Starting phenix.real_space_refine on Sun Sep 13 17:28:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ef0_9042/09_2026/6ef0_9042.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ef0_9042/09_2026/6ef0_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6ef0_9042/09_2026/6ef0_9042.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ef0_9042/09_2026/6ef0_9042.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ef0_9042/09_2026/6ef0_9042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ef0_9042/09_2026/6ef0_9042.map" model { file = "/net/cci-nas-00/data/ceres_data/6ef0_9042/09_2026/6ef0_9042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ef0_9042/09_2026/6ef0_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 5.31, per 1000 atoms: 0.21 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: 2.18 Conformation dependent library (CDL) restraints added in 1.2 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: 0.74 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: 3.98 Time building geometry restraints manager: 2.88 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: 15077 35.73 - 71.45: 127 71.45 - 107.18: 6 107.18 - 142.90: 2 142.90 - 178.63: 2 Dihedral angle restraints: 15214 sinusoidal: 5693 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 15211 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: 2.860 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.060 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 12.588 178.628 9096 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/Z covalent geometry : bond 0.01074 / 0.49 (25141) covalent geometry : angle 1.07384 / 0.63 (34112) hydrogen bonds : bond 0.32858 / 22.15 ( 698) hydrogen bonds : angle 11.32578 / 7.81 ( 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 : 0.978 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: 0.8462 (p0) cc_final: 0.7453 (t0) REVERT: A 106 TYR cc_start: 0.7792 (t80) cc_final: 0.6624 (m-10) REVERT: A 231 ASP cc_start: 0.7271 (t70) cc_final: 0.7070 (t70) REVERT: B 97 TYR cc_start: 0.6933 (t80) cc_final: 0.6507 (t80) REVERT: B 99 ARG cc_start: 0.8281 (mtt90) cc_final: 0.7898 (mtt90) REVERT: B 111 VAL cc_start: 0.9021 (p) cc_final: 0.8762 (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: 0.4812 (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: 0.8275 (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: 0.7580 (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: 0.7682 (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: 0.8763 (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: 0.8043 (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: 0.8899 (m110) cc_final: 0.8471 (m-40) REVERT: L 359 GLU cc_start: 0.9302 (mp0) cc_final: 0.8993 (mp0) outliers start: 0 outliers final: 0 residues processed: 641 average time/residue: 0.1920 time to fit residues: 185.4246 Evaluate side-chains 423 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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... ** 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 E 216 ASN F 210 ASN I 238 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.087000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.073937 restraints weight = 88894.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.075806 restraints weight = 57667.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.077537 restraints weight = 37913.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.077866 restraints weight = 27355.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.078307 restraints weight = 23082.327| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25141 Z= 0.180 Angle : 0.788 7.755 34112 Z= 0.404 Chirality : 0.049 0.173 3976 Planarity : 0.005 0.054 4421 Dihedral : 8.465 152.597 3601 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.28 % Allowed : 5.16 % Favored : 94.56 % 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: -4.21 (0.13), residues: 3288 helix: -2.59 (0.12), residues: 1146 sheet: -3.40 (0.22), residues: 392 loop : -2.81 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 294 TYR 0.018 0.002 TYR H 249 PHE 0.021 0.002 PHE A 205 TRP 0.011 0.002 TRP G 218 HIS 0.007 0.001 HIS M 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (25141) covalent geometry : angle 0.78752 / 0.40 (34112) hydrogen bonds : bond 0.05258 / 3.58 ( 698) hydrogen bonds : angle 6.84468 / 4.73 ( 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: 7 poor density : 593 time to evaluate : 0.948 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: A 49 ASP cc_start: 0.8517 (t70) cc_final: 0.8189 (t0) REVERT: A 89 ASP cc_start: 0.8297 (p0) cc_final: 0.7692 (t0) REVERT: A 162 TYR cc_start: 0.6921 (p90) cc_final: 0.6632 (p90) REVERT: A 175 GLN cc_start: 0.8200 (pm20) cc_final: 0.7787 (pm20) REVERT: A 231 ASP cc_start: 0.7580 (t70) cc_final: 0.7099 (t70) REVERT: B 75 TYR cc_start: 0.8171 (p90) cc_final: 0.7795 (p90) REVERT: B 99 ARG cc_start: 0.8316 (mtt90) cc_final: 0.8096 (mtt90) REVERT: B 117 ILE cc_start: 0.8961 (mm) cc_final: 0.8602 (mm) REVERT: B 149 GLN cc_start: 0.8414 (tm-30) cc_final: 0.7956 (tm-30) REVERT: B 241 GLN cc_start: 0.7794 (pm20) cc_final: 0.7352 (pm20) REVERT: C 1 MET cc_start: 0.5472 (ptm) cc_final: 0.4904 (ptt) REVERT: C 114 ARG cc_start: 0.8822 (tpm170) cc_final: 0.8497 (tpp-160) REVERT: C 120 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8336 (tm-30) REVERT: C 213 PHE cc_start: 0.8296 (p90) cc_final: 0.8009 (p90) REVERT: D 56 ASP cc_start: 0.7533 (t70) cc_final: 0.6905 (m-30) REVERT: D 120 TYR cc_start: 0.8134 (m-80) cc_final: 0.7478 (m-80) REVERT: D 149 GLN cc_start: 0.7460 (tm-30) cc_final: 0.7085 (tm-30) REVERT: D 163 THR cc_start: 0.9479 (p) cc_final: 0.9149 (t) REVERT: E 84 ASP cc_start: 0.8762 (p0) cc_final: 0.8457 (p0) REVERT: E 90 GLU cc_start: 0.8349 (tt0) cc_final: 0.7618 (tp30) REVERT: F 19 LEU cc_start: 0.8804 (mp) cc_final: 0.8180 (mp) REVERT: F 23 GLU cc_start: 0.8513 (mp0) cc_final: 0.7966 (mp0) REVERT: F 24 TYR cc_start: 0.8820 (m-80) cc_final: 0.8506 (m-10) REVERT: F 144 LEU cc_start: 0.9084 (tp) cc_final: 0.8852 (tp) REVERT: F 147 PHE cc_start: 0.8583 (t80) cc_final: 0.7949 (t80) REVERT: F 228 GLU cc_start: 0.8485 (mp0) cc_final: 0.8260 (mm-30) REVERT: G 18 ASP cc_start: 