Starting phenix.real_space_refine on Sun Sep 13 17:05:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ef2_9044/09_2026/6ef2_9044.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ef2_9044/09_2026/6ef2_9044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ef2_9044/09_2026/6ef2_9044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ef2_9044/09_2026/6ef2_9044.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ef2_9044/09_2026/6ef2_9044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ef2_9044/09_2026/6ef2_9044.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ef2_9044/09_2026/6ef2_9044.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ef2_9044/09_2026/6ef2_9044.cif" } resolution = 4.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 89 5.16 5 C 15527 2.51 5 N 4289 2.21 5 O 4738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s 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: 24659 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1835 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1816 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 12, 'TRANS': 236} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 11, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1795 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 235} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1782 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 230} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 62 Chain: "E" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1869 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 242} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1739 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 225} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "G" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1778 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 9, 'TRANS': 236} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "H" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1986 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 13, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "I" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1958 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 249} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 43 Chain: "J" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1976 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 250} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "K" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1956 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 247} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "L" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1860 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 14, 'TRANS': 249} Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 10, 'PHE:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 136 Chain: "M" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2035 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 259} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "s" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 96 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.92, per 1000 atoms: 0.24 Number of scatterers: 24659 At special positions: 0 Unit cell: (136.99, 138.02, 125.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 89 16.00 P 16 15.00 O 4738 8.00 N 4289 7.00 C 15527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.3 seconds 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6070 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 27 sheets defined 42.3% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 Processing helix chain 'A' and resid 86 through 109 removed outlier: 3.632A pdb=" N ALA A 90 " --> pdb=" O PRO A 86 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 128 removed outlier: 3.539A pdb=" N TYR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 188 removed outlier: 3.997A pdb=" N GLU A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 215 removed outlier: 3.563A pdb=" N VAL A 203 " --> pdb=" O TRP A 199 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA A 213 " --> pdb=" O HIS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'B' and resid 20 through 31 removed outlier: 3.949A pdb=" N THR B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 27 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 97 removed outlier: 4.081A pdb=" N VAL B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 107 through 119 removed outlier: 4.475A pdb=" N GLU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 178 Processing helix chain 'B' and resid 185 through 197 removed outlier: 3.518A pdb=" N ILE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 245 removed outlier: 3.738A pdb=" N ASP B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 249 Processing helix chain 'C' and resid 19 through 27 removed outlier: 3.844A pdb=" N GLU C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 81 through 103 removed outlier: 4.436A pdb=" N ILE C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN C 96 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR C 101 " --> pdb=" O ASN C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 117 removed outlier: 3.727A pdb=" N LEU C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.737A pdb=" N THR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N MET C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 207 through 211 removed outlier: 3.583A pdb=" N LEU C 211 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 234 Processing helix chain 'C' and resid 235 through 241 removed outlier: 3.637A pdb=" N LEU C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL C 240 " --> pdb=" O LYS C 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 28 Processing helix chain 'D' and resid 79 through 101 removed outlier: 3.871A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 118 Processing helix chain 'D' and resid 118 through 123 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.608A pdb=" N VAL D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU D 176 " --> pdb=" O ARG D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 196 removed outlier: 3.505A pdb=" N CYS D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 4.144A pdb=" N GLN D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 removed outlier: 3.615A pdb=" N ASN D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 239 removed outlier: 3.688A pdb=" N ILE D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 32 removed outlier: 3.633A pdb=" N LEU E 28 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA E 30 " --> pdb=" O TYR E 26 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS E 32 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 removed outlier: 3.600A pdb=" N ILE E 64 " --> pdb=" O SER E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 removed outlier: 3.770A pdb=" N ALA E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARG E 86 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N HIS E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 103 removed outlier: 3.620A pdb=" N THR E 98 " --> pdb=" O THR E 94 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN E 100 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 121 removed outlier: 3.546A pdb=" N LEU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU E 121 " --> pdb=" O CYS E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 124 No H-bonds generated for 'chain 'E' and resid 122 through 124' Processing helix chain 'E' and resid 178 through 183 removed outlier: 3.598A pdb=" N GLU E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 186 No H-bonds generated for 'chain 'E' and resid 184 through 186' Processing helix chain 'E' and resid 196 through 207 removed outlier: 3.535A pdb=" N LEU E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 248 removed outlier: 3.639A pdb=" N LEU E 239 " --> pdb=" O LYS E 235 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE E 240 " --> pdb=" O THR E 236 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS E 244 " --> pdb=" O ILE E 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 26 Processing helix chain 'F' and resid 27 through 32 removed outlier: 3.761A pdb=" N LYS F 30 " --> pdb=" O GLU F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.903A pdb=" N VAL F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 122 removed outlier: 3.613A pdb=" N ALA F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY F 109 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP