 0.048 0.259 3976 Planarity : 0.004 0.065 4421 Dihedral : 8.443 97.899 3694 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -3.11 (0.14), residues: 3288 helix: -1.67 (0.14), residues: 1185 sheet: -2.26 (0.23), residues: 433 loop : -2.28 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 169 TYR 0.021 0.002 TYR I 222 PHE 0.024 0.002 PHE D 174 TRP 0.012 0.002 TRP C 160 HIS 0.008 0.001 HIS J 240 Details of bonding type rmsd covalent geometry : bond 0.00464 (25141) covalent geometry : angle 0.74773 (34112) hydrogen bonds : bond 0.04202 ( 698) hydrogen bonds : angle 6.00852 ( 1935) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 499 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8285 (p0) cc_final: 0.7803 (t0) REVERT: A 199 TRP cc_start: 0.8352 (p-90) cc_final: 0.8121 (p-90) REVERT: A 224 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7774 (tm-30) REVERT: B 75 TYR cc_start: 0.8722 (p90) cc_final: 0.8448 (p90) REVERT: B 99 ARG cc_start: 0.8324 (mtt90) cc_final: 0.7991 (mtt90) REVERT: B 103 GLU cc_start: 0.8247 (pm20) cc_final: 0.7999 (pm20) REVERT: C 93 ILE cc_start: 0.8606 (pt) cc_final: 0.8321 (mp) REVERT: C 114 ARG cc_start: 0.9014 (tpm170) cc_final: 0.8687 (tpp-160) REVERT: D 16 HIS cc_start: 0.8760 (m90) cc_final: 0.8016 (m90) REVERT: D 19 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8355 (mm-40) REVERT: D 56 ASP cc_start: 0.8111 (t70) cc_final: 0.7365 (m-30) REVERT: D 120 TYR cc_start: 0.8205 (m-80) cc_final: 0.7595 (m-80) REVERT: E 84 ASP cc_start: 0.8689 (p0) cc_final: 0.8318 (p0) REVERT: E 121 LEU cc_start: 0.7773 (mt) cc_final: 0.7376 (tp) REVERT: G 9 ASP cc_start: 0.7170 (p0) cc_final: 0.6882 (p0) REVERT: G 18 ASP cc_start: 0.9095 (p0) cc_final: 0.8831 (p0) REVERT: G 53 LEU cc_start: 0.8486 (tt) cc_final: 0.8208 (pp) REVERT: G 104 LYS cc_start: 0.2989 (mttt) cc_final: 0.2784 (mttt) REVERT: G 110 PRO cc_start: 0.9269 (Cg_exo) cc_final: 0.9025 (Cg_endo) REVERT: G 150 MET cc_start: 0.7976 (ttm) cc_final: 0.7360 (tpp) REVERT: G 225 ASN cc_start: 0.7521 (t0) cc_final: 0.7270 (t0) REVERT: G 237 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8679 (tp40) REVERT: H 428 MET cc_start: 0.6254 (tpt) cc_final: 0.5550 (ttm) REVERT: I 253 ILE cc_start: 0.9262 (mp) cc_final: 0.8992 (mm) REVERT: I 395 MET cc_start: 0.8417 (tpp) cc_final: 0.8197 (tpp) REVERT: J 249 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7452 (mm-30) REVERT: J 269 GLN cc_start: 0.9223 (tt0) cc_final: 0.8590 (tm-30) REVERT: J 327 ILE cc_start: 0.9368 (mm) cc_final: 0.9138 (mm) REVERT: K 161 MET cc_start: 0.8104 (ppp) cc_final: 0.7735 (ppp) REVERT: K 221 MET cc_start: 0.8253 (ppp) cc_final: 0.8036 (ppp) REVERT: K 222 LEU cc_start: 0.9276 (tt) cc_final: 0.9073 (tp) REVERT: K 253 MET cc_start: 0.7870 (ppp) cc_final: 0.7493 (tmm) REVERT: K 292 VAL cc_start: 0.9205 (m) cc_final: 0.8933 (p) REVERT: L 311 GLN cc_start: 0.8149 (tp40) cc_final: 0.7933 (tp40) REVERT: L 328 ASN cc_start: 0.8706 (m-40) cc_final: 0.8259 (m-40) REVERT: L 359 GLU cc_start: 0.9041 (mp0) cc_final: 0.8750 (mp0) REVERT: M 397 GLU cc_start: 0.9008 (mp0) cc_final: 0.8616 (mp0) outliers start: 1 outliers final: 0 residues processed: 499 average time/residue: 0.1599 time to fit residues: 125.1741 Evaluate side-chains 405 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 291 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 280 optimal weight: 8.9990 chunk 286 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 231 optimal weight: 7.9990 chunk 284 optimal weight: 9.9990 chunk 227 optimal weight: 0.6980 chunk 270 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 268 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 84 ASN C 152 ASN C 177 GLN D 70 HIS F 86 ASN I 410 GLN K 302 GLN M 390 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.079722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.066377 restraints weight = 88577.