0.9000 (p0) cc_final: 0.8678 (p0) REVERT: G 53 LEU cc_start: 0.8623 (tt) cc_final: 0.8066 (pp) REVERT: G 84 ASP cc_start: 0.8371 (p0) cc_final: 0.8169 (p0) REVERT: G 212 PHE cc_start: 0.8757 (p90) cc_final: 0.8445 (p90) REVERT: G 225 ASN cc_start: 0.7157 (t0) cc_final: 0.6852 (t0) REVERT: H 392 HIS cc_start: 0.7505 (m-70) cc_final: 0.7042 (m90) REVERT: H 448 ASP cc_start: 0.8814 (t0) cc_final: 0.8599 (t0) REVERT: I 326 MET cc_start: 0.8482 (pmm) cc_final: 0.8210 (pmm) REVERT: I 352 ASN cc_start: 0.8313 (m-40) cc_final: 0.8066 (m-40) REVERT: I 395 MET cc_start: 0.8929 (tpp) cc_final: 0.8664 (tpp) REVERT: I 417 LYS cc_start: 0.9248 (tttm) cc_final: 0.8932 (tptt) REVERT: J 327 ILE cc_start: 0.9366 (mm) cc_final: 0.9055 (mm) REVERT: J 359 LYS cc_start: 0.9182 (ptmt) cc_final: 0.8849 (tttt) REVERT: J 368 TYR cc_start: 0.7773 (t80) cc_final: 0.7191 (t80) REVERT: K 161 MET cc_start: 0.7486 (ppp) cc_final: 0.7127 (ppp) REVERT: K 221 MET cc_start: 0.7596 (ppp) cc_final: 0.7366 (ppp) REVERT: K 285 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8917 (mm-40) REVERT: K 292 VAL cc_start: 0.9206 (m) cc_final: 0.8940 (p) REVERT: K 322 ASP cc_start: 0.7876 (p0) cc_final: 0.7668 (p0) REVERT: L 306 MET cc_start: 0.8344 (mtt) cc_final: 0.8021 (mtt) REVERT: L 328 ASN cc_start: 0.8680 (m-40) cc_final: 0.8293 (m-40) REVERT: L 359 GLU cc_start: 0.8953 (mp0) cc_final: 0.8714 (mp0) REVERT: M 303 ARG cc_start: 0.8545 (mtt90) cc_final: 0.8064 (ptp-170) REVERT: M 368 MET cc_start: 0.6695 (ptp) cc_final: 0.6306 (ptt) outliers start: 7 outliers final: 4 residues processed: 596 average time/residue: 0.1706 time to fit residues: 157.8059 Evaluate side-chains 455 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 451 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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: 0.0370 chunk 172 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 211 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 320 optimal weight: 0.2980 chunk 146 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 210 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 129 optimal weight: 0.0370 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 84 ASN A 209 HIS B 123 GLN B 218 ASN D 117 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN H 392 HIS ** K 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 310 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.090201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.077274 restraints weight = 87313.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.079224 restraints weight = 55610.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.081056 restraints weight = 36615.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.081365 restraints weight = 26324.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.081789 restraints weight = 22425.432| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25141 Z= 0.122 Angle : 0.699 8.771 34112 Z= 0.351 Chirality : 0.045 0.177 3976 Planarity : 0.004 0.047 4421 Dihedral : 7.178 121.499 3601 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.04 % Allowed : 5.16 % Favored : 94.80 % 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: -3.48 (0.14), residues: 3288 helix: -1.98 (0.13), residues: 1178 sheet: -2.80 (0.23), residues: 412 loop : -2.41 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 169 TYR 0.017 0.001 TYR L 221 PHE 0.026 0.001 PHE A 205 TRP 0.007 0.001 TRP G 218 HIS 0.008 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (25141) covalent geometry : angle 0.69852 / 0.35 (34112) hydrogen bonds : bond 0.04279 / 2.91 ( 698) hydrogen bonds : angle 6.04942 / 4.21 ( 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 595 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 594 time to evaluate : 0.945 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: A 49 ASP cc_start: 0.8292 (t70) cc_final: 0.7799 (t0) REVERT: A 89 ASP cc_start: 0.8430 (p0) cc_final: 0.7445 (t0) REVERT: A 162 TYR cc_start: 0.6895 (p90) cc_final: 0.6639 (p90) REVERT: A 231 ASP cc_start: 0.7507 (t70) cc_final: 0.7116 (t70) REVERT: B 99 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7853 (mtt90) REVERT: B 117 ILE cc_start: 0.8879 (mm) cc_final: 0.8584 (mm) REVERT: B 119 GLN cc_start: 0.7926 (tp-100) cc_final: 0.7669 (tp-100) REVERT: B 241 GLN cc_start: 0.7716 (pm20) cc_final: 0.7362 (pm20) REVERT: C 1 MET cc_start: 0.5175 (ptm) cc_final: 0.4892 (ptt) REVERT: C 114 ARG cc_start: 0.8817 (tpm170) cc_final: 0.8437 (tpp-160) REVERT: C 120 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8334 (tm-30) REVERT: C 134 SER cc_start: 0.9406 (t) cc_final: 0.9024 (m) REVERT: D 56 ASP cc_start: 0.7343 (t70) cc_final: 0.7022 (m-30) REVERT: D 120 TYR cc_start: 0.7996 (m-80) cc_final: 0.7556 (m-80) REVERT: D 149 GLN cc_start: 0.7559 (tm-30) cc_final: 0.7050 (tm-30) REVERT: D 153 SER cc_start: 0.9116 (p) cc_final: 0.8862 (p) REVERT: E 84 ASP cc_start: 0.8791 (p0) cc_final: 0.8487 (p0) REVERT: E 90 GLU cc_start: 0.8233 (tt0) cc_final: 0.7964 (tt0) REVERT: F 24 TYR cc_start: 0.8764 (m-80) cc_final: 0.8521 (m-10) REVERT: G 18 ASP cc_start: 0.9011 (p0) cc_final: 0.8647 (p0) REVERT: G 53 LEU cc_start: 0.8727 (tt) cc_final: 0.8328 (pp) REVERT: G 86 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7279 (ttm-80) REVERT: G 110 PRO cc_start: 0.9099 (Cg_exo) cc_final: 0.8785 (Cg_endo) REVERT: G 206 ASP cc_start: 0.8924 (p0) cc_final: 0.8714 (p0) REVERT: G 225 ASN cc_start: 0.7124 (t0) cc_final: 0.6818 (t0) REVERT: H 387 ASN cc_start: 0.8683 (m-40) cc_final: 0.8346 (m110) REVERT: H 392 HIS cc_start: 0.7122 (m90) cc_final: 0.6744 (m90) REVERT: H 448 ASP cc_start: 0.8919 (t0) cc_final: 0.8610 (t0) REVERT: I 219 VAL cc_start: 0.8610 (p) cc_final: 0.8010 (m) REVERT: I 343 ARG cc_start: 0.6871 (mtt90) cc_final: 0.6542 (mtt90) REVERT: I 395 MET cc_start: 0.8929 (tpp) cc_final: 0.8552 (tpp) REVERT: I 417 LYS cc_start: 0.9115 (tttm) cc_final: 0.8761 (tptt) REVERT: J 240 HIS cc_start: 0.7353 (m90) cc_final: 0.6877 (m90) REVERT: J 311 ASP cc_start: 0.8726 (p0) cc_final: 0.8408 (m-30) REVERT: J 327 ILE cc_start: 0.9269 (mm) cc_final: 0.8969 (mm) REVERT: J 359 LYS cc_start: 0.9125 (ptmt) cc_final: 0.8767 (tttt) REVERT: J 368 TYR cc_start: 0.7685 (t80) cc_final: 0.7272 (t80) REVERT: K 161 MET cc_start: 0.7597 (ppp) cc_final: 0.7226 (ppp) REVERT: K 194 GLN cc_start: 0.8732 (mt0) cc_final: 0.8516 (mt0) REVERT: K 221 MET cc_start: 0.7783 (ppp) cc_final: 0.7461 (ppp) REVERT: K 285 GLN cc_start: 0.9259 (mm-40) cc_final: 0.9041 (mm-40) REVERT: K 292 VAL cc_start: 0.8674 (m) cc_final: 0.8324 (p) REVERT: K 322 ASP cc_start: 0.7957 (p0) cc_final: 0.7720 (p0) REVERT: K 334 LEU cc_start: 0.8575 (mt) cc_final: 0.7871 (mt) REVERT: L 167 VAL cc_start: 0.8878 (t) cc_final: 0.8524 (p) REVERT: L 281 ASP cc_start: 0.7694 (p0) cc_final: 0.6686 (p0) REVERT: L 301 ILE cc_start: 0.9285 (pt) cc_final: 0.9059 (pt) REVERT: L 311 GLN cc_start: 0.7845 (tp40) cc_final: 0.7639 (tp40) REVERT: L 328 ASN cc_start: 0.8517 (m-40) cc_final: 0.8123 (m-40) REVERT: L 354 GLU cc_start: 0.8095 (pp20) cc_final: 0.7729 (pp20) REVERT: L 359 GLU cc_start: 0.8925 (mp0) cc_final: 0.8700 (mp0) REVERT: M 303 ARG cc_start: 0.8387 (mtt90) cc_final: 0.7999 (mtm-85) outliers start: 1 outliers final: 1 residues processed: 594 average time/residue: 0.1730 time to fit residues: 160.0893 Evaluate side-chains 453 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 452 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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: 4.9990 chunk 188 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 229 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 309 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 185 optimal weight: 0.6980 chunk 300 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS A 84 ASN B 119 GLN B 123 GLN B 218 ASN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.076208 restraints weight = 87122.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.078313 restraints weight = 55104.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.079976 restraints weight = 35140.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.080495 restraints weight = 26128.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.081256 restraints weight = 20149.176| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4061 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= 0.123 Angle : 0.675 9.130 34112 Z= 0.341 Chirality : 0.045 0.170 3976 Planarity : 0.004 0.046 4421 Dihedral : 6.621 97.131 3601 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % 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: -3.16 (0.14), residues: 3288 helix: -1.77 (0.14), residues: 1183 sheet: -2.28 (0.24), residues: 411 loop : -2.28 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 169 TYR 0.018 0.001 TYR D 232 PHE 0.035 0.001 PHE D 174 TRP 0.007 0.001 TRP G 218 HIS 0.016 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (25141) covalent geometry : angle 0.67524 / 0.34 (34112) hydrogen bonds : bond 0.03769 / 2.58 ( 698) hydrogen bonds : angle 5.78557 / 4.04 ( 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 557 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 556 time to evaluate : 1.174 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: 0.8328 (t70) cc_final: 0.7829 (t0) REVERT: A 89 ASP cc_start: 0.8314 (p0) cc_final: 0.7543 (t70) REVERT: A 162 TYR cc_start: 0.6992 (p90) cc_final: 0.6721 (p90) REVERT: A 231 ASP cc_start: 0.7332 (t70) cc_final: 0.6690 (t70) REVERT: B 99 ARG cc_start: 0.8192 (mtt90) cc_final: 0.7890 (mtt90) REVERT: B 117 ILE cc_start: 0.8750 (mm) cc_final: 0.8495 (mm) REVERT: C 1 MET cc_start: 0.5066 (ptm) cc_final: 0.4745 (ptt) REVERT: C 114 ARG cc_start: 0.8859 (tpm170) cc_final: 0.8507 (tpp-160) REVERT: C 120 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8358 (tm-30) REVERT: C 134 SER cc_start: 0.9333 (t) cc_final: 0.9018 (m) REVERT: D 120 TYR cc_start: 0.8099 (m-80) cc_final: 0.7735 (m-80) REVERT: D 167 ASN cc_start: 0.9223 (m110) cc_final: 0.8995 (m-40) REVERT: E 84 ASP cc_start: 0.8686 (p0) cc_final: 0.8369 (p0) REVERT: E 143 LEU cc_start: 0.8446 (mt) cc_final: 0.8229 (mt) REVERT: G 18 ASP cc_start: 0.9030 (p0) cc_final: 0.8661 (p0) REVERT: G 53 LEU cc_start: 0.8671 (tt) cc_final: 0.8444 (pp) REVERT: G 84 ASP cc_start: 0.8376 (p0) cc_final: 0.8080 (p0) REVERT: G 86 ARG cc_start: 0.7766 (ttm-80) cc_final: 0.7420 (ttm-80) REVERT: G 110 PRO cc_start: 0.9122 (Cg_exo) cc_final: 0.8837 (Cg_endo) REVERT: G 206 ASP cc_start: 0.8986 (p0) cc_final: 0.8652 (p0) REVERT: G 212 PHE cc_start: 0.8899 (p90) cc_final: 0.8458 (p90) REVERT: G 225 ASN cc_start: 0.7173 (t0) cc_final: 0.6859 (t0) REVERT: H 387 ASN cc_start: 0.8820 (m-40) cc_final: 0.8367 (m110) REVERT: H 448 ASP cc_start: 0.8955 (t0) cc_final: 0.8701 (t0) REVERT: I 219 VAL cc_start: 0.8696 (p) cc_final: 0.8183 (m) REVERT: I 343 ARG cc_start: 0.6913 (mtt90) cc_final: 0.6612 (mtt90) REVERT: I 417 LYS cc_start: 0.9084 (tttm) cc_final: 0.8737 (tptt) REVERT: J 161 LYS cc_start: 0.8466 (mtmm) cc_final: 0.8104 (tptt) REVERT: J 327 ILE cc_start: 0.9264 (mm) cc_final: 0.8935 (mm) REVERT: J 332 SER cc_start: 0.8956 (p) cc_final: 0.8632 (t) REVERT: J 359 LYS cc_start: 0.9192 (ptmt) cc_final: 0.8897 (tttt) REVERT: J 368 TYR cc_start: 0.7497 (t80) cc_final: 0.7119 (t80) REVERT: K 161 MET cc_start: 0.7683 (ppp) cc_final: 0.7266 (ppp) REVERT: K 164 ASN cc_start: 0.7976 (p0) cc_final: 0.7660 (p0) REVERT: K 204 ASP cc_start: 0.8240 (p0) cc_final: 0.7903 (p0) REVERT: K 221 MET cc_start: 0.8030 (ppp) cc_final: 0.7823 (ppp) REVERT: K 245 LYS cc_start: 0.8231 (ttpp) cc_final: 0.8013 (ttpt) REVERT: K 292 VAL cc_start: 0.8632 (m) cc_final: 0.8311 (p) REVERT: K 322 ASP cc_start: 0.7986 (p0) cc_final: 0.7731 (p0) REVERT: K 325 ASP cc_start: 0.8800 (p0) cc_final: 0.8594 (p0) REVERT: K 334 LEU cc_start: 0.8665 (mt) cc_final: 0.8310 (mt) REVERT: K 377 SER cc_start: 0.8306 (m) cc_final: 0.8029 (p) REVERT: L 167 VAL cc_start: 0.8861 (t) cc_final: 0.8502 (p) REVERT: L 203 ASN cc_start: 0.8669 (p0) cc_final: 0.8416 (p0) REVERT: L 328 ASN cc_start: 0.8599 (m-40) cc_final: 0.8161 (m-40) REVERT: L 349 ILE cc_start: 0.9136 (pt) cc_final: 0.8417 (pt) REVERT: L 354 GLU cc_start: 0.8108 (pp20) cc_final: 0.7666 (pp20) REVERT: L 359 GLU cc_start: 0.9045 (mp0) cc_final: 0.8723 (mp0) REVERT: M 303 ARG cc_start: 0.8423 (mtt90) cc_final: 0.7999 (mtm-85) REVERT: M 397 GLU cc_start: 0.8866 (mp0) cc_final: 0.8481 (mp0) outliers start: 1 outliers final: 0 residues processed: 556 average time/residue: 0.1695 time to fit residues: 148.6736 Evaluate side-chains 441 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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: 6.9990 chunk 258 optimal weight: 1.9990 chunk 179 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 275 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 190 optimal weight: 0.0470 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS A 27 GLN B 119 GLN B 123 GLN B 218 ASN D 178 ASN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 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 = 0.3348 r_free = 0.3348 target = 0.087122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.073943 restraints weight = 87710.