F 114 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 176 removed outlier: 3.742A pdb=" N THR F 170 " --> pdb=" O GLN F 166 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N TYR F 171 " --> pdb=" O GLY F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 198 removed outlier: 3.979A pdb=" N LEU F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 211 removed outlier: 3.744A pdb=" N LEU F 211 " --> pdb=" O VAL F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 230 removed outlier: 4.145A pdb=" N ALA F 229 " --> pdb=" O ASP F 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.573A pdb=" N GLU G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU G 32 " --> pdb=" O VAL G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 97 removed outlier: 3.843A pdb=" N VAL G 89 " --> pdb=" O GLY G 85 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG G 91 " --> pdb=" O HIS G 87 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA G 97 " --> pdb=" O ARG G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 104 Processing helix chain 'G' and resid 108 through 123 removed outlier: 4.708A pdb=" N GLN G 121 " --> pdb=" O GLY G 117 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 176 removed outlier: 3.679A pdb=" N ALA G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 183 removed outlier: 3.785A pdb=" N VAL G 180 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 205 removed outlier: 3.938A pdb=" N LYS G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA G 197 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LYS G 198 " --> pdb=" O LYS G 194 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE G 199 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU G 205 " --> pdb=" O TYR G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'G' and resid 235 through 240 Processing helix chain 'G' and resid 240 through 248 removed outlier: 4.409A pdb=" N GLU G 246 " --> pdb=" O PHE G 242 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN G 248 " --> pdb=" O GLN G 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 199 Processing helix chain 'H' and resid 216 through 225 removed outlier: 3.637A pdb=" N LEU H 221 " --> pdb=" O GLN H 217 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU H 223 " --> pdb=" O GLU H 219 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL H 224 " --> pdb=" O LYS H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 231 removed outlier: 3.545A pdb=" N LEU H 229 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 239 removed outlier: 3.775A pdb=" N LEU H 238 " --> pdb=" O ARG H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 268 removed outlier: 4.314A pdb=" N ALA H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG H 266 " --> pdb=" O ALA H 262 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP H 268 " --> pdb=" O ALA H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 301 removed outlier: 4.289A pdb=" N VAL H 291 " --> pdb=" O GLY H 287 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG H 292 " --> pdb=" O ALA H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 341 removed outlier: 3.903A pdb=" N THR H 332 " --> pdb=" O GLU H 328 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU H 335 " --> pdb=" O ARG H 331 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU H 336 " --> pdb=" O THR H 332 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE H 337 " --> pdb=" O MET H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 361 removed outlier: 3.880A pdb=" N THR H 360 " --> pdb=" O ARG H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 386 Processing helix chain 'H' and resid 388 through 393 removed outlier: 3.759A pdb=" N HIS H 392 " --> pdb=" O ILE H 388 " (cutoff:3.500A) Processing helix chain 'H' and resid 403 through 411 removed outlier: 3.904A pdb=" N ILE H 407 " --> pdb=" O ARG H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 433 removed outlier: 3.523A pdb=" N SER H 421 " --> pdb=" O ALA H 417 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL H 422 " --> pdb=" O GLU H 418 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N CYS H 423 " --> pdb=" O LEU H 419 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA H 430 " --> pdb=" O ALA H 426 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE H 431 " --> pdb=" O GLY H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 452 removed outlier: 3.543A pdb=" N LEU H 444 " --> pdb=" O GLU H 440 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS H 445 " --> pdb=" O LYS H 441 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS H 449 " --> pdb=" O LYS H 445 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL H 450 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE H 451 " --> pdb=" O VAL H 447 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER H 452 " --> pdb=" O ASP H 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 198 removed outlier: 3.513A pdb=" N LYS I 195 " --> pdb=" O ILE I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 212 removed outlier: 3.604A pdb=" N MET I 211 " --> pdb=" O LEU I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 239 removed outlier: 3.560A pdb=" N ASN I 238 " --> pdb=" O LYS I 234 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN I 239 " --> pdb=" O ALA I 235 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 274 removed outlier: 3.561A pdb=" N CYS I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG I 265 " --> pdb=" O PRO I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 Processing helix chain 'I' and resid 299 through 314 removed outlier: 3.907A pdb=" N GLN I 303 " --> pdb=" O GLU I 299 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR I 305 " --> pdb=" O GLU I 301 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU I 309 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU I 310 " --> pdb=" O MET I 306 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 366 removed outlier: 3.735A pdb=" N LYS I 359 " --> pdb=" O LEU I 355 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS I 360 " --> pdb=" O SER I 356 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY I 363 " --> pdb=" O LYS I 359 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS I 365 " --> pdb=" O ILE I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 376 through 381 removed outlier: 3.538A pdb=" N LEU I 380 " --> pdb=" O ASN I 376 " (cutoff:3.500A) Processing helix chain 'I' and resid 390 through 405 removed outlier: 3.958A pdb=" N ALA I 394 " --> pdb=" O ALA I 390 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY I 400 " --> pdb=" O CYS I 396 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU I 401 " --> pdb=" O THR I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 412 through 424 removed outlier: 4.260A pdb=" N PHE I 416 " --> pdb=" O THR I 412 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA I 419 " --> pdb=" O ASP I 415 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET I 424 " --> pdb=" O LYS I 420 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 161 removed outlier: 3.814A pdb=" N LYS J 161 " --> pdb=" O ILE J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 170 removed outlier: 3.781A pdb=" N VAL J 168 " --> pdb=" O ILE J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 177 Processing helix chain 'J' and resid 194 through 205 removed outlier: 3.614A pdb=" N ALA J 199 " --> pdb=" O LYS J 195 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA J 203 " --> pdb=" O ALA J 199 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS J 204 " --> pdb=" O ARG J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 239 removed outlier: 3.865A pdb=" N LEU J 233 " --> pdb=" O MET J 229 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL J 235 " --> pdb=" O ARG J 231 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET J 236 " --> pdb=" O GLU J 232 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU J 239 " --> pdb=" O VAL J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 276 removed outlier: 4.009A pdb=" N ARG J 270 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU J 274 " --> pdb=" O ARG J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 285 removed outlier: 3.664A pdb=" N GLU J 283 " --> pdb=" O LEU J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 306 removed outlier: 4.547A pdb=" N LEU J 305 " --> pdb=" O ASP J 301 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 through 331 removed outlier: 3.579A pdb=" N ILE J 327 " --> pdb=" O ALA J 323 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU J 328 " --> pdb=" O ARG J 324 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG J 329 " --> pdb=" O ALA J 325 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 348 Processing helix chain 'J' and resid 355 through 371 removed outlier: 3.681A pdb=" N LYS J 359 " --> pdb=" O GLY J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 390 removed outlier: 3.789A pdb=" N GLU J 383 " --> pdb=" O GLN J 379 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET J 390 " --> pdb=" O VAL J 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 395 Processing helix chain 'K' and resid 179 through 188 removed outlier: 4.111A pdb=" N GLU K 183 " --> pdb=" O MET K 179 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE K 184 " --> pdb=" O GLN K 180 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG K 185 " --> pdb=" O LYS K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 194 removed outlier: 4.389A pdb=" N LEU K 192 " --> pdb=" O VAL K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 202 Processing helix chain 'K' and resid 219 through 229 removed outlier: 3.997A pdb=" N VAL K 223 " --> pdb=" O LYS K 219 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS K 224 " --> pdb=" O THR K 220 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 242 Processing helix chain 'K' and resid 248 through 264 removed outlier: 3.857A pdb=" N ARG K 252 " --> pdb=" O GLY K 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 304 removed outlier: 4.055A pdb=" N GLN K 293 " --> pdb=" O ASP K 289 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG K 294 " --> pdb=" O ARG K 290 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU K 299 " --> pdb=" O ILE K 295 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN K 302 " --> pdb=" O GLU K 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 359 removed outlier: 3.762A pdb=" N ARG K 349 " --> pdb=" O ASP K 345 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY K 354 " --> pdb=" O ARG K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 396 removed outlier: 3.860A pdb=" N ALA K 384 " --> pdb=" O GLY K 380 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA K 394 " --> pdb=" O ALA K 390 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL K 395 " --> pdb=" O GLY K 391 " (cutoff:3.500A) Processing helix chain 'K' and resid 407 through 414 removed outlier: 3.553A pdb=" N TYR K 411 " --> pdb=" O LEU K 407 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA K 412 " --> pdb=" O GLU K 408 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 424 Processing helix chain 'L' and resid 171 through 175 removed outlier: 3.714A pdb=" N GLU L 174 " --> pdb=" O THR L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 197 removed outlier: 3.680A pdb=" N GLU L 195 " --> pdb=" O ARG L 191 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL L 196 " --> pdb=" O GLU L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 203 removed outlier: 3.521A pdb=" N LEU L 201 " --> pdb=" O ILE L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 211 Processing helix chain 'L' and resid 229 through 240 removed outlier: 3.555A pdb=" N LYS L 233 " --> pdb=" O THR L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 251 Processing helix chain 'L' and resid 259 through 273 removed outlier: 3.889A pdb=" N ILE L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 286 Processing helix chain 'L' and resid 294 through 313 removed outlier: 4.580A pdb=" N GLU L 300 " --> pdb=" O SER L 296 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN L 302 " --> pdb=" O ASP L 298 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG L 303 " --> pdb=" O ARG L 299 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP L 313 " --> pdb=" O LEU L 309 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 365 removed outlier: 4.539A pdb=" N LEU L 358 " --> pdb=" O GLU L 354 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU L 359 " --> pdb=" O ALA L 355 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE L 363 " --> pdb=" O GLU L 359 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS L 364 " --> pdb=" O ILE L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 383 Processing helix chain 'L' and resid 387 through 403 removed outlier: 3.717A pdb=" N ILE L 391 " --> pdb=" O ASN L 387 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA L 402 " --> pdb=" O ALA L 398 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE L 403 " --> pdb=" O GLY L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 423 removed outlier: 4.048A pdb=" N LEU L 415 " --> pdb=" O ASN L 411 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG L 420 " --> pdb=" O MET L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 424 through 429 Processing helix chain 'M' and resid 186 through 198 removed outlier: 4.190A pdb=" N ILE M 190 " --> pdb=" O LEU M 186 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU M 191 " --> pdb=" O ASP M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 198 through 203 Processing helix chain 'M' and resid 205 through 210 Processing helix chain 'M' and resid 227 through 240 removed outlier: 3.676A pdb=" N LEU M 231 " --> pdb=" O GLY M 227 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA M 232 " --> pdb=" O LYS M 228 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG M 233 " --> pdb=" O THR M 229 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 253 Processing helix chain 'M' and resid 258 through 272 removed outlier: 3.657A pdb=" N VAL M 263 " --> pdb=" O GLY M 259 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE M 267 " --> pdb=" O VAL M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 311 removed outlier: 3.612A pdb=" N GLN M 302 " --> pdb=" O ASP M 298 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR M 304 " --> pdb=" O GLU M 300 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 364 removed outlier: 4.469A pdb=" N GLN M 359 " --> pdb=" O ASP M 355 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE M 360 " --> pdb=" O SER M 356 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS M 364 " --> pdb=" O ILE M 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 382 removed outlier: 4.622A pdb=" N LEU M 379 " --> pdb=" O ASN M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 387 through 406 removed outlier: 3.918A pdb=" N ALA M 393 " --> pdb=" O ALA M 389 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL M 394 " --> pdb=" O GLN M 390 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY M 399 " --> pdb=" O THR M 395 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU M 403 " --> pdb=" O GLY M 399 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG M 404 " --> pdb=" O MET M 400 " (cutoff:3.500A) Processing helix chain 'M' and resid 411 through 423 removed outlier: 3.588A pdb=" N PHE M 415 " --> pdb=" O LYS M 411 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN M 423 " --> pdb=" O ILE M 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 46 removed outlier: 3.715A pdb=" N LEU A 43 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 225 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 236 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR A 229 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 232 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 82 removed outlier: 3.602A pdb=" N SER A 145 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 153 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.538A pdb=" N SER B 65 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 73 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 138 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU B 147 " --> pdb=" O TRP B 159 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 149 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.577A pdb=" N ALA C 214 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 74 through 76 removed outlier: 3.707A pdb=" N GLY C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 161 through 162 removed outlier: 3.703A pdb=" N GLN D 162 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL D 42 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 222 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 71 through 77 removed outlier: 3.678A pdb=" N ALA D 136 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 137 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS D 146 " --> pdb=" O GLY D 137 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 151 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 169 through 171 removed outlier: 3.506A