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.068040 restraints weight = 56328.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.069204 restraints weight = 39798.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.070022 restraints weight = 30534.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.070607 restraints weight = 25005.215| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25141 Z= 0.244 Angle : 0.776 9.162 34112 Z= 0.404 Chirality : 0.049 0.206 3976 Planarity : 0.004 0.052 4421 Dihedral : 8.352 95.028 3694 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.98 (0.14), residues: 3288 helix: -1.57 (0.14), residues: 1199 sheet: -2.15 (0.23), residues: 440 loop : -2.21 (0.16), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 132 TYR 0.014 0.002 TYR D 232 PHE 0.032 0.002 PHE D 174 TRP 0.009 0.002 TRP G 218 HIS 0.009 0.001 HIS J 240 Details of bonding type rmsd covalent geometry : bond 0.00548 (25141) covalent geometry : angle 0.77640 (34112) hydrogen bonds : bond 0.04348 ( 698) hydrogen bonds : angle 6.06478 ( 1935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 476 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8533 (t0) cc_final: 0.8149 (t0) REVERT: A 89 ASP cc_start: 0.8323 (p0) cc_final: 0.7864 (t0) REVERT: A 92 ASN cc_start: 0.8726 (p0) cc_final: 0.8494 (p0) REVERT: A 224 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 4 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7301 (ttp80) REVERT: B 75 TYR cc_start: 0.8829 (p90) cc_final: 0.8526 (p90) REVERT: B 103 GLU cc_start: 0.8322 (pm20) cc_final: 0.8013 (pm20) REVERT: B 108 LYS cc_start: 0.7199 (ttpt) cc_final: 0.6783 (tmtt) REVERT: B 117 ILE cc_start: 0.9020 (mm) cc_final: 0.8804 (mm) REVERT: C 114 ARG cc_start: 0.9016 (tpm170) cc_final: 0.8739 (tpp-160) REVERT: D 16 HIS cc_start: 0.8883 (m90) cc_final: 0.8043 (m90) REVERT: D 120 TYR cc_start: 0.8136 (m-80) cc_final: 0.7371 (m-80) REVERT: D 167 ASN cc_start: 0.9092 (m110) cc_final: 0.8762 (m110) REVERT: E 22 PHE cc_start: 0.7964 (m-80) cc_final: 0.7607 (m-80) REVERT: E 84 ASP cc_start: 0.8718 (p0) cc_final: 0.8406 (p0) REVERT: E 121 LEU cc_start: 0.7987 (mt) cc_final: 0.7562 (tp) REVERT: E 182 GLU cc_start: 0.8492 (pm20) cc_final: 0.8262 (pm20) REVERT: F 60 GLN cc_start: 0.7303 (tp40) cc_final: 0.6996 (tp40) REVERT: G 9 ASP cc_start: 0.7255 (p0) cc_final: 0.7000 (p0) REVERT: G 18 ASP cc_start: 0.9140 (p0) cc_final: 0.8914 (p0) REVERT: G 53 LEU cc_start: 0.8456 (tt) cc_final: 0.8178 (pp) REVERT: G 110 PRO cc_start: 0.9281 (Cg_exo) cc_final: 0.9040 (Cg_endo) REVERT: G 150 MET cc_start: 0.8027 (ttm) cc_final: 0.7513 (tpp) REVERT: G 170 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8453 (mm-40) REVERT: G 212 PHE cc_start: 0.8835 (p90) cc_final: 0.8449 (p90) REVERT: G 225 ASN cc_start: 0.7515 (t0) cc_final: 0.7279 (t0) REVERT: G 237 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8543 (tp40) REVERT: I 351 GLU cc_start: 0.8332 (pm20) cc_final: 0.8132 (pm20) REVERT: J 249 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7441 (mm-30) REVERT: J 311 ASP cc_start: 0.8680 (p0) cc_final: 0.8348 (m-30) REVERT: J 327 ILE cc_start: 0.9370 (mm) cc_final: 0.9006 (tt) REVERT: K 161 MET cc_start: 0.8125 (ppp) cc_final: 0.7921 (ppp) REVERT: K 221 MET cc_start: 0.8358 (ppp) cc_final: 