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.075874 restraints weight = 55825.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.077645 restraints weight = 36177.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.078131 restraints weight = 27116.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.078878 restraints weight = 20682.897| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25141 Z= 0.141 Angle : 0.677 8.541 34112 Z= 0.341 Chirality : 0.046 0.180 3976 Planarity : 0.004 0.053 4421 Dihedral : 6.415 82.210 3601 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.16 % Allowed : 4.14 % Favored : 95.69 % 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: -2.88 (0.14), residues: 3288 helix: -1.53 (0.14), residues: 1177 sheet: -1.96 (0.24), residues: 424 loop : -2.16 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 169 TYR 0.014 0.001 TYR E 167 PHE 0.025 0.002 PHE D 174 TRP 0.006 0.001 TRP G 218 HIS 0.012 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (25141) covalent geometry : angle 0.67720 / 0.34 (34112) hydrogen bonds : bond 0.03697 / 2.52 ( 698) hydrogen bonds : angle 5.63765 / 3.95 ( 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 535 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 531 time to evaluate : 1.024 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: A 49 ASP cc_start: 0.8381 (t70) cc_final: 0.7755 (t0) REVERT: A 89 ASP cc_start: 0.8362 (p0) cc_final: 0.7545 (t0) REVERT: A 162 TYR cc_start: 0.7048 (p90) cc_final: 0.6742 (p90) REVERT: A 231 ASP cc_start: 0.7344 (t70) cc_final: 0.6849 (t70) REVERT: B 99 ARG cc_start: 0.8184 (mtt90) cc_final: 0.7857 (mtt90) REVERT: B 113 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7082 (mt-10) REVERT: B 123 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7892 (tt0) REVERT: C 1 MET cc_start: 0.5214 (ptm) cc_final: 0.4951 (ptt) REVERT: C 64 GLU cc_start: 0.8063 (pp20) cc_final: 0.7774 (pp20) REVERT: C 114 ARG cc_start: 0.8976 (tpm170) cc_final: 0.8640 (tpp-160) REVERT: C 120 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8452 (tm-30) REVERT: C 134 SER cc_start: 0.9351 (t) cc_final: 0.9034 (m) REVERT: D 16 HIS cc_start: 0.8584 (m90) cc_final: 0.8226 (m90) REVERT: D 56 ASP cc_start: 0.7715 (t70) cc_final: 0.7186 (m-30) REVERT: D 119 ARG cc_start: 0.8236 (mtp180) cc_final: 0.7973 (ttm110) REVERT: D 120 TYR cc_start: 0.8088 (m-80) cc_final: 0.7692 (m-80) REVERT: D 167 ASN cc_start: 0.9047 (m110) cc_final: 0.8807 (m-40) REVERT: E 84 ASP cc_start: 0.8648 (p0) cc_final: 0.8261 (p0) REVERT: F 19 LEU cc_start: 0.8641 (mp) cc_final: 0.8247 (mp) REVERT: G 9 ASP cc_start: 0.7009 (p0) cc_final: 0.6701 (p0) REVERT: G 18 ASP cc_start: 0.9100 (p0) cc_final: 0.8776 (p0) REVERT: G 84 ASP cc_start: 0.8487 (p0) cc_final: 0.8186 (p0) REVERT: G 86 ARG cc_start: 0.7753 (ttm-80) cc_final: 0.7330 (ttm-80) REVERT: G 110 PRO cc_start: 0.9158 (Cg_exo) cc_final: 0.8877 (Cg_endo) REVERT: G 206 ASP cc_start: 0.9058 (p0) cc_final: 0.8771 (p0) REVERT: G 212 PHE cc_start: 0.9017 (p90) cc_final: 0.8585 (p90) REVERT: G 225 ASN cc_start: 0.7247 (t0) cc_final: 0.6967 (t0) REVERT: H 383 GLU cc_start: 0.8255 (tp30) cc_final: 0.7975 (tp30) REVERT: H 387 ASN cc_start: 0.8932 (m-40) cc_final: 0.8384 (m110) REVERT: H 392 HIS cc_start: 0.7512 (m90) cc_final: 0.6980 (m90) REVERT: H 448 ASP cc_start: 0.9070 (t0) cc_final: 0.8816 (t0) REVERT: I 219 VAL cc_start: 0.8735 (p) cc_final: 0.8280 (m) REVERT: I 343 ARG cc_start: 0.7003 (mtt90) cc_final: 0.6681 (mtt90) REVERT: I 351 GLU cc_start: 0.7900 (pm20) cc_final: 0.7676 (pm20) REVERT: J 161 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8234 (tptt) REVERT: J 222 TYR cc_start: 0.7893 (m-80) cc_final: 0.7660 (m-80) REVERT: J 269 GLN cc_start: 0.9039 (tt0) cc_final: 0.8615 (tm-30) REVERT: J 327 ILE cc_start: 0.9224 (mm) cc_final: 0.8941 (mm) REVERT: J 332 SER cc_start: 0.9098 (p) cc_final: 0.8696 (t) REVERT: J 350 MET cc_start: 0.8078 (ptp) cc_final: 0.7831 (ptm) REVERT: K 161 MET cc_start: 0.7878 (ppp) cc_final: 0.7564 (ppp) REVERT: K 164 ASN cc_start: 0.8081 (p0) cc_final: 0.7880 (p0) REVERT: K 221 MET cc_start: 0.8203 (ppp) cc_final: 0.7949 (ppp) REVERT: K 292 VAL cc_start: 0.8902 (m) cc_final: 0.8597 (p) REVERT: K 316 MET cc_start: 0.9244 (mmm) cc_final: 0.8966 (mmp) REVERT: K 322 ASP cc_start: 0.7978 (p0) cc_final: 0.7652 (p0) REVERT: K 334 LEU cc_start: 0.8781 (mt) cc_final: 0.8486 (mt) REVERT: K 377 SER cc_start: 0.8286 (m) cc_final: 0.7984 (p) REVERT: L 167 VAL cc_start: 0.8874 (t) cc_final: 0.8543 (p) REVERT: L 203 ASN cc_start: 0.8781 (p0) cc_final: 0.8558 (p0) REVERT: L 309 LEU cc_start: 0.9301 (tt) cc_final: 0.9095 (tp) REVERT: L 328 ASN cc_start: 0.8585 (m-40) cc_final: 0.8124 (m-40) REVERT: L 354 GLU cc_start: 0.8198 (pp20) cc_final: 0.7718 (pp20) REVERT: L 359 GLU cc_start: 0.9006 (mp0) cc_final: 0.8712 (mp0) REVERT: M 215 PRO cc_start: 0.7176 (Cg_endo) cc_final: 0.6809 (Cg_exo) REVERT: M 303 ARG cc_start: 0.8406 (mtt90) cc_final: 0.8087 (ptp-170) REVERT: M 397 GLU cc_start: 0.8902 (mp0) cc_final: 0.8453 (mp0) outliers start: 4 outliers final: 0 residues processed: 533 average time/residue: 0.1620 time to fit residues: 137.0712 Evaluate side-chains 434 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 433 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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: 0.5980 chunk 215 optimal weight: 8.9990 chunk 280 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 9 optimal weight: 0.1980 chunk 231 optimal weight: 8.9990 chunk 284 optimal weight: 6.9990 chunk 227 optimal weight: 8.9990 chunk 270 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 268 optimal weight: 6.