pdb=" N VAL E 46 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER E 220 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS E 229 " --> pdb=" O CYS E 221 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR E 223 " --> pdb=" O GLY E 227 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 74 through 75 Processing sheet with id=AB2, first strand: chain 'E' and resid 157 through 158 Processing sheet with id=AB3, first strand: chain 'F' and resid 159 through 161 removed outlier: 3.771A pdb=" N VAL F 45 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA F 44 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR F 223 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLY F 217 " --> pdb=" O PRO F 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.837A pdb=" N ILE F 63 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU F 74 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LYS F 65 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU F 72 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET F 70 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY F 71 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE F 135 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY F 131 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY F 136 " --> pdb=" O HIS F 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 38 through 40 removed outlier: 3.589A pdb=" N GLY G 39 " --> pdb=" O ALA G 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 46 through 48 removed outlier: 3.658A pdb=" N LYS G 229 " --> pdb=" O TRP G 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 51 through 53 removed outlier: 3.580A pdb=" N LYS G 52 " --> pdb=" O GLU G 213 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 67 through 70 removed outlier: 3.686A pdb=" N ILE G 74 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER G 79 " --> pdb=" O SER G 135 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER G 135 " --> pdb=" O SER G 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 67 through 70 removed outlier: 3.686A pdb=" N ILE G 74 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER G 79 " --> pdb=" O SER G 135 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER G 135 " --> pdb=" O SER G 79 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE G 138 " --> pdb=" O TYR G 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 247 through 249 Processing sheet with id=AC2, first strand: chain 'H' and resid 270 through 274 Processing sheet with id=AC3, first strand: chain 'I' and resid 326 through 327 removed outlier: 6.523A pdb=" N VAL I 219 " --> pdb=" O MET I 326 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE I 220 " --> pdb=" O ILE I 348 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'I' and resid 277 through 279 Processing sheet with id=AC5, first strand: chain 'J' and resid 209 through 213 removed outlier: 5.818A pdb=" N LYS J 209 " --> pdb=" O ILE J 244 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N PHE J 246 " --> pdb=" O LYS J 209 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE J 211 " --> pdb=" O PHE J 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 269 through 270 removed outlier: 6.541A pdb=" N ILE K 269 " --> pdb=" O ILE K 315 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY K 208 " --> pdb=" O ARG K 336 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE K 338 " --> pdb=" O GLY K 208 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU K 210 " --> pdb=" O ILE K 338 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 325 through 326 removed outlier: 7.185A pdb=" N LEU L 219 " --> pdb=" O VAL L 347 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 276 through 277 removed outlier: 6.583A pdb=" N CYS L 276 " --> pdb=" O LYS L 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'M' and resid 276 through 280 removed outlier: 3.849A pdb=" N ALA M 326 " --> pdb=" O ILE M 280 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA M 325 " --> pdb=" O ALA M 218 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR M 327 " --> pdb=" O MET M 220 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N ILE M 347 " --> pdb=" O GLY M 217 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU M 219 " --> pdb=" O ILE M 347 " (cutoff:3.500A) 814 hydrogen bonds defined for protein. 2271 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.21 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8107 1.34 - 1.45: 4149 1.45 - 1.57: 12627 1.57 - 1.69: 27 1.69 - 1.81: 149 Bond restraints: 25059 Sorted by residual: bond pdb=" C4 ATP M 501 " pdb=" C5 ATP M 501 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.27e+01 bond pdb=" C4 ATP H 501 " pdb=" C5 ATP H 501 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C4 ATP I 501 " pdb=" C5 ATP I 501 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.41e+01 bond pdb=" C4 ATP J 501 " pdb=" C5 ATP J 501 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.35e+01 bond pdb=" C5 ATP J 501 " pdb=" N7 ATP J 501 " ideal model delta sigma weight residual 1.387 1.330 0.057 1.00e-02 1.00e+04 3.29e+01 ... (remaining 25054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.98: 33888 4.98 - 9.96: 129 9.96 - 14.94: 0 14.94 - 19.93: 1 19.93 - 24.91: 7 Bond angle restraints: 34025 Sorted by residual: angle pdb=" PB ATP H 501 " pdb=" O3B ATP H 501 " pdb=" PG ATP H 501 " ideal model delta sigma weight residual 139.87 114.96 24.91 1.00e+00 1.00e+00 6.20e+02 angle pdb=" PB ATP M 501 " pdb=" O3B ATP M 501 " pdb=" PG ATP M 501 " ideal model delta sigma weight residual 139.87 116.27 23.60 1.00e+00 1.00e+00 5.57e+02 angle pdb=" PA ATP M 501 " pdb=" O3A ATP M 501 " pdb=" PB ATP M 501 " ideal model delta sigma weight residual 136.83 113.84 22.99 1.00e+00 1.00e+00 5.28e+02 angle pdb=" PB ATP J 501 " pdb=" O3B ATP J 501 " pdb=" PG ATP J 501 " ideal model delta sigma weight residual 139.87 118.59 21.28 1.00e+00 1.00e+00 4.53e+02 angle pdb=" PA ATP J 501 " pdb=" O3A ATP J 501 " pdb=" PB ATP J 501 " ideal model delta sigma weight residual 136.83 115.58 21.25 1.00e+00 1.00e+00 4.52e+02 ... (remaining 34020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 14264 18.09 - 36.18: 733 36.18 - 54.26: 69 54.26 - 72.35: 22 72.35 - 90.44: 10 Dihedral angle restraints: 15098 sinusoidal: 5645 harmonic: 9453 Sorted by residual: dihedral pdb=" CA PHE B 157 " pdb=" C PHE B 157 " pdb=" N PRO B 158 " pdb=" CA PRO B 158 " ideal model delta harmonic sigma weight residual 180.00 146.90 33.10 0 5.00e+00 4.00e-02 4.38e+01 dihedral pdb=" CA VAL K 401 " pdb=" C VAL K 401 " pdb=" N ILE K 402 " pdb=" CA ILE K 402 " ideal model delta harmonic sigma weight residual -180.00 -149.20 -30.80 0 5.00e+00 4.00e-02 3.79e+01 dihedral pdb=" CA PHE M 207 " pdb=" C PHE M 207 " pdb=" N LYS M 208 " pdb=" CA LYS M 208 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 15095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2169 0.041 - 0.082: 1238 0.082 - 0.123: 441 0.123 - 0.164: 117 0.164 - 0.205: 12 Chirality restraints: 3977 Sorted by residual: chirality pdb=" CB ILE K 277 " pdb=" CA ILE K 277 " pdb=" CG1 ILE K 277 " pdb=" CG2 ILE K 277 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL J 268 " pdb=" CA VAL J 268 " pdb=" CG1 VAL J 268 " pdb=" CG2 VAL J 268 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE G 40 " pdb=" CA ILE G 40 " pdb=" CG1 ILE G 40 " pdb=" CG2 ILE G 40 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 3974 not shown) Planarity restraints: 4395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 157 " -0.051 5.00e-02 4.00e+02 7.61e-02 9.26e+00 pdb=" N PRO B 158 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 158 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 158 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 14 " 0.048 5.00e-02 4.00e+02 7.37e-02 8.69e+00 pdb=" N PRO F 15 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 15 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 15 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 106 " 0.041 5.00e-02 4.00e+02 6.07e-02 5.90e+00 pdb=" N PRO C 107 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 107 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 107 " 0.034 5.00e-02 4.00e+02 ... (remaining 4392 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1025 2.69 - 3.24: 27127 3.24 - 3.80: 36325 3.80 - 4.35: 47267 4.35 - 4.90: 75630 Nonbonded interactions: 187374 Sorted by model distance: nonbonded pdb=" OD2 ASP K 304 " pdb=" NH2 ARG K 330 " model vdw 2.139 3.120 nonbonded pdb=" OG SER D 153 " pdb=" OE1 GLN H 465 " model vdw 2.141 3.040 