0.8122 (ppp) REVERT: K 235 ILE cc_start: 0.8706 (pt) cc_final: 0.8029 (mm) REVERT: K 253 MET cc_start: 0.8190 (ppp) cc_final: 0.7777 (tmm) REVERT: K 273 GLU cc_start: 0.7340 (tt0) cc_final: 0.6861 (tt0) REVERT: K 292 VAL cc_start: 0.9328 (m) cc_final: 0.9073 (p) REVERT: K 303 MET cc_start: 0.8837 (mtp) cc_final: 0.8571 (tpp) REVERT: L 280 MET cc_start: 0.8143 (mmm) cc_final: 0.7935 (mmm) REVERT: L 328 ASN cc_start: 0.8805 (m-40) cc_final: 0.8413 (m-40) REVERT: L 339 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8208 (ttp80) REVERT: L 359 GLU cc_start: 0.9032 (mp0) cc_final: 0.8772 (mp0) REVERT: M 303 ARG cc_start: 0.8701 (mtt90) cc_final: 0.8142 (ptp-170) REVERT: M 397 GLU cc_start: 0.9048 (mp0) cc_final: 0.8599 (mp0) outliers start: 2 outliers final: 0 residues processed: 476 average time/residue: 0.1626 time to fit residues: 121.8132 Evaluate side-chains 399 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 85 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 228 optimal weight: 0.0770 chunk 223 optimal weight: 0.0470 chunk 104 optimal weight: 5.9990 chunk 260 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 27 GLN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN B 119 GLN B 139 HIS C 173 GLN D 178 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN M 390 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.070466 restraints weight = 87015.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.072195 restraints weight = 55022.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.073308 restraints weight = 38750.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074220 restraints weight = 29887.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.074845 restraints weight = 24352.811| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25141 Z= 0.124 Angle : 0.710 10.218 34112 Z= 0.355 Chirality : 0.046 0.178 3976 Planarity : 0.004 0.070 4421 Dihedral : 7.773 85.467 3694 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.68 (0.14), residues: 3288 helix: -1.34 (0.14), residues: 1205 sheet: -2.08 (0.23), residues: 443 loop : -1.98 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 48 TYR 0.019 0.001 TYR D 108 PHE 0.026 0.002 PHE D 174 TRP 0.017 0.002 TRP H 404 HIS 0.007 0.001 HIS J 240 Details of bonding type rmsd covalent geometry : bond 0.00277 (25141) covalent geometry : angle 0.71034 (34112) hydrogen bonds : bond 0.03656 ( 698) hydrogen bonds : angle 5.59954 ( 1935) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 512 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8397 (p0) cc_final: 0.7749 (t0) REVERT: A 92 ASN cc_start: 0.8364 (p0) cc_final: 0.8110 (t0) REVERT: A 175 GLN cc_start: 0.7416 (pm20) cc_final: 0.7009 (pm20) REVERT: B 4 ARG cc_start: 0.7660 (ttp80) cc_final: 0.6902 (ttp80) REVERT: B 103 GLU cc_start: 0.8242 (pm20) cc_final: 0.7960 (pm20) REVERT: B 117 ILE cc_start: 0.9023 (mm) cc_final: 0.8818 (mm) REVERT: C 114 ARG cc_start: 0.8942 (tpm170) cc_final: 0.8591 (tpp-160) REVERT: C 212 GLU cc_start: 0.8075 (pm20) cc_final: 0.7490 (pm20) REVERT: D 16 HIS cc_start: 0.8819 (m90) cc_final: 0.8128 (m90) REVERT: D 19 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8631 (mm110) REVERT: D 120 TYR cc_start: 0.8031 (m-80) cc_final: 0.7419 (m-80) REVERT: D 167 ASN cc_start: 0.8939 (m110) cc_final: 0.8668 (m110) REVERT: E 84 ASP cc_start: 0.8698 (p0) cc_final: 0.8320 (p0) REVERT: E 121 LEU cc_start: 0.8506 (mt) cc_final: 0.8190 (tp) REVERT: E 132 ARG cc_start: 0.5443 (tpp80) cc_final: 0.5155 (tpt-90) REVERT: F 60 GLN cc_start: 0.7309 (tp40) cc_final: 0.7087 (tp40) REVERT: F 80 ASP cc_start: 0.8537 (m-30) cc_final: 0.8318 (m-30) REVERT: F 197 ILE cc_start: 0.9047 (mp) cc_final: 0.8746 (mm) REVERT: G 9 ASP cc_start: 0.7234 (p0) cc_final: 0.6943 (p0) REVERT: G 18 ASP cc_start: 0.9157 (p0) cc_final: 0.8955 (p0) REVERT: G 53 LEU cc_start: 0.8480 (tt) cc_final: 0.8194 (pp) REVERT: G 84 ASP cc_start: 0.8673 (p0) cc_final: 0.8383 (p0) REVERT: G 86 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7249 (ttm-80) REVERT: G 110 PRO cc_start: 0.9269 (Cg_exo) cc_final: 0.9009 (Cg_endo) REVERT: G 212 PHE cc_start: 0.8805 (p90) cc_final: 0.8399 (p90) REVERT: G 225 ASN cc_start: 0.7291 (t0) cc_final: 0.7035 (t0) REVERT: G 237 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8696 (tp40) REVERT: H 404 TRP cc_start: 0.7839 (m-10) cc_final: 0.7575 (m-10) REVERT: H 428 MET cc_start: 0.6270 (tpt) cc_final: 0.5777 (ttm) REVERT: I 191 ILE cc_start: 0.7289 (tt) cc_final: 0.7011 (tp) REVERT: I 417 LYS cc_start: 0.9262 (tttm) cc_final: 0.9015 (tptt) REVERT: I 420 LYS cc_start: 0.9131 (tttt) cc_final: 0.8888 (tttt) REVERT: J 249 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7484 (mm-30) REVERT: J 269 GLN cc_start: 0.9046 (tt0) cc_final: 0.8516 (tm-30) REVERT: J 273 LEU cc_start: 0.8070 (tt) cc_final: 0.7833 (tt) REVERT: J 327 ILE cc_start: 0.9315 (mm) cc_final: 0.9102 (mm) REVERT: K 161 MET cc_start: 0.7998 (ppp) cc_final: 0.7770 (ppp) REVERT: K 253 MET cc_start: 0.8020 (ppp) cc_final: 0.7615 (tmm) REVERT: K 303 MET cc_start: 0.8830 (mtp) cc_final: 0.8579 (tpp) REVERT: L 255 TYR cc_start: 0.8499 (m-10) cc_final: 0.8245 (m-80) REVERT: L 328 ASN cc_start: 0.8789 (m-40) cc_final: 0.8389 (m-40) REVERT: L 359 GLU cc_start: 0.9000 (mp0) cc_final: 0.8687 (mp0) REVERT: M 303 ARG cc_start: 0.8634 (mtt90) cc_final: 0.8179 (ptp-170) REVERT: M 397 GLU cc_start: 0.8943 (mp0) cc_final: 0.8516 (mp0) outliers start: 3 outliers final: 0 residues processed: 513 average time/residue: 0.1698 time to fit residues: 136.6602 Evaluate side-chains 407 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 39 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 270 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 chunk 233 optimal weight: 7.9990 chunk 283 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 27 GLN A 84 ASN B 123 GLN C 152 ASN C 173 GLN D 178 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 390 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.082938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.069526 restraints weight = 86881.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.071224 restraints weight = 54778.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.072431 restraints weight = 38807.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.073301 restraints weight = 29661.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.073911 restraints weight = 24133.806| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25141 Z= 0.138 Angle : 0.705 11.698 34112 Z= 0.356 Chirality : 0.046 0.195 3976 Planarity : 0.004 0.049 4421 Dihedral : 7.584 77.690 3694 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.04 % Allowed : 1.87 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.49 (0.14), residues: 3288 helix: -1.14 (0.14), residues: 1195 sheet: -1.97 (0.22), residues: 459 loop : -1.89 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 48 TYR 0.023 0.001 TYR G 78 PHE 0.049 0.002 PHE D 174 TRP 0.016 0.001 TRP C 160 HIS 0.009 0.001 HIS J 240 Details of bonding type rmsd covalent geometry : bond 0.00316 (25141) covalent geometry : angle 0.70471 (34112) hydrogen bonds : bond 0.03677 ( 698) hydrogen bonds : angle 5.57365 ( 1935) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 489 time to evaluate : 1.062 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 89 ASP cc_start: 0.8375 (p0) cc_final: 0.7749 (t0) REVERT: A 175 GLN cc_start: 0.7511 (pm20) cc_final: 0.7017 (pm20) REVERT: A 205 PHE cc_start: 0.8854 (t80) cc_final: 0.8441 (t80) REVERT: A 231 ASP cc_start: 0.7631 (t70) cc_final: 0.7321 (t70) REVERT: A 243 GLU cc_start: 0.8276 (tt0) cc_final: 0.7988 (tm-30) REVERT: B 4 ARG cc_start: 0.7737 (ttp80) cc_final: 0.7089 (ttp80) REVERT: B 103 GLU cc_start: 0.8244 (pm20) cc_final: 0.7979 (pm20) REVERT: C 114 ARG cc_start: 0.8977 (tpm170) cc_final: 0.8622 (tpp-160) REVERT: C 211 LEU cc_start: 0.9213 (tt) cc_final: 0.8972 (tt) REVERT: C 212 GLU cc_start: 0.7985 (pm20) cc_final: 0.7264 (pm20) REVERT: D 16 HIS cc_start: 0.8822 (m90) cc_final: 0.8076 (m90) REVERT: D 108 TYR cc_start: 0.8384 (t80) cc_final: 0.8155 (t80) REVERT: D 120 TYR cc_start: 0.8036 (m-80) cc_final: 0.7445 (m-80) REVERT: D 167 ASN cc_start: 0.8996 (m110) cc_final: 0.8670 (m-40) REVERT: E 84 ASP cc_start: 0.8666 (p0) cc_final: 0.8385 (p0) REVERT: E 121 LEU cc_start: 0.8625 (mt) cc_final: 0.8333 (tp) REVERT: E 132 ARG cc_start: 0.5418 (tpp80) cc_final: 0.5120 (tpt-90) REVERT: F 60 GLN cc_start: 0.7272 (tp40) cc_final: 0.7036 (tp40) REVERT: F 80 ASP cc_start: 0.8561 (m-30) cc_final: 0.8328 (m-30) REVERT: F 190 ILE cc_start: 0.8940 (pt) cc_final: 0.8441 (mt) REVERT: F 197 ILE cc_start: 0.9066 (mp) cc_final: 0.8779 (mm) REVERT: G 18 ASP cc_start: 0.9126 (p0) cc_final: 0.8922 (p0) REVERT: G 53 LEU cc_start: 0.8498 (tt) cc_final: 0.8191 (pp) REVERT: G 84 ASP cc_start: 0.8706 (p0) cc_final: 0.8456 (p0) REVERT: G 110 PRO cc_start: 0.9223 (Cg_exo) cc_final: 0.8999 (Cg_endo) REVERT: G 212 PHE cc_start: 0.8782 (p90) cc_final: 0.8501 (p90) REVERT: G 225 ASN cc_start: 0.7346 (t0) cc_final: 0.7075 (t0) REVERT: I 191 ILE cc_start: 0.7378 (tt) cc_final: 0.7060 (tp) REVERT: I 343 ARG cc_start: 0.7810 (mtt90) cc_final: 0.7234 (mtt90) REVERT: I 351 GLU cc_start: 0.8237 (pm20) cc_final: 0.8022 (pm20) REVERT: I 417 LYS cc_start: 0.9216 (tttm) cc_final: 0.8828 (tptt) REVERT: I 420 LYS cc_start: 0.9112 (tttt) cc_final: 0.8865 (tttt) REVERT: J 249 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7559 (mm-30) REVERT: J 269 GLN cc_start: 0.9110 (tt0) cc_final: 0.8579 (tm-30) REVERT: J 327 ILE cc_start: 0.9294 (mm) cc_final: 0.8890 (tt) REVERT: K 253 MET cc_start: 0.8095 (ppp) cc_final: 0.7792 (tmm) REVERT: K 273 GLU cc_start: 0.6943 (tt0) cc_final: 0.6588 (tt0) REVERT: K 303 MET cc_start: 0.8908 (mtp) cc_final: 0.8558 (tpp) REVERT: K 316 MET cc_start: 0.9207 (mmm) cc_final: 0.8983 (mmp) REVERT: L 203 ASN cc_start: 0.8900 (p0) cc_final: 0.8618 (p0) REVERT: L 255 TYR cc_start: 0.8470 (m-10) cc_final: 0.8242 (m-80) REVERT: L 328 ASN cc_start: 0.8878 (m-40) cc_final: 0.8483 (m-40) REVERT: L 359 GLU cc_start: 0.8999 (mp0) cc_final: 0.8683 (mp0) REVERT: L 397 GLU cc_start: 0.8484 (tp30) cc_final: 0.7999 (tp30) REVERT: M 303 ARG cc_start: 0.8657 (mtt90) cc_final: 0.8207 (ptp-170) REVERT: M 397 GLU cc_start: 0.8950 (mp0) cc_final: 0.8474 (mp0) outliers start: 1 outliers final: 0 residues processed: 489 average time/residue: 0.1704 time to fit residues: 131.4142 Evaluate side-chains 404 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 321 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 287 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 167 optimal weight: 20.0000 chunk 300 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 308 optimal weight: 7.9990 chunk 230 optimal weight: 4.9990 chunk 303 optimal weight: 0.0870 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 84 ASN C 227 GLN D 178 ASN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.084229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.070749 restraints weight = 87495.