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS A 27 GLN B 218 ASN C 227 GLN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN D 204 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 217 GLN I 254 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.082036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.068693 restraints weight = 88879.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.070410 restraints weight = 56441.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.071602 restraints weight = 39669.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.072442 restraints weight = 30303.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.073018 restraints weight = 24729.016| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4661 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= 0.221 Angle : 0.755 9.431 34112 Z= 0.389 Chirality : 0.048 0.167 3976 Planarity : 0.004 0.043 4421 Dihedral : 6.682 85.316 3601 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 0.16 % Allowed : 4.55 % Favored : 95.29 % 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: -2.76 (0.14), residues: 3288 helix: -1.42 (0.14), residues: 1179 sheet: -1.97 (0.23), residues: 450 loop : -2.07 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 169 TYR 0.014 0.002 TYR G 119 PHE 0.024 0.002 PHE M 279 TRP 0.012 0.002 TRP B 179 HIS 0.009 0.001 HIS J 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (25141) covalent geometry : angle 0.75514 / 0.39 (34112) hydrogen bonds : bond 0.04170 / 2.84 ( 698) hydrogen bonds : angle 5.90304 / 4.12 ( 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 501 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 497 time to evaluate : 0.907 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: 0.8349 (p0) cc_final: 0.7704 (t0) REVERT: A 231 ASP cc_start: 0.7275 (t70) cc_final: 0.6832 (t70) REVERT: B 82 TYR cc_start: 0.8644 (t80) cc_final: 0.8399 (t80) REVERT: C 114 ARG cc_start: 0.9038 (tpm170) cc_final: 0.8735 (tpp-160) REVERT: D 16 HIS cc_start: 0.8624 (m90) cc_final: 0.8084 (m90) REVERT: D 56 ASP cc_start: 0.7944 (t70) cc_final: 0.7494 (m-30) REVERT: D 120 TYR cc_start: 0.8117 (m-80) cc_final: 0.7605 (m-80) REVERT: D 167 ASN cc_start: 0.9142 (m110) cc_final: 0.8827 (m-40) REVERT: E 22 PHE cc_start: 0.7858 (m-80) cc_final: 0.7545 (m-10) REVERT: E 84 ASP cc_start: 0.8601 (p0) cc_final: 0.8261 (p0) REVERT: E 132 ARG cc_start: 0.4907 (ttp-170) cc_final: 0.4391 (ttt180) REVERT: E 206 GLN cc_start: 0.8358 (tm-30) cc_final: 0.7976 (tm-30) REVERT: G 9 ASP cc_start: 0.7291 (p0) cc_final: 0.6964 (p0) REVERT: G 18 ASP cc_start: 0.9122 (p0) cc_final: 0.8837 (p0) REVERT: G 94 GLU cc_start: 0.8533 (pp20) cc_final: 0.8085 (pt0) REVERT: G 110 PRO cc_start: 0.9190 (Cg_exo) cc_final: 0.8940 (Cg_endo) REVERT: G 212 PHE cc_start: 0.8852 (p90) cc_final: 0.8630 (p90) REVERT: G 225 ASN cc_start: 0.7477 (t0) cc_final: 0.7206 (t0) REVERT: I 219 VAL cc_start: 0.8594 (p) cc_final: 0.8035 (m) REVERT: I 395 MET cc_start: 0.8698 (tpp) cc_final: 0.8443 (tpp) REVERT: J 161 LYS cc_start: 0.8859 (mtmm) cc_final: 0.8359 (mtmm) REVERT: J 222 TYR cc_start: 0.8216 (m-80) cc_final: 0.7940 (m-80) REVERT: J 327 ILE cc_start: 0.9290 (mm) cc_final: 0.9078 (mm) REVERT: J 332 SER cc_start: 0.9152 (p) cc_final: 0.8722 (t) REVERT: J 367 MET cc_start: 0.8145 (tpt) cc_final: 0.7792 (tpt) REVERT: K 221 MET cc_start: 0.8247 (ppp) cc_final: 0.7916 (ppp) REVERT: K 222 LEU cc_start: 0.9300 (tt) cc_final: 0.9098 (tp) REVERT: K 292 VAL cc_start: 0.9154 (m) cc_final: 0.8878 (p) REVERT: L 203 ASN cc_start: 0.8866 (p0) cc_final: 0.8590 (p0) REVERT: L 306 MET cc_start: 0.8246 (mmt) cc_final: 0.7943 (mmt) REVERT: L 328 ASN cc_start: 0.8736 (m-40) cc_final: 0.8247 (m-40) REVERT: L 359 GLU cc_start: 0.9011 (mp0) cc_final: 0.8745 (mp0) REVERT: M 215 PRO cc_start: 0.7365 (Cg_endo) cc_final: 0.7084 (Cg_exo) REVERT: M 397 GLU cc_start: 0.8975 (mp0) cc_final: 0.8530 (mp0) outliers start: 4 outliers final: 0 residues processed: 499 average time/residue: 0.1668 time to fit residues: 131.2904 Evaluate side-chains 418 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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: 4.9990 chunk 27 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 228 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 260 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS A 27 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN C 227 GLN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN E 157 HIS ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS J 181 GLN K 302 GLN K 398 ASN ** M 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.084029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.070708 restraints weight = 87455.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.072418 restraints weight = 54964.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.073628 restraints weight = 38795.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.074484 restraints weight = 29671.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.075113 restraints weight = 24143.409| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25141 Z= 0.139 Angle : 0.707 13.399 34112 Z= 0.353 Chirality : 0.046 0.231 3976 Planarity : 0.004 0.080 4421 Dihedral : 6.393 82.469 3601 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.20 % Allowed : 1.99 % Favored : 97.81 % 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: -2.56 (0.14), residues: 3288 helix: -1.23 (0.14), residues: 1173 sheet: -1.88 (0.23), residues: 448 loop : -1.97 (0.16), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 169 TYR 0.022 0.001 TYR L 269 PHE 0.022 0.002 PHE A 186 TRP 0.013 0.002 TRP C 160 HIS 0.017 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (25141) covalent geometry : angle 0.70725 / 0.35 (34112) hydrogen bonds : bond 0.03682 / 2.50 ( 698) hydrogen bonds : angle 5.62459 / 3.95 ( 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 524 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 519 