nonbonded pdb=" O ASP C 42 " pdb=" OH TYR C 146 " model vdw 2.150 3.040 nonbonded pdb=" O ILE J 330 " pdb=" NH1 ARG J 333 " model vdw 2.150 3.120 nonbonded pdb=" NH1 ARG H 385 " pdb=" O CYS H 411 " model vdw 2.153 3.120 ... (remaining 187369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.950 Find NCS groups from input model: 0.480 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.098 25059 Z= 0.483 Angle : 1.024 24.907 34025 Z= 0.627 Chirality : 0.056 0.205 3977 Planarity : 0.006 0.076 4395 Dihedral : 11.426 90.439 9028 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 13.44 % Favored : 86.53 % Rotamer: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.32 (0.12), residues: 3260 helix: -3.88 (0.09), residues: 1150 sheet: -3.82 (0.19), residues: 476 loop : -3.12 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG F 126 TYR 0.034 0.003 TYR E 26 PHE 0.031 0.003 PHE J 382 TRP 0.017 0.003 TRP H 404 HIS 0.013 0.003 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.01108 / 0.48 (25059) covalent geometry : angle 1.02423 / 0.63 (34025) hydrogen bonds : bond 0.32090 / 21.46 ( 807) hydrogen bonds : angle 11.41555 / 7.95 ( 2271) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 633 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 THR cc_start: 0.7838 (p) cc_final: 0.7585 (p) REVERT: B 57 MET cc_start: 0.7779 (mpp) cc_final: 0.7270 (mtm) REVERT: B 123 GLN cc_start: 0.6943 (pt0) cc_final: 0.6715 (pt0) REVERT: B 186 GLU cc_start: 0.8220 (tp30) cc_final: 0.7414 (tp30) REVERT: B 194 LEU cc_start: 0.9159 (pp) cc_final: 0.8750 (pp) REVERT: B 245 ASP cc_start: 0.8009 (p0) cc_final: 0.7686 (p0) REVERT: C 26 LEU cc_start: 0.9129 (mp) cc_final: 0.8927 (mp) REVERT: C 51 LYS cc_start: 0.8148 (tptm) cc_final: 0.7912 (tttm) REVERT: C 89 ASN cc_start: 0.7848 (m110) cc_final: 0.7623 (t0) REVERT: C 160 TRP cc_start: 0.7714 (m100) cc_final: 0.7101 (m100) REVERT: C 173 GLN cc_start: 0.8192 (mm110) cc_final: 0.7910 (mm-40) REVERT: C 194 LEU cc_start: 0.8835 (tp) cc_final: 0.8485 (tt) REVERT: C 213 PHE cc_start: 0.8838 (m-80) cc_final: 0.8633 (m-80) REVERT: D 5 ASP cc_start: 0.7837 (p0) cc_final: 0.7446 (p0) REVERT: D 22 TYR cc_start: 0.7749 (m-10) cc_final: 0.7494 (m-10) REVERT: D 102 ASP cc_start: 0.8397 (t0) cc_final: 0.8128 (t0) REVERT: E 59 LEU cc_start: 0.7876 (tt) cc_final: 0.7632 (tt) REVERT: E 122 ARG cc_start: 0.9050 (tpp80) cc_final: 0.8799 (tpp80) REVERT: E 213 ASP cc_start: 0.8420 (t70) cc_final: 0.8083 (t70) REVERT: E 221 CYS cc_start: 0.7290 (p) cc_final: 0.6904 (p) REVERT: E 232 ASP cc_start: 0.8417 (t70) cc_final: 0.7976 (p0) REVERT: F 31 GLN cc_start: 0.8774 (pt0) cc_final: 0.8566 (tt0) REVERT: F 80 ASP cc_start: 0.7839 (t70) cc_final: 0.7627 (t0) REVERT: F 145 LEU cc_start: 0.8350 (mp) cc_final: 0.8043 (mt) REVERT: G 9 ASP cc_start: 0.8186 (m-30) cc_final: 0.7580 (m-30) REVERT: G 26 TYR cc_start: 0.8062 (m-80) cc_final: 0.7587 (m-80) REVERT: G 177 GLU cc_start: 0.7599 (tp30) cc_final: 0.7337 (tp30) REVERT: G 238 GLU cc_start: 0.8407 (pp20) cc_final: 0.7973 (pp20) REVERT: H 314 VAL cc_start: 0.9141 (m) cc_final: 0.8800 (p) REVERT: I 259 ASP cc_start: 0.7695 (p0) cc_final: 0.7274 (p0) REVERT: I 265 ARG cc_start: 0.8528 (mtm110) cc_final: 0.8111 (ttp-110) REVERT: I 306 MET cc_start: 0.8589 (ttp) cc_final: 0.8320 (ttt) REVERT: I 329 ASN cc_start: 0.8232 (m-40) cc_final: 0.7987 (m-40) REVERT: J 243 SER cc_start: 0.9037 (t) cc_final: 0.8711 (m) REVERT: J 274 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7696 (tm-30) REVERT: J 404 PHE cc_start: 0.8184 (p90) cc_final: 0.7645 (p90) REVERT: K 224 LYS cc_start: 0.9044 (mtmt) cc_final: 0.7966 (tptt) REVERT: L 307 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7413 (tm-30) REVERT: M 307 GLU cc_start: 0.8533 (tt0) cc_final: 0.7896 (tp30) REVERT: M 390 GLN cc_start: 0.8717 (mp10) cc_final: 0.8308 (mp10) REVERT: s 125 ILE cc_start: 0.9319 (mm) cc_final: 0.9040 (mm) REVERT: s 127 VAL cc_start: 0.9050 (p) cc_final: 0.8792 (m) outliers start: 0 outliers final: 0 residues processed: 633 average time/residue: 0.1992 time to fit residues: 188.0519 Evaluate side-chains 390 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0170 chunk 298 optimal weight: 0.0020 overall best weight: 0.5428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 ASN A 92 ASN A 175 GLN C 124 GLN D 118 GLN F 21 GLN F 119 ASN G 33 ASN G 68 GLN G 118 GLN H 356 ASN I 238 ASN I 418 GLN J 295 ASN J 391 ASN ** K 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.087148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.076676 restraints weight = 68454.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.078076 restraints weight = 42044.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.078764 restraints weight = 28994.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.079151 restraints weight = 21283.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.079259 restraints weight = 20302.070| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25059 Z= 0.142 Angle : 0.710 10.253 34025 Z= 0.362 Chirality : 0.047 0.180 3977 Planarity : 0.005 0.048 4395 Dihedral : 6.932 66.849 3592 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.04 % Allowed : 4.25 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.11 (0.13), residues: 3260 helix: -2.56 (0.12), residues: 1234 sheet: -2.98 (0.20), residues: 476 loop : -2.70 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 333 TYR 0.023 0.001 TYR B 82 PHE 0.018 0.002 PHE B 204 TRP 0.031 0.003 TRP M 376 HIS 0.012 0.001 HIS F 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (25059) covalent geometry : angle 0.70974 / 0.36 (34025) hydrogen bonds : bond 0.04968 / 3.35 ( 807) hydrogen bonds : angle 6.23307 / 4.30 ( 2271) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 557 time to evaluate : 0.985 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: A 49 ASP cc_start: 0.8089 (p0) cc_final: 0.7750 (p0) REVERT: B 4 ARG cc_start: 0.7645 (ttt90) cc_final: 0.6795 (ttm110) REVERT: B 148 TYR cc_start: 0.8523 (m-80) cc_final: 0.8148 (m-10) REVERT: C 68 LYS cc_start: 0.8862 (tttt) cc_final: 0.8614 (tttm) REVERT: C 114 ARG cc_start: 0.7941 (tmt-80) cc_final: 0.7731 (tmt-80) REVERT: C 160 TRP cc_start: 0.8027 (m100) cc_final: 0.7554 (m100) REVERT: C 173 GLN cc_start: 0.8414 (mm110) cc_final: 0.8031 (mm-40) REVERT: D 5 ASP cc_start: 0.7463 (p0) cc_final: 0.7034 (p0) REVERT: D 22 TYR cc_start: 0.7926 (m-10) cc_final: 0.7598 (m-80) REVERT: D 102 ASP cc_start: 0.8416 (t0) cc_final: 0.8115 (t0) REVERT: D 139 ASP cc_start: 0.8439 (t0) cc_final: 0.8231 (t0) REVERT: D 175 LEU cc_start: 0.8150 (mp) cc_final: 0.7871 (mt) REVERT: E 122 ARG cc_start: 0.8863 (tpp80) cc_final: 0.8531 (tpt170) REVERT: E 151 ASP cc_start: 0.7395 (p0) cc_final: 0.6683 (t0) REVERT: E 213 ASP cc_start: 0.7959 (t70) cc_final: 0.7617 (t70) REVERT: E 221 CYS cc_start: 0.7384 (p) cc_final: 0.7152 (p) REVERT: F 27 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7366 (mt-10) REVERT: F 31 GLN cc_start: 0.8965 (pt0) cc_final: 0.8476 (tt0) REVERT: F 42 THR cc_start: 0.8395 (p) cc_final: 0.8115 (p) REVERT: F 114 ASP cc_start: 0.7799 (m-30) cc_final: 0.7588 (m-30) REVERT: F 118 LYS cc_start: 0.8575 (ptmt) cc_final: 0.8270 (ptpp) REVERT: F 138 ASP cc_start: 0.8377 (p0) cc_final: 0.7976 (p0) REVERT: F 152 ASN cc_start: 0.8604 (m110) cc_final: 0.8321 (m-40) REVERT: G 9 ASP cc_start: 0.8219 (m-30) cc_final: 0.7519 (m-30) REVERT: G 26 TYR cc_start: 0.7970 (m-80) cc_final: 0.7751 (m-80) REVERT: G 238 GLU cc_start: 0.8219 (pp20) cc_final: 0.7981 (pp20) REVERT: H 320 ASP cc_start: 0.6850 (p0) cc_final: 0.6364 (p0) REVERT: I 246 ARG cc_start: 0.4511 (pmt-80) cc_final: 0.3046 (mtt90) REVERT: I 259 ASP cc_start: 0.7525 (p0) cc_final: 0.7083 (p0) REVERT: I 306 MET cc_start: 0.8603 (ttp) cc_final: 0.8310 (ttt) REVERT: I 406 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6896 (tm-30) REVERT: J 148 ASP cc_start: 0.8310 (p0) cc_final: 0.8081 (p0) REVERT: J 243 SER cc_start: 0.9243 (t) cc_final: 0.8774 (m) REVERT: J 274 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8131 (tm-30) REVERT: J 351 ASN cc_start: 0.5419 (p0) cc_final: 0.5128 (p0) REVERT: J 370 LEU cc_start: 0.9029 (tt) cc_final: 0.8584 (tt) REVERT: K 224 LYS cc_start: 0.9025 (mtmt) cc_final: 0.8100 (tptt) REVERT: L 189 GLN cc_start: 0.7652 (mp10) cc_final: 0.7230 (mm-40) REVERT: L 269 TYR cc_start: 0.7948 (t80) cc_final: 0.7714 (t80) REVERT: L 271 LYS cc_start: 0.8790 (mtpp) cc_final: 0.8459 (mtpp) REVERT: M 307 GLU cc_start: 0.8196 (tt0) cc_final: 0.7802 (tp30) REVERT: s 127 VAL cc_start: 0.9011 (p) cc_final: 0.8720 (m) outliers start: 1 outliers final: 0 residues processed: 557 average time/residue: 0.1695 time to fit residues: 147.1732 Evaluate side-chains 369 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 268 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 221 optimal weight: 0.9980 chunk 172 optimal weight: 0.7980 chunk 254 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 ASN F 143 HIS G 121 GLN G 127 ASN J 269 GLN J 295 ASN K 285 GLN ** K 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 364 HIS M 412 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.082988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.072116 restraints weight = 69033.