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.072469 restraints weight = 55130.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.073697 restraints weight = 38790.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.074480 restraints weight = 29731.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.075132 restraints weight = 24585.219| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25141 Z= 0.123 Angle : 0.711 10.991 34112 Z= 0.353 Chirality : 0.046 0.247 3976 Planarity : 0.004 0.046 4421 Dihedral : 7.386 82.278 3694 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.30 (0.15), residues: 3288 helix: -0.99 (0.15), residues: 1180 sheet: -1.82 (0.22), residues: 475 loop : -1.79 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG L 342 TYR 0.023 0.001 TYR I 222 PHE 0.045 0.002 PHE D 174 TRP 0.015 0.002 TRP C 160 HIS 0.006 0.001 HIS J 240 Details of bonding type rmsd covalent geometry : bond 0.00277 (25141) covalent geometry : angle 0.71096 (34112) hydrogen bonds : bond 0.03527 ( 698) hydrogen bonds : angle 5.44588 ( 1935) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 503 time to evaluate : 0.908 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 89 ASP cc_start: 0.8522 (p0) cc_final: 0.7687 (t0) REVERT: A 205 PHE cc_start: 0.8857 (t80) cc_final: 0.8486 (t80) REVERT: A 231 ASP cc_start: 0.7535 (t70) cc_final: 0.7311 (t70) REVERT: B 189 ILE cc_start: 0.9335 (mt) cc_final: 0.9128 (mm) REVERT: B 241 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8238 (tp40) REVERT: C 108 VAL cc_start: 0.9355 (t) cc_final: 0.8885 (t) REVERT: C 114 ARG cc_start: 0.8939 (tpm170) cc_final: 0.8601 (tpp-160) REVERT: C 210 ARG cc_start: 0.8313 (ttp-110) cc_final: 0.8053 (ttp-110) REVERT: C 233 GLN cc_start: 0.8444 (mm-40) cc_final: 0.7534 (tm-30) REVERT: D 16 HIS cc_start: 0.8811 (m90) cc_final: 0.8074 (m90) REVERT: D 120 TYR cc_start: 0.7994 (m-80) cc_final: 0.7441 (m-80) REVERT: D 167 ASN cc_start: 0.8967 (m110) cc_final: 0.8661 (m-40) REVERT: E 78 MET cc_start: 0.8405 (mtp) cc_final: 0.8067 (mmm) REVERT: E 84 ASP cc_start: 0.8514 (p0) cc_final: 0.8195 (p0) REVERT: E 121 LEU cc_start: 0.8572 (mt) cc_final: 0.8276 (tp) REVERT: E 132 ARG cc_start: 0.5362 (tpp80) cc_final: 0.5077 (tpt-90) REVERT: F 60 GLN cc_start: 0.7365 (tp40) cc_final: 0.7128 (tp40) REVERT: F 190 ILE cc_start: 0.8949 (pt) cc_final: 0.8527 (mt) REVERT: F 197 ILE cc_start: 0.8925 (mp) cc_final: 0.8690 (mm) REVERT: G 10 LEU cc_start: 0.8636 (pt) cc_final: 0.8038 (tt) REVERT: G 53 LEU cc_start: 0.8524 (tt) cc_final: 0.8204 (pp) REVERT: G 212 PHE cc_start: 0.8874 (p90) cc_final: 0.8564 (p90) REVERT: G 225 ASN cc_start: 0.7277 (t0) cc_final: 0.7033 (t0) REVERT: I 191 ILE cc_start: 0.7337 (tt) cc_final: 0.7098 (tp) REVERT: I 313 LEU cc_start: 0.9047 (pp) cc_final: 0.8753 (tp) REVERT: I 326 MET cc_start: 0.8557 (ptp) cc_final: 0.8002 (pmm) REVERT: I 417 LYS cc_start: 0.9220 (tttm) cc_final: 0.8802 (tptt) REVERT: J 249 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7599 (mm-30) REVERT: J 269 GLN cc_start: 0.9035 (tt0) cc_final: 0.8732 (tm-30) REVERT: J 327 ILE cc_start: 0.9272 (mm) cc_final: 0.8870 (tt) REVERT: J 332 SER cc_start: 0.8960 (p) cc_final: 0.7990 (p) REVERT: K 253 MET cc_start: 0.8097 (ppp) cc_final: 0.7778 (tmm) REVERT: K 273 GLU cc_start: 0.6821 (tt0) cc_final: 0.6589 (tt0) REVERT: K 303 MET cc_start: 0.8942 (mtp) cc_final: 0.8611 (tpp) REVERT: K 316 MET cc_start: 0.9186 (mmm) cc_final: 0.8979 (mmp) REVERT: L 203 ASN cc_start: 0.8858 (p0) cc_final: 0.8648 (p0) REVERT: L 255 TYR cc_start: 0.8557 (m-10) cc_final: 0.8308 (m-80) REVERT: L 328 ASN cc_start: 0.8852 (m-40) cc_final: 0.8465 (m-40) REVERT: L 354 GLU cc_start: 0.8255 (pp20) cc_final: 0.7744 (pp20) REVERT: L 359 GLU cc_start: 0.9155 (mp0) cc_final: 0.8842 (mp0) REVERT: L 397 GLU cc_start: 0.8484 (tp30) cc_final: 0.8012 (tp30) REVERT: M 303 ARG cc_start: 0.8634 (mtt90) cc_final: 0.8121 (ptp-170) REVERT: M 397 GLU cc_start: 0.8903 (mp0) cc_final: 0.8443 (mp0) outliers start: 0 outliers final: 0 residues processed: 503 average time/residue: 0.1617 time to fit residues: 130.2898 Evaluate side-chains 411 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 297 optimal weight: 5.9990 chunk 290 optimal weight: 0.9980 chunk 305 optimal weight: 10.0000 chunk 54 optimal weight: 0.3980 chunk 227 optimal weight: 4.9990 chunk 243 optimal weight: 0.4980 chunk 181 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 299 optimal weight: 0.0870 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 84 ASN C 152 ASN C 173 GLN C 227 GLN D 178 ASN E 180 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 413 ASN ** J 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.085063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.071637 restraints weight = 86470.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.073374 restraints weight = 54435.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.074591 restraints weight = 38302.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.075360 restraints weight = 29219.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.076009 restraints weight = 24090.177| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25141 Z= 0.119 Angle : 0.704 9.223 34112 Z= 0.350 Chirality : 0.045 0.169 3976 Planarity : 0.004 0.045 4421 Dihedral : 7.201 84.760 3694 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.08 % Allowed : 0.53 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.17 (0.15), residues: 3288 helix: -0.92 (0.15), residues: 1192 sheet: -1.66 (0.22), residues: 479 loop : -1.70 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 296 TYR 0.020 0.001 TYR D 108 PHE 0.042 0.001 PHE D 174 TRP 0.015 0.001 TRP C 160 HIS 0.018 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00268 (25141) covalent geometry : angle 0.70383 (34112) hydrogen bonds : bond 0.03355 ( 698) hydrogen bonds : angle 5.31979 ( 1935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 510 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8519 (p0) cc_final: 0.7774 (t0) REVERT: A 205 PHE cc_start: 0.8857 (t80) cc_final: 0.8471 (t80) REVERT: A 231 ASP cc_start: 0.7446 (t70) cc_final: 0.7187 (t70) REVERT: B 241 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8283 (tp40) REVERT: C 114 ARG cc_start: 0.8859 (tpm170) cc_final: 0.8510 (tpp-160) REVERT: C 120 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8598 (tm-30) REVERT: C 212 GLU cc_start: 0.8131 (pm20) cc_final: 0.7300 (pm20) REVERT: C 233 GLN cc_start: 0.8458 (mm-40) cc_final: 0.7468 (tm-30) REVERT: D 16 HIS cc_start: 0.8825 (m90) cc_final: 0.8056 (m90) REVERT: D 120 TYR cc_start: 0.7971 (m-80) cc_final: 0.7428 (m-80) REVERT: D 167 ASN cc_start: 0.8929 (m110) cc_final: 0.8612 (m110) REVERT: E 78 MET cc_start: 0.8143 (mtp) cc_final: 0.7871 (mmm) REVERT: E 84 ASP cc_start: 0.8550 (p0) cc_final: 0.8291 (p0) REVERT: E 