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8432 (p0) cc_final: 0.7601 (t0) REVERT: A 231 ASP cc_start: 0.7381 (t70) cc_final: 0.6998 (t70) REVERT: B 108 LYS cc_start: 0.6916 (ttpt) cc_final: 0.6632 (tmtt) REVERT: C 114 ARG cc_start: 0.8977 (tpm170) cc_final: 0.8655 (tpp-160) REVERT: C 233 GLN cc_start: 0.8546 (mm-40) cc_final: 0.7470 (tm-30) REVERT: D 56 ASP cc_start: 0.7638 (t70) cc_final: 0.7396 (m-30) REVERT: D 120 TYR cc_start: 0.8014 (m-80) cc_final: 0.7518 (m-80) REVERT: D 167 ASN cc_start: 0.9060 (m110) cc_final: 0.8763 (m-40) REVERT: E 84 ASP cc_start: 0.8615 (p0) cc_final: 0.8256 (p0) REVERT: E 132 ARG cc_start: 0.4812 (ttp-170) cc_final: 0.4247 (ttt180) REVERT: F 226 ASP cc_start: 0.8992 (t70) cc_final: 0.8664 (t0) REVERT: G 18 ASP cc_start: 0.9151 (p0) cc_final: 0.8895 (p0) REVERT: G 86 ARG cc_start: 0.7861 (ttm-80) cc_final: 0.7398 (ttm-80) REVERT: G 110 PRO cc_start: 0.9221 (Cg_exo) cc_final: 0.8982 (Cg_endo) REVERT: G 212 PHE cc_start: 0.8949 (p90) cc_final: 0.8520 (p90) REVERT: G 225 ASN cc_start: 0.7301 (t0) cc_final: 0.7045 (t0) REVERT: I 191 ILE cc_start: 0.7295 (tp) cc_final: 0.7089 (tp) REVERT: I 193 GLU cc_start: 0.8800 (mp0) cc_final: 0.8544 (mp0) REVERT: I 219 VAL cc_start: 0.8520 (p) cc_final: 0.8074 (m) REVERT: J 161 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8483 (mtmm) REVERT: J 222 TYR cc_start: 0.8204 (m-80) cc_final: 0.7929 (m-80) REVERT: J 327 ILE cc_start: 0.9231 (mm) cc_final: 0.9010 (mm) REVERT: J 332 SER cc_start: 0.8980 (p) cc_final: 0.8749 (t) REVERT: K 161 MET cc_start: 0.7843 (ppp) cc_final: 0.7633 (ppp) REVERT: K 221 MET cc_start: 0.8170 (ppp) cc_final: 0.7817 (ppp) REVERT: K 222 LEU cc_start: 0.9296 (tt) cc_final: 0.9076 (tp) REVERT: K 235 ILE cc_start: 0.8144 (pt) cc_final: 0.7744 (pt) REVERT: K 292 VAL cc_start: 0.9037 (m) cc_final: 0.8737 (p) REVERT: L 167 VAL cc_start: 0.9160 (t) cc_final: 0.8937 (p) REVERT: L 203 ASN cc_start: 0.8929 (p0) cc_final: 0.8669 (p0) REVERT: L 328 ASN cc_start: 0.8727 (m-40) cc_final: 0.8259 (m-40) REVERT: L 354 GLU cc_start: 0.8207 (pp20) cc_final: 0.7938 (pp20) REVERT: L 359 GLU cc_start: 0.9149 (mp0) cc_final: 0.8710 (mp0) REVERT: M 215 PRO cc_start: 0.7435 (Cg_endo) cc_final: 0.7068 (Cg_exo) REVERT: M 303 ARG cc_start: 0.8512 (mtt90) cc_final: 0.8060 (ptp-170) REVERT: M 397 GLU cc_start: 0.8921 (mp0) cc_final: 0.8486 (mp0) outliers start: 5 outliers final: 0 residues processed: 522 average time/residue: 0.1654 time to fit residues: 136.7028 Evaluate side-chains 428 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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: 10.0000 chunk 319 optimal weight: 0.0670 chunk 270 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 293 optimal weight: 8.9990 chunk 167 optimal weight: 20.0000 chunk 233 optimal weight: 4.9990 chunk 283 optimal weight: 3.9990 chunk 211 optimal weight: 0.0970 chunk 93 optimal weight: 10.0000 overall best weight: 2.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS A 27 GLN C 227 GLN ** 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** ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 302 GLN ** M 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.082614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.069407 restraints weight = 88544.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.071135 restraints weight = 55867.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.072323 restraints weight = 39293.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.073185 restraints weight = 30083.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.073823 restraints weight = 24486.914| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25141 Z= 0.153 Angle : 0.708 11.791 34112 Z= 0.357 Chirality : 0.046 0.235 3976 Planarity : 0.004 0.044 4421 Dihedral : 6.313 88.132 3601 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.04 % Allowed : 2.27 % Favored : 97.68 % 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: -2.46 (0.14), residues: 3288 helix: -1.15 (0.14), residues: 1173 sheet: -1.82 (0.23), residues: 446 loop : -1.90 (0.16), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 169 TYR 0.015 0.001 TYR E 167 PHE 0.038 0.002 PHE D 174 TRP 0.014 0.002 TRP H 404 HIS 0.008 0.001 HIS J 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (25141) covalent geometry : angle 0.70840 / 0.36 (34112) hydrogen bonds : bond 0.03658 / 2.48 ( 698) hydrogen bonds : angle 5.61201 / 3.94 ( 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 492 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 491 time to evaluate : 0.965 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: 0.8472 (p0) cc_final: 0.7581 (t0) REVERT: A 231 ASP cc_start: 0.7357 (t70) cc_final: 0.7082 (t70) REVERT: B 108 LYS cc_start: 0.6991 (ttpt) cc_final: 0.6746 (tmtt) REVERT: B 241 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8197 (tp40) REVERT: C 50 ARG cc_start: 0.7089 (mpp80) cc_final: 0.6210 (mtt180) REVERT: C 114 ARG cc_start: 0.8988 (tpm170) cc_final: 0.8678 (tpp-160) REVERT: C 233 GLN cc_start: 0.8534 (mm-40) cc_final: 0.7441 (tm-30) REVERT: D 16 HIS cc_start: 0.8666 (m90) cc_final: 0.8115 (m90) REVERT: D 120 TYR cc_start: 0.8007 (m-80) cc_final: 0.7498 (m-80) REVERT: E 78 MET cc_start: 0.8397 (mtp) cc_final: 0.8189 (mtp) REVERT: E 84 ASP cc_start: 0.8582 (p0) cc_final: 0.8247 (p0) REVERT: E 132 ARG cc_start: 0.4864 (ttp-170) cc_final: 0.4275 (ttt180) REVERT: F 190 ILE cc_start: 0.9013 (pt) cc_final: 0.8458 (mt) REVERT: G 9 ASP cc_start: 0.7367 (p0) cc_final: 0.6509 (p0) REVERT: G 18 ASP cc_start: 0.9149 (p0) cc_final: 0.8896 (p0) REVERT: G 86 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7461 (ttm-80) REVERT: G 110 PRO cc_start: 0.9234 (Cg_exo) cc_final: 0.9015 (Cg_endo) REVERT: G 212 PHE cc_start: 0.8831 (p90) cc_final: 0.8596 (p90) REVERT: G 225 ASN cc_start: 0.7331 (t0) cc_final: 0.7080 (t0) REVERT: I 193 GLU cc_start: 0.8835 (mp0) cc_final: 0.8415 (mp0) REVERT: I 219 VAL cc_start: 0.8486 (p) cc_final: 0.8161 (m) REVERT: J 222 TYR cc_start: 0.8207 (m-80) cc_final: 0.7942 (m-80) REVERT: J 332 SER cc_start: 0.9049 (p) cc_final: 0.8778 (t) REVERT: K 221 MET cc_start: 0.8262 (ppp) cc_final: 0.7932 (ppp) REVERT: K 222 LEU cc_start: 0.9318 (tt) cc_final: 0.9081 (tp) REVERT: K 292 VAL cc_start: 0.9110 (m) cc_final: 0.8834 (p) REVERT: L 203 ASN cc_start: 0.8865 (p0) cc_final: 0.8309 (p0) REVERT: L 206 ILE cc_start: 0.7800 (mm) cc_final: 0.7051 (mm) REVERT: L 281 ASP cc_start: 0.7482 (p0) cc_final: 0.7189 (p0) REVERT: L 328 ASN cc_start: 0.8813 (m-40) cc_final: 0.8381 (m-40) REVERT: L 354 GLU cc_start: 0.8238 (pp20) cc_final: 0.7815 (pp20) REVERT: L 359 GLU cc_start: 0.9061 (mp0) cc_final: 0.8636 (mp0) REVERT: L 386 PHE cc_start: 0.8029 (m-80) cc_final: 0.7507 (m-80) REVERT: M 215 PRO cc_start: 0.7627 (Cg_endo) cc_final: 0.7275 (Cg_exo) REVERT: M 303 ARG cc_start: 0.8547 (mtt90) cc_final: 0.8062 (ptp-170) REVERT: M 397 GLU cc_start: 0.8887 (mp0) cc_final: 0.8479 (mp0) outliers start: 1 outliers final: 0 residues processed: 492 average time/residue: 0.1641 time to fit residues: 128.0776 Evaluate side-chains 416 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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: 0.0870 chunk 221 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 287 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 300 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 308 optimal weight: 0.0370 chunk 230 optimal weight: 1.9990 chunk 303 optimal weight: 20.0000 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS A 27 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN C 227 GLN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 413 ASN I 190 GLN ** M 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.084130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.071076 restraints weight = 88603.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.073091 restraints weight = 55803.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.074583 restraints weight = 35446.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.074997 restraints weight = 27221.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.075816 restraints weight = 21802.164| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5360 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 : 0.713 12.621 34112 Z= 0.352 Chirality : 0.046 0.169 3976 Planarity : 0.004 0.044 4421 Dihedral : 6.097 86.443 3601 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.08 % Allowed : 1.10 % Favored : 98.82 % 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: -2.29 (0.15), residues: 3288 helix: -0.98 (0.15), residues: 1180 sheet: -1.76 (0.23), residues: 454 loop : -1.82 (0.16), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 169 TYR 0.022 0.001 TYR I 222 PHE 0.035 0.002 PHE D 174 TRP 0.011 0.001 TRP C 160 HIS 0.007 0.001 HIS J 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (25141) covalent geometry : angle 0.71343 / 0.35 (34112) hydrogen bonds : bond 0.03518 / 2.39 ( 698) hydrogen bonds : angle 5.42936 / 3.81 ( 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 496 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 494 time to evaluate : 1.017 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: 0.8443 (p0) cc_final: 0.7468 (t0) REVERT: A 195 ASN cc_start: 0.8668 (m-40) cc_final: 0.8247 (m-40) REVERT: A 231 ASP cc_start: 0.7429 (t70) cc_final: 0.7156 (t70) REVERT: B 4 ARG cc_start: 0.7328 (ttp80) cc_final: 0.6903 (ttp80) REVERT: B 99 ARG cc_start: 0.8343 (mtt90) cc_final: 0.8006 (mtt90) REVERT: B 241 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8312 (tp40) REVERT: C 50 ARG cc_start: 0.6846 (mpp80) cc_final: 0.6476 (mtt180) REVERT: C 114 ARG cc_start: 0.8933 (tpm170) cc_final: 0.8629 (tpp-160) REVERT: C 233 GLN cc_start: 0.8494 (mm-40) cc_final: 0.7339 (tm-30) REVERT: D 16 HIS cc_start: 0.8662 (m90) cc_final: 0.7997 (m90) REVERT: D 120 TYR cc_start: 0.7961 (m-80) cc_final: 0.7499 (m-80) REVERT: E 78 MET cc_start: 0.8313 (mtp) cc_final: 0.8058 (mtp) REVERT: E 84 ASP cc_start: 0.8561 (p0) cc_final: 0.8211 (p0) REVERT: E 132 ARG cc_start: 0.4851 (ttp-170) cc_final: 0.4268 (ttt180) REVERT: E 143 LEU cc_start: 0.8676 (mt) cc_final: 0.8413 (mt) REVERT: E 208 MET cc_start: 0.8055 (mmm) cc_final: 0.7763 (tpp) REVERT: F 190 ILE cc_start: 0.8956 (pt) cc_final: 0.8444 (mt) REVERT: F 213 ILE cc_start: 0.9144 (mp) cc_final: 0.8916 (mm) REVERT: G 18 ASP cc_start: 0.9168 (p0) cc_final: 0.8930 (p0) REVERT: G 86 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7330 (ttm-80) REVERT: G 110 PRO cc_start: 0.9238 (Cg_exo) cc_final: 0.9010 (Cg_endo) REVERT: G 225 ASN cc_start: 0.7253 (t0) cc_final: 0.6997 (t0) REVERT: I 196 GLU cc_start: 0.7525 (pp20) cc_final: 0.6843 (tm-30) REVERT: I 219 VAL cc_start: 0.8602 (p) cc_final: 0.8178 (m) REVERT: I 261 PRO cc_start: 0.8207 (Cg_exo) cc_final: 0.7998 (Cg_endo) REVERT: J 269 GLN cc_start: 0.9023 (tt0) cc_final: 0.8500 (tm-30) REVERT: J 311 ASP cc_start: 0.8765 (p0) cc_final: 0.8231 (m-30) REVERT: J 327 ILE cc_start: 0.9178 (mm) cc_final: 0.8724 (tt) REVERT: J 332 SER cc_start: 0.8988 (p) cc_final: 0.8738 (t) REVERT: K 221 MET cc_start: 0.8235 (ppp) cc_final: 0.7971 (ppp) REVERT: L 203 ASN cc_start: 0.8863 (p0) cc_final: 0.8573 (p0) REVERT: L 281 ASP cc_start: 0.7352 (p0) cc_final: 0.7025 (p0) REVERT: L 328 ASN cc_start: 0.8818 (m-40) cc_final: 0.8401 (m-40) REVERT: L 354 GLU cc_start: 0.8181 (pp20) cc_final: 0.7694 (pp20) REVERT: L 359 GLU cc_start: 0.9062 (mp0) cc_final: 0.8708 (mp0) REVERT: M 215 PRO cc_start: 0.7688 (Cg_endo) cc_final: 0.7375 (Cg_exo) REVERT: M 303 ARG cc_start: 0.8524 (mtt90) cc_final: 0.8062 (ptp-170) REVERT: M 397 GLU cc_start: 0.8911 (mp0) cc_final: 0.8468 (mp0) outliers start: 2 outliers final: 0 residues processed: 495 average time/residue: 0.1621 time to fit residues: 129.2158 Evaluate side-chains 417 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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: 8.9990 chunk 290 optimal weight: 0.9990 chunk 305 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 243 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 299 optimal weight: 0.0020 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS A 27 GLN C 227 GLN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 413 ASN ** 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 = 0.3307 r_free = 0.3307 target = 0.084726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.071491 restraints weight = 88381.