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.073275 restraints weight = 44842.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.073957 restraints weight = 31585.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.074517 restraints weight = 23905.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.075331 restraints weight = 21267.218| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25059 Z= 0.151 Angle : 0.664 9.896 34025 Z= 0.339 Chirality : 0.046 0.170 3977 Planarity : 0.005 0.055 4395 Dihedral : 6.423 68.091 3592 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.04 % Allowed : 5.22 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.13), residues: 3260 helix: -1.93 (0.13), residues: 1243 sheet: -2.46 (0.21), residues: 486 loop : -2.42 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 342 TYR 0.028 0.001 TYR E 26 PHE 0.016 0.002 PHE I 268 TRP 0.044 0.002 TRP M 376 HIS 0.007 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (25059) covalent geometry : angle 0.66388 / 0.34 (34025) hydrogen bonds : bond 0.04111 / 2.73 ( 807) hydrogen bonds : angle 5.33571 / 3.67 ( 2271) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 500 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8067 (p0) cc_final: 0.7785 (p0) REVERT: A 78 THR cc_start: 0.7796 (p) cc_final: 0.7567 (p) REVERT: A 81 MET cc_start: 0.8724 (ttp) cc_final: 0.8478 (ttp) REVERT: A 210 MET cc_start: 0.7828 (ptm) cc_final: 0.7485 (ttm) REVERT: B 57 MET cc_start: 0.7875 (mpp) cc_final: 0.7229 (mtm) REVERT: C 68 LYS cc_start: 0.8911 (tttt) cc_final: 0.8591 (tttm) REVERT: C 160 TRP cc_start: 0.7991 (m100) cc_final: 0.7620 (m100) REVERT: C 173 GLN cc_start: 0.8523 (mm110) cc_final: 0.8180 (mm-40) REVERT: D 5 ASP cc_start: 0.7569 (p0) cc_final: 0.7117 (p0) REVERT: D 22 TYR cc_start: 0.8261 (m-10) cc_final: 0.7982 (m-10) REVERT: D 139 ASP cc_start: 0.8539 (t0) cc_final: 0.8168 (t0) REVERT: D 175 LEU cc_start: 0.8294 (mp) cc_final: 0.8026 (mt) REVERT: E 134 MET cc_start: 0.8493 (mtp) cc_final: 0.7791 (mtm) REVERT: E 151 ASP cc_start: 0.7440 (p0) cc_final: 0.6647 (t0) REVERT: E 182 GLU cc_start: 0.8600 (pp20) cc_final: 0.8340 (pp20) REVERT: F 31 GLN cc_start: 0.9027 (pt0) cc_final: 0.8741 (pt0) REVERT: F 226 ASP cc_start: 0.7429 (p0) cc_final: 0.7115 (p0) REVERT: G 26 TYR cc_start: 0.8261 (m-80) cc_final: 0.8038 (m-80) REVERT: G 218 TRP cc_start: 0.8286 (p-90) cc_final: 0.7478 (p-90) REVERT: G 238 GLU cc_start: 0.8300 (pp20) cc_final: 0.8051 (pp20) REVERT: H 333 MET cc_start: 0.8537 (ttt) cc_final: 0.8230 (ttt) REVERT: I 259 ASP cc_start: 0.7371 (p0) cc_final: 0.6924 (p0) REVERT: I 306 MET cc_start: 0.8623 (ttp) cc_final: 0.8289 (ttt) REVERT: I 329 ASN cc_start: 0.7957 (m-40) cc_final: 0.7694 (m-40) REVERT: J 148 ASP cc_start: 0.8400 (p0) cc_final: 0.8170 (p0) REVERT: J 243 SER cc_start: 0.9339 (t) cc_final: 0.8811 (m) REVERT: J 245 ILE cc_start: 0.8911 (pt) cc_final: 0.8655 (pt) REVERT: J 269 GLN cc_start: 0.8252 (tm130) cc_final: 0.7530 (tm-30) REVERT: J 274 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8192 (tm-30) REVERT: J 351 ASN cc_start: 0.5169 (p0) cc_final: 0.4969 (p0) REVERT: J 367 MET cc_start: 0.8346 (mmp) cc_final: 0.7746 (mmp) REVERT: K 221 MET cc_start: 0.7490 (ptp) cc_final: 0.7271 (ptp) REVERT: K 224 LYS cc_start: 0.9085 (mtmt) cc_final: 0.8197 (tptt) REVERT: K 291 GLU cc_start: 0.8214 (tp30) cc_final: 0.7754 (tp30) REVERT: K 389 GLU cc_start: 0.8699 (pp20) cc_final: 0.8497 (pp20) REVERT: L 271 LYS cc_start: 0.8752 (mtpp) cc_final: 0.8497 (mtpp) REVERT: M 307 GLU cc_start: 0.8251 (tt0) cc_final: 0.7802 (tp30) REVERT: s 127 VAL cc_start: 0.8993 (p) cc_final: 0.8615 (m) outliers start: 1 outliers final: 0 residues processed: 500 average time/residue: 0.1651 time to fit residues: 130.1402 Evaluate side-chains 353 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 254 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 282 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 124 GLN D 55 GLN D 118 GLN D 122 GLN D 149 GLN ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 GLN H 356 ASN J 220 GLN J 287 ASN J 295 ASN K 285 GLN L 175 GLN L 364 HIS M 310 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.080228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.069225 restraints weight = 69648.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.070803 restraints weight = 44437.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.071392 restraints weight = 28030.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.071693 restraints weight = 22655.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.071766 restraints weight = 21517.648| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25059 Z= 0.175 Angle : 0.675 9.717 34025 Z= 0.343 Chirality : 0.047 0.243 3977 Planarity : 0.004 0.056 4395 Dihedral : 6.282 68.593 3592 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.12 % Allowed : 5.51 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.99 (0.14), residues: 3260 helix: -1.60 (0.13), residues: 1241 sheet: -2.11 (0.22), residues: 494 loop : -2.19 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 50 TYR 0.038 0.002 TYR E 26 PHE 0.032 0.002 PHE A 32 TRP 0.048 0.003 TRP M 376 HIS 0.008 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (25059) covalent geometry : angle 0.67453 / 0.34 (34025) hydrogen bonds : bond 0.03704 / 2.47 ( 807) hydrogen bonds : angle 5.12922 / 3.53 ( 2271) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 467 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8133 (p0) cc_final: 0.7787 (p0) REVERT: A 62 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6812 (ptpt) REVERT: B 57 MET cc_start: 0.7890 (mpp) cc_final: 0.7416 (mtp) REVERT: B 180 ASN cc_start: 0.8772 (t0) cc_final: 0.7978 (t0) REVERT: C 68 LYS cc_start: 0.8991 (tttt) cc_final: 0.8615 (tttm) REVERT: C 114 ARG cc_start: 0.8093 (tmt-80) cc_final: 0.7838 (tmt-80) REVERT: C 173 GLN cc_start: 0.8602 (mm110) cc_final: 0.8225 (tp40) REVERT: D 5 ASP cc_start: 0.7604 (p0) cc_final: 0.7274 (p0) REVERT: D 22 TYR cc_start: 0.8443 (m-10) cc_final: 0.8240 (m-80) REVERT: D 139 ASP cc_start: 0.8596 (t0) cc_final: 0.8160 (t0) REVERT: E 134 MET cc_start: 0.8565 (mtp) cc_final: 0.7824 (mtm) REVERT: E 151 ASP cc_start: 0.7541 (p0) cc_final: 0.6803 (t0) REVERT: E 182 GLU cc_start: 0.8623 (pp20) cc_final: 0.8378 (pp20) REVERT: E 213 ASP cc_start: 0.8081 (t70) cc_final: 0.7481 (t70) REVERT: E 221 CYS cc_start: 0.7364 (p) cc_final: 0.7159 (p) REVERT: F 60 GLN cc_start: 0.7725 (mt0) cc_final: 0.7511 (mt0) REVERT: G 218 TRP cc_start: 0.8359 (p-90) cc_final: 0.7654 (p-90) REVERT: G 238 GLU cc_start: 0.8309 (pp20) cc_final: 0.8082 (pp20) REVERT: H 310 GLU cc_start: 0.8057 (tp30) cc_final: 0.7738 (mm-30) REVERT: H 320 ASP cc_start: 0.7160 (p0) cc_final: 0.6541 (p0) REVERT: H 333 MET cc_start: 0.8521 (ttt) cc_final: 0.8174 (ttt) REVERT: H 352 MET cc_start: 0.8596 (ptp) cc_final: 0.8369 (ptp) REVERT: H 396 MET cc_start: 0.8684 (mtp) cc_final: 0.8392 (mtt) REVERT: I 259 ASP cc_start: 0.7465 (p0) cc_final: 0.6960 (p0) REVERT: I 306 MET cc_start: 0.8615 (ttp) cc_final: 0.8276 (ttt) REVERT: I 329 ASN cc_start: 0.7883 (m-40) cc_final: 0.7678 (m-40) REVERT: J 148 ASP cc_start: 0.8447 (p0) cc_final: 0.8177 (p0) REVERT: J 243 SER cc_start: 0.9362 (t) cc_final: 0.8891 (m) REVERT: J 265 ASP cc_start: 0.8063 (t70) cc_final: 0.7849 (t70) REVERT: J 269 GLN cc_start: 0.8329 (tm-30) cc_final: 0.7692 (tm-30) REVERT: J 274 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8263 (tm-30) REVERT: J 357 ASP cc_start: 0.8824 (p0) cc_final: 0.8311 (p0) REVERT: J 367 MET cc_start: 0.8272 (mmp) cc_final: 0.8035 (mmp) REVERT: L 271 LYS cc_start: 0.8712 (mtpp) cc_final: 0.8501 (mtpp) REVERT: L 307 GLU cc_start: 0.7990 (tp30) cc_final: 0.7419 (tm-30) REVERT: M 307 GLU cc_start: 0.8158 (tt0) cc_final: 0.7716 (tp30) REVERT: s 127 VAL cc_start: 0.8896 (p) cc_final: 0.8482 (m) outliers start: 3 outliers final: 2 residues processed: 468 average time/residue: 0.1625 time to fit residues: 121.0745 Evaluate side-chains 364 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 362 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 132 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 154 optimal weight: 0.0370 chunk 73 optimal weight: 3.9990 chunk 278 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 124 GLN ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 ASN F 31 GLN G 195 GLN J 295 ASN K 285 GLN L 175 GLN L 364 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.080456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.069583 restraints weight = 69310.