121 LEU cc_start: 0.8564 (mt) cc_final: 0.8311 (tp) REVERT: E 132 ARG cc_start: 0.5250 (tpp80) cc_final: 0.4987 (tpt-90) REVERT: F 60 GLN cc_start: 0.7370 (tp40) cc_final: 0.7127 (tp40) REVERT: F 102 LYS cc_start: 0.8201 (mmpt) cc_final: 0.7521 (mtmt) REVERT: F 190 ILE cc_start: 0.8936 (pt) cc_final: 0.8560 (mt) REVERT: F 197 ILE cc_start: 0.8775 (mp) cc_final: 0.8548 (mm) REVERT: G 10 LEU cc_start: 0.8659 (pt) cc_final: 0.8138 (tt) REVERT: G 53 LEU cc_start: 0.8503 (tt) cc_final: 0.8195 (pp) REVERT: G 212 PHE cc_start: 0.9018 (p90) cc_final: 0.8594 (p90) REVERT: G 225 ASN cc_start: 0.7217 (t0) cc_final: 0.6984 (t0) REVERT: H 226 GLU cc_start: 0.8222 (pm20) cc_final: 0.7879 (pm20) REVERT: I 191 ILE cc_start: 0.7314 (tt) cc_final: 0.7023 (tp) REVERT: I 313 LEU cc_start: 0.9040 (pp) cc_final: 0.8734 (tp) REVERT: I 417 LYS cc_start: 0.9206 (tttm) cc_final: 0.8809 (tptt) REVERT: J 327 ILE cc_start: 0.9262 (mm) cc_final: 0.8846 (tt) REVERT: J 335 MET cc_start: 0.6965 (mpp) cc_final: 0.5776 (mpp) REVERT: K 221 MET cc_start: 0.8116 (ppp) cc_final: 0.7768 (ppp) REVERT: K 253 MET cc_start: 0.8154 (ppp) cc_final: 0.7838 (tmm) REVERT: K 273 GLU cc_start: 0.6852 (tt0) cc_final: 0.6605 (tt0) REVERT: K 303 MET cc_start: 0.8974 (mtp) cc_final: 0.8637 (tpp) REVERT: K 337 LYS cc_start: 0.8807 (mptt) cc_final: 0.8597 (mmtt) REVERT: K 377 SER cc_start: 0.8311 (m) cc_final: 0.8047 (p) REVERT: L 203 ASN cc_start: 0.8839 (p0) cc_final: 0.8592 (p0) REVERT: L 328 ASN cc_start: 0.8877 (m-40) cc_final: 0.8478 (m-40) REVERT: L 359 GLU cc_start: 0.9098 (mp0) cc_final: 0.8715 (mp0) REVERT: L 397 GLU cc_start: 0.8488 (tp30) cc_final: 0.8012 (tp30) REVERT: M 303 ARG cc_start: 0.8614 (mtt90) cc_final: 0.8016 (ptp-170) REVERT: M 397 GLU cc_start: 0.8907 (mp0) cc_final: 0.8473 (mp0) outliers start: 2 outliers final: 0 residues processed: 511 average time/residue: 0.1614 time to fit residues: 132.2405 Evaluate side-chains 435 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 214 optimal weight: 0.8980 chunk 282 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS B 94 HIS C 227 GLN D 178 ASN E 180 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 413 ASN ** J 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.084814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.071499 restraints weight = 86293.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.073202 restraints weight = 54400.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.074399 restraints weight = 38354.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.075178 restraints weight = 29391.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.075824 restraints weight = 24124.771| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25141 Z= 0.123 Angle : 0.713 15.771 34112 Z= 0.353 Chirality : 0.046 0.165 3976 Planarity : 0.004 0.043 4421 Dihedral : 7.123 87.736 3694 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.08 % Allowed : 0.57 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.07 (0.15), residues: 3288 helix: -0.86 (0.15), residues: 1185 sheet: -1.63 (0.22), residues: 479 loop : -1.62 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 169 TYR 0.015 0.001 TYR E 167 PHE 0.040 0.001 PHE D 174 TRP 0.023 0.001 TRP C 160 HIS 0.006 0.001 HIS J 240 Details of bonding type rmsd covalent geometry : bond 0.00280 (25141) covalent geometry : angle 0.71345 (34112) hydrogen bonds : bond 0.03356 ( 698) hydrogen bonds : angle 5.26813 ( 1935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3868.89 seconds wall clock time: 67 minutes 51.16 seconds (4071.16 seconds total)