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.073453 restraints weight = 56600.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.075198 restraints weight = 36537.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.075724 restraints weight = 27406.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.076505 restraints weight = 20849.077| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25141 Z= 0.122 Angle : 0.700 12.889 34112 Z= 0.346 Chirality : 0.045 0.188 3976 Planarity : 0.004 0.044 4421 Dihedral : 5.906 85.160 3601 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.08 % Allowed : 0.28 % Favored : 99.63 % 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: -0.93 (0.15), residues: 1185 sheet: -1.66 (0.23), residues: 458 loop : -1.70 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 169 TYR 0.028 0.001 TYR A 162 PHE 0.027 0.002 PHE F 147 TRP 0.016 0.001 TRP C 160 HIS 0.032 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (25141) covalent geometry : angle 0.70031 / 0.35 (34112) hydrogen bonds : bond 0.03387 / 2.28 ( 698) hydrogen bonds : angle 5.34597 / 3.75 ( 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 504 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 502 time to evaluate : 1.059 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 49 ASP cc_start: 0.8408 (t0) cc_final: 0.8035 (t0) REVERT: A 89 ASP cc_start: 0.8456 (p0) cc_final: 0.7438 (t0) REVERT: A 169 THR cc_start: 0.8896 (t) cc_final: 0.8570 (m) REVERT: A 175 GLN cc_start: 0.7585 (pm20) cc_final: 0.7312 (pm20) REVERT: A 231 ASP cc_start: 0.7399 (t70) cc_final: 0.7119 (t70) REVERT: B 4 ARG cc_start: 0.7398 (ttp80) cc_final: 0.6992 (ttp80) REVERT: B 99 ARG cc_start: 0.8287 (mtt90) cc_final: 0.7897 (mtt90) REVERT: B 241 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8357 (tp40) REVERT: C 50 ARG cc_start: 0.7119 (mpp80) cc_final: 0.6847 (mpp80) REVERT: C 52 VAL cc_start: 0.8470 (t) cc_final: 0.8149 (p) REVERT: C 114 ARG cc_start: 0.8897 (tpm170) cc_final: 0.8588 (tpp-160) REVERT: C 120 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8484 (tm-30) REVERT: C 233 GLN cc_start: 0.8468 (mm-40) cc_final: 0.7403 (tm-30) REVERT: C 234 GLU cc_start: 0.8185 (pt0) cc_final: 0.7981 (pt0) REVERT: D 120 TYR cc_start: 0.7910 (m-80) cc_final: 0.7511 (m-80) REVERT: E 78 MET cc_start: 0.8242 (mtp) cc_final: 0.7911 (mmm) REVERT: E 84 ASP cc_start: 0.8501 (p0) cc_final: 0.8167 (p0) REVERT: E 132 ARG cc_start: 0.4862 (ttp-170) cc_final: 0.4345 (ttt180) REVERT: E 208 MET cc_start: 0.8084 (mmm) cc_final: 0.7669 (tpp) REVERT: F 23 GLU cc_start: 0.8465 (mp0) cc_final: 0.8252 (mp0) REVERT: F 213 ILE cc_start: 0.9159 (mp) cc_final: 0.8956 (mm) REVERT: G 10 LEU cc_start: 0.8566 (pt) cc_final: 0.7947 (tt) REVERT: G 18 ASP cc_start: 0.9178 (p0) cc_final: 0.8939 (p0) REVERT: G 84 ASP cc_start: 0.8693 (p0) cc_final: 0.8349 (p0) REVERT: G 86 ARG cc_start: 0.7739 (ttm-80) cc_final: 0.7392 (ttm-80) REVERT: G 110 PRO cc_start: 0.9220 (Cg_exo) cc_final: 0.8987 (Cg_endo) REVERT: G 212 PHE cc_start: 0.8917 (p90) cc_final: 0.8351 (p90) REVERT: G 225 ASN cc_start: 0.7217 (t0) cc_final: 0.6963 (t0) REVERT: I 219 VAL cc_start: 0.8651 (p) cc_final: 0.8244 (m) REVERT: J 269 GLN cc_start: 0.9051 (tt0) cc_final: 0.8539 (tm-30) REVERT: J 311 ASP cc_start: 0.8652 (p0) cc_final: 0.8176 (m-30) REVERT: J 327 ILE cc_start: 0.9152 (mm) cc_final: 0.8673 (tt) REVERT: J 332 SER cc_start: 0.8960 (p) cc_final: 0.8701 (t) REVERT: K 221 MET cc_start: 0.8236 (ppp) cc_final: 0.7948 (ppp) REVERT: K 222 LEU cc_start: 0.9317 (tp) cc_final: 0.9089 (tt) REVERT: K 377 SER cc_start: 0.8284 (m) cc_final: 0.8035 (p) REVERT: L 203 ASN cc_start: 0.8858 (p0) cc_final: 0.8263 (p0) REVERT: L 206 ILE cc_start: 0.7819 (mm) cc_final: 0.7014 (mm) REVERT: L 280 MET cc_start: 0.8333 (mmm) cc_final: 0.8105 (mmm) REVERT: L 281 ASP cc_start: 0.7461 (p0) cc_final: 0.7163 (p0) REVERT: L 282 GLU cc_start: 0.7657 (pm20) cc_final: 0.7448 (pm20) REVERT: L 328 ASN cc_start: 0.8850 (m-40) cc_final: 0.8431 (m-40) REVERT: M 215 PRO cc_start: 0.7670 (Cg_endo) cc_final: 0.7345 (Cg_exo) REVERT: M 303 ARG cc_start: 0.8492 (mtt90) cc_final: 0.7937 (ptp-170) REVERT: M 397 GLU cc_start: 0.8952 (mp0) cc_final: 0.8521 (mp0) outliers start: 2 outliers final: 0 residues processed: 503 average time/residue: 0.1575 time to fit residues: 127.8155 Evaluate side-chains 433 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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: 5.9990 chunk 282 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 141 optimal weight: 0.3980 chunk 249 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 19 optimal weight: 0.0870 chunk 156 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 237 optimal weight: 3.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 413 ASN ** M 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.084721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.071408 restraints weight = 87163.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.073145 restraints weight = 54496.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.074376 restraints weight = 38234.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.075275 restraints weight = 29029.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.075882 restraints weight = 23551.040| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25141 Z= 0.120 Angle : 0.703 13.267 34112 Z= 0.346 Chirality : 0.045 0.200 3976 Planarity : 0.004 0.051 4421 Dihedral : 5.828 81.889 3601 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.08 % Allowed : 0.45 % Favored : 99.47 % 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: -2.06 (0.15), residues: 3288 helix: -0.85 (0.15), residues: 1188 sheet: -1.50 (0.23), residues: 464 loop : -1.67 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 169 TYR 0.022 0.001 TYR I 222 PHE 0.028 0.001 PHE F 147 TRP 0.009 0.001 TRP A 199 HIS 0.011 0.001 HIS M 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (25141) covalent geometry : angle 0.70303 / 0.35 (34112) hydrogen bonds : bond 0.03357 / 2.26 ( 698) hydrogen bonds : angle 5.29639 / 3.72 ( 1935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3939.94 seconds wall clock time: 69 minutes 10.63 seconds (4150.63 seconds total)