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.070832 restraints weight = 43937.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.071581 restraints weight = 30081.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.071772 restraints weight = 24202.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.071834 restraints weight = 21792.306| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25059 Z= 0.133 Angle : 0.643 10.389 34025 Z= 0.323 Chirality : 0.045 0.170 3977 Planarity : 0.004 0.054 4395 Dihedral : 6.113 67.027 3592 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.66 (0.14), residues: 3260 helix: -1.27 (0.14), residues: 1250 sheet: -1.95 (0.23), residues: 489 loop : -2.05 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 342 TYR 0.036 0.001 TYR F 24 PHE 0.017 0.001 PHE L 180 TRP 0.054 0.003 TRP M 376 HIS 0.005 0.001 HIS M 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (25059) covalent geometry : angle 0.64261 / 0.32 (34025) hydrogen bonds : bond 0.03432 / 2.27 ( 807) hydrogen bonds : angle 4.91692 / 3.38 ( 2271) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 495 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8166 (p0) cc_final: 0.7849 (p0) REVERT: A 78 THR cc_start: 0.7894 (p) cc_final: 0.7620 (p) REVERT: A 209 HIS cc_start: 0.7996 (t-90) cc_final: 0.7705 (t-90) REVERT: B 4 ARG cc_start: 0.7684 (ttp80) cc_final: 0.7355 (ttp80) REVERT: B 57 MET cc_start: 0.7902 (mpp) cc_final: 0.7455 (mtp) REVERT: C 23 GLU cc_start: 0.8295 (pm20) cc_final: 0.8038 (pm20) REVERT: C 68 LYS cc_start: 0.8982 (tttt) cc_final: 0.8653 (tttm) REVERT: C 88 ILE cc_start: 0.8580 (pt) cc_final: 0.8119 (mt) REVERT: C 173 GLN cc_start: 0.8565 (mm110) cc_final: 0.8160 (tp40) REVERT: C 212 GLU cc_start: 0.8319 (pm20) cc_final: 0.7873 (pm20) REVERT: D 5 ASP cc_start: 0.7415 (p0) cc_final: 0.7075 (p0) REVERT: D 139 ASP cc_start: 0.8575 (t0) cc_final: 0.8225 (t0) REVERT: D 187 THR cc_start: 0.8631 (t) cc_final: 0.8361 (p) REVERT: E 28 LEU cc_start: 0.9119 (mm) cc_final: 0.8674 (mp) REVERT: E 134 MET cc_start: 0.8479 (mtp) cc_final: 0.7823 (mtm) REVERT: E 151 ASP cc_start: 0.7563 (p0) cc_final: 0.6797 (t0) REVERT: F 24 TYR cc_start: 0.8906 (m-80) cc_final: 0.8602 (m-80) REVERT: F 60 GLN cc_start: 0.7738 (mt0) cc_final: 0.7474 (mt0) REVERT: G 177 GLU cc_start: 0.7261 (tp30) cc_final: 0.6426 (tp30) REVERT: G 218 TRP cc_start: 0.8335 (p-90) cc_final: 0.7692 (p-90) REVERT: G 238 GLU cc_start: 0.8332 (pp20) cc_final: 0.8119 (pp20) REVERT: H 310 GLU cc_start: 0.8036 (tp30) cc_final: 0.7728 (mm-30) REVERT: H 333 MET cc_start: 0.8546 (ttt) cc_final: 0.8216 (ttt) REVERT: H 352 MET cc_start: 0.8566 (ptp) cc_final: 0.8337 (ptp) REVERT: H 445 LYS cc_start: 0.8566 (pttt) cc_final: 0.8271 (ttpt) REVERT: I 259 ASP cc_start: 0.7517 (p0) cc_final: 0.7137 (p0) REVERT: I 306 MET cc_start: 0.8608 (ttp) cc_final: 0.8234 (ttt) REVERT: J 243 SER cc_start: 0.9348 (t) cc_final: 0.8862 (m) REVERT: J 269 GLN cc_start: 0.8440 (tm-30) cc_final: 0.7746 (tm-30) REVERT: J 271 THR cc_start: 0.9369 (t) cc_final: 0.9162 (t) REVERT: J 274 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8218 (tm-30) REVERT: J 357 ASP cc_start: 0.8717 (p0) cc_final: 0.8247 (p0) REVERT: J 367 MET cc_start: 0.8535 (mmp) cc_final: 0.8049 (mmp) REVERT: K 389 GLU cc_start: 0.8644 (pp20) cc_final: 0.8062 (pp20) REVERT: L 271 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8295 (ttmt) REVERT: L 307 GLU cc_start: 0.7944 (tp30) cc_final: 0.7343 (tm-30) REVERT: M 307 GLU cc_start: 0.8191 (tt0) cc_final: 0.7925 (tp30) REVERT: s 127 VAL cc_start: 0.8814 (p) cc_final: 0.8366 (m) outliers start: 0 outliers final: 0 residues processed: 495 average time/residue: 0.1604 time to fit residues: 127.0236 Evaluate side-chains 337 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 24 optimal weight: 8.9990 chunk 201 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 310 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 316 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 295 optimal weight: 8.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 124 GLN D 122 GLN E 215 ASN F 4 ASN F 31 GLN G 195 GLN H 356 ASN J 295 ASN K 285 GLN L 175 GLN L 203 ASN L 208 GLN L 364 HIS M 362 GLN M 412 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.077771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.066712 restraints weight = 70068.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.068151 restraints weight = 44545.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.068762 restraints weight = 29735.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.068962 restraints weight = 23193.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.069013 restraints weight = 22371.582| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25059 Z= 0.185 Angle : 0.686 9.136 34025 Z= 0.348 Chirality : 0.047 0.168 3977 Planarity : 0.004 0.058 4395 Dihedral : 6.156 68.102 3592 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.14), residues: 3260 helix: -1.19 (0.14), residues: 1254 sheet: -1.80 (0.23), residues: 486 loop : -2.02 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 5 TYR 0.025 0.002 TYR F 24 PHE 0.019 0.002 PHE H 429 TRP 0.075 0.003 TRP M 376 HIS 0.004 0.001 HIS D 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (25059) covalent geometry : angle 0.68608 / 0.35 (34025) hydrogen bonds : bond 0.03609 / 2.38 ( 807) hydrogen bonds : angle 4.95635 / 3.42 ( 2271) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 454 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8161 (p0) cc_final: 0.7872 (p0) REVERT: A 218 PHE cc_start: 0.8185 (m-10) cc_final: 0.7860 (m-10) REVERT: B 5 TYR cc_start: 0.6610 (m-10) cc_final: 0.6206 (m-10) REVERT: B 21 ILE cc_start: 0.8675 (pt) cc_final: 0.8395 (mt) REVERT: B 57 MET cc_start: 0.8206 (mpp) cc_final: 0.7635 (mtm) REVERT: B 103 GLU cc_start: 0.8192 (pp20) cc_final: 0.7921 (pp20) REVERT: C 88 ILE cc_start: 0.8647 (pt) cc_final: 0.8178 (mt) REVERT: C 212 GLU cc_start: 0.8219 (pm20) cc_final: 0.7825 (pm20) REVERT: D 5 ASP cc_start: 0.7447 (p0) cc_final: 0.7237 (p0) REVERT: D 139 ASP cc_start: 0.8595 (t0) cc_final: 0.8262 (t0) REVERT: D 187 THR cc_start: 0.8721 (t) cc_final: 0.8446 (p) REVERT: E 28 LEU cc_start: 0.9122 (mm) cc_final: 0.8718 (mp) REVERT: E 134 MET cc_start: 0.8615 (mtp) cc_final: 0.7988 (mtm) REVERT: E 151 ASP cc_start: 0.7640 (p0) cc_final: 0.7014 (t0) REVERT: E 233 ASN cc_start: 0.8283 (m110) cc_final: 0.7997 (m-40) REVERT: F 60 GLN cc_start: 0.7793 (mt0) cc_final: 0.7542 (mt0) REVERT: G 218 TRP cc_start: 0.8465 (p-90) cc_final: 0.7876 (p-90) REVERT: H 310 GLU cc_start: 0.8087 (tp30) cc_final: 0.7773 (mm-30) REVERT: H 396 MET cc_start: 0.8744 (mtp) cc_final: 0.8347 (mmt) REVERT: I 196 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8240 (mt-10) REVERT: I 259 ASP cc_start: 0.7474 (p0) cc_final: 0.6979 (p0) REVERT: I 306 MET cc_start: 0.8585 (ttp) cc_final: 0.8178 (ttt) REVERT: I 351 GLU cc_start: 0.7930 (pm20) cc_final: 0.7729 (pm20) REVERT: J 148 ASP cc_start: 0.8404 (p0) cc_final: 0.8201 (p0) REVERT: J 269 GLN cc_start: 0.8527 (tm-30) cc_final: 0.7973 (tm-30) REVERT: J 357 ASP cc_start: 0.8754 (p0) cc_final: 0.8328 (p0) REVERT: J 367 MET cc_start: 0.8498 (mmp) cc_final: 0.7925 (mmp) REVERT: K 319 ASN cc_start: 0.8123 (m110) cc_final: 0.7699 (m-40) REVERT: K 320 ARG cc_start: 0.7286 (tmm160) cc_final: 0.7011 (ttp80) REVERT: K 389 GLU cc_start: 0.8706 (pp20) cc_final: 0.8066 (pp20) REVERT: L 271 LYS cc_start: 0.8752 (mtpp) cc_final: 0.8406 (ttmt) REVERT: L 307 GLU cc_start: 0.8012 (tp30) cc_final: 0.7480 (tm-30) REVERT: M 307 GLU cc_start: 0.8224 (tt0) cc_final: 0.7825 (tp30) REVERT: M 311 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8622 (tm-30) REVERT: s 127 VAL cc_start: 0.8770 (p) cc_final: 0.8370 (m) outliers start: 1 outliers final: 1 residues processed: 455 average time/residue: 0.1578 time to fit residues: 116.0166 Evaluate side-chains 351 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 350 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 304 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 285 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 243 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN E 215 ASN F 4 ASN J 295 ASN K 285 GLN L 175 GLN L 208 GLN L 364 HIS M 253 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.078196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.067335 restraints weight = 69977.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.068475 restraints weight = 45066.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.068995 restraints weight = 32176.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.069138 restraints weight = 26383.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.069635 restraints weight = 24136.142| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25059 Z= 0.150 Angle : 0.662 10.430 34025 Z= 0.332 Chirality : 0.046 0.159 3977 Planarity : 0.004 0.057 4395 Dihedral : 6.057 67.567 3592 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.14), residues: 3260 helix: -1.07 (0.14), residues: 1271 sheet: -1.72 (0.23), residues: 481 loop : -1.94 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 50 TYR 0.014 0.001 TYR K 212 PHE 0.018 0.002 PHE L 180 TRP 0.047 0.002 TRP M 376 HIS 0.008 0.001 HIS F 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (25059) covalent geometry : angle 0.66162 / 0.33 (34025) hydrogen bonds : bond 0.03410 / 2.27 ( 807) hydrogen bonds : angle 4.85455 / 3.36 ( 2271) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8150 (p0) cc_final: 0.7844 (p0) REVERT: B 4 ARG cc_start: 0.7542 (ttp80) cc_final: 0.7285 (ttp80) REVERT: B 5 TYR cc_start: 0.6500 (m-10) cc_final: 0.6179 (m-10) REVERT: B 21 ILE cc_start: 0.8687 (pt) cc_final: 0.8403 (mt) REVERT: B 57 MET cc_start: 0.8112 (mpp) cc_final: 0.7519 (mtm) REVERT: B 186 GLU cc_start: 0.8199 (tp30) cc_final: 0.7648 (tp30) REVERT: C 27 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8140 (mm-30) REVERT: C 88 ILE cc_start: 0.8658 (pt) cc_final: 0.8210 (mt) REVERT: C 212 GLU cc_start: 0.8093 (pm20) cc_final: 0.7878 (pm20) REVERT: D 5 ASP cc_start: 0.7562 (p0) cc_final: 0.7324 (p0) REVERT: D 139 ASP cc_start: 0.8612 (t0) cc_final: 0.8351 (t0) REVERT: D 162 GLN cc_start: 0.8894 (tp40) cc_final: 0.8493 (tp40) REVERT: D 187 THR cc_start: 0.8692 (t) cc_final: 0.8431 (p) REVERT: E 28 LEU cc_start: 0.9063 (mm) cc_final: 0.8669 (mp) REVERT: E 134 MET cc_start: 0.8567 (mtp) cc_final: 0.7847 (mtm) REVERT: E 151 ASP cc_start: 0.7623 (p0) cc_final: 0.6987 (t0) REVERT: E 221 CYS cc_start: 0.7460 (p) cc_final: 0.6821 (p) REVERT: E 231 TYR cc_start: 0.8589 (m-10) cc_final: 0.8372 (m-10) REVERT: E 233 ASN cc_start: 0.8346 (m110) cc_final: 0.8097 (m-40) REVERT: F 60 GLN cc_start: 0.7864 (mt0) cc_final: 0.7513 (mt0) REVERT: G 167 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7676 (mmtm) REVERT: G 218 TRP cc_start: 0.8488 (p-90) cc_final: 0.7926 (p-90) REVERT: H 310 GLU cc_start: 0.8089 (tp30) cc_final: 0.7786 (mm-30) REVERT: H 333 MET cc_start: 0.8601 (ttt) cc_final: 0.8297 (ttt) REVERT: H 396 MET cc_start: 0.8713 (mtp) cc_final: 0.8269 (mmt) REVERT: H 445 LYS cc_start: 0.8622 (pttt) cc_final: 0.8412 (ttpt) REVERT: I 259 ASP cc_start: 0.7503 (p0) cc_final: 0.6984 (p0) REVERT: I 306 MET cc_start: 0.8594 (ttp) cc_final: 0.8105 (ttt) REVERT: I 329 ASN cc_start: 0.8082 (m-40) cc_final: 0.7861 (m-40) REVERT: I 421 GLU cc_start: 0.8269 (pp20) cc_final: 0.7965 (tm-30) REVERT: J 229 MET cc_start: 0.7050 (mtt) cc_final: 0.6768 (mtt) REVERT: J 269 GLN cc_start: 0.8493 (tm-30) cc_final: 0.7940 (tm-30) REVERT: J 357 ASP cc_start: 0.8761 (p0) cc_final: 0.8364 (p0) REVERT: J 367 MET cc_start: 0.8381 (mmp) cc_final: 0.7830 (mmm) REVERT: K 221 MET cc_start: 0.7442 (ptp) cc_final: 0.6928 (ptp) REVERT: K 319 ASN cc_start: 0.8165 (m110) cc_final: 0.7741 (m-40) REVERT: K 320 ARG cc_start: 0.7293 (tmm160) cc_final: 0.7051 (ttp80) REVERT: L 191 ARG cc_start: 0.6915 (ptm-80) cc_final: 0.6473 (ptm-80) REVERT: L 271 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8404 (ttmt) REVERT: L 307 GLU cc_start: 0.7954 (tp30) cc_final: 0.7459 (tm-30) REVERT: L 394 CYS cc_start: 0.6259 (p) cc_final: 0.6002 (p) REVERT: M 307 GLU cc_start: 0.8134 (tt0) cc_final: 0.7778 (tp30) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.1607 time to fit residues: 117.8867 Evaluate side-chains 349 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 169 optimal weight: 0.4980 chunk 222 optimal weight: 0.9980 chunk 223 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 296 optimal weight: 0.0010 chunk 83 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 124 GLN F 4 ASN F 31 GLN G 144 ASN H 356 ASN ** I 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 311 ASN J 295 ASN K 285 GLN L 175 GLN L 208 GLN L 364 HIS M 253 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.080416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.069690 restraints weight = 69087.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.070704 restraints weight = 44149.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.071100 restraints weight = 32316.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.071450 restraints weight = 28774.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.071504 restraints weight = 23868.239| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25059 Z= 0.110 Angle : 0.644 11.493 34025 Z= 0.318 Chirality : 0.044 0.306 3977 Planarity : 0.004 0.055 4395 Dihedral : 5.781 66.988 3592 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.04 % Allowed : 1.54 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.14), residues: 3260 helix: -0.86 (0.14), residues: 1285 sheet: -1.47 (0.23), residues: 479 loop : -1.79 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 233 TYR 0.026 0.001 TYR F 24 PHE 0.018 0.001 PHE M 279 TRP 0.042 0.002 TRP M 376 HIS 0.010 0.001 HIS F 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (25059) covalent geometry : angle 0.64446 / 0.32 (34025) hydrogen bonds : bond 0.03041 / 2.01 ( 807) hydrogen bonds : angle 4.62751 / 3.18 ( 2271) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 479 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8125 (p0) cc_final: 0.7861 (p0) REVERT: A 81 MET cc_start: 0.8838 (ttp) cc_final: 0.8612 (ttp) REVERT: A 218 PHE cc_start: 0.8233 (m-10) cc_final: 0.7907 (m-10) REVERT: B 4 ARG cc_start: 0.7575 (ttp80) cc_final: 0.7273 (ttp80) REVERT: B 21 ILE cc_start: 0.8555 (pt) cc_final: 0.8270 (mt) REVERT: B 57 MET cc_start: 0.8133 (mpp) cc_final: 0.7815 (mtp) REVERT: C 23 GLU cc_start: 0.8311 (pm20) cc_final: 0.8091 (pm20) REVERT: C 68 LYS cc_start: 0.9024 (tttt) cc_final: 0.8768 (tttm) REVERT: C 88 ILE cc_start: 0.8592 (pt) cc_final: 0.8190 (mt) REVERT: C 173 GLN cc_start: 0.8452 (mm110) cc_final: 0.8134 (tp40) REVERT: D 5 ASP cc_start: 0.7425 (p0) cc_final: 0.7193 (p0) REVERT: D 139 ASP cc_start: 0.8553 (t0) cc_final: 0.8280 (t0) REVERT: D 162 GLN cc_start: 0.8843 (tp40) cc_final: 0.8439 (tp40) REVERT: D 187 THR cc_start: 0.8669 (t) cc_final: 0.8441 (p) REVERT: E 28 LEU cc_start: 0.9093 (mm) cc_final: 0.8650 (mp) REVERT: E 134 MET cc_start: 0.8394 (mtp) cc_final: 0.7908 (mtm) REVERT: E 151 ASP cc_start: 0.7743 (p0) cc_final: 0.6988 (t0) REVERT: E 221 CYS cc_start: 0.7531 (p) cc_final: 0.6904 (p) REVERT: E 233 ASN cc_start: 0.8320 (m110) cc_final: 0.8036 (m-40) REVERT: F 60 GLN cc_start: 0.7782 (mt0) cc_final: 0.7415 (mt0) REVERT: G 167 LYS cc_start: 0.7870 (mmmt) cc_final: 0.7620 (mmtm) REVERT: G 218 TRP cc_start: 0.8456 (p-90) cc_final: 0.7881 (p-90) REVERT: H 310 GLU cc_start: 0.8173 (tp30) cc_final: 0.7759 (mm-30) REVERT: H 333 MET cc_start: 0.8517 (ttt) cc_final: 0.8244 (ttt) REVERT: H 352 MET cc_start: 0.8469 (ptp) cc_final: 0.8248 (ptp) REVERT: H 396 MET cc_start: 0.8735 (mtp) cc_final: 0.8475 (mmt) REVERT: I 259 ASP cc_start: 0.7472 (p0) cc_final: 0.7099 (p0) REVERT: I 306 MET cc_start: 0.8548 (ttp) cc_final: 0.8114 (ttt) REVERT: I 329 ASN cc_start: 0.7937 (m-40) cc_final: 0.7732 (m-40) REVERT: I 376 ASN cc_start: 0.7871 (t0) cc_final: 0.7630 (t0) REVERT: I 421 GLU cc_start: 0.8288 (pp20) cc_final: 0.7881 (tm-30) REVERT: J 148 ASP cc_start: 0.8275 (p0) cc_final: 0.8067 (p0) REVERT: J 229 MET cc_start: 0.6943 (mtt) cc_final: 0.6643 (mtt) REVERT: J 243 SER cc_start: 0.9346 (t) cc_final: 0.8846 (m) REVERT: J 256 THR cc_start: 0.8426 (m) cc_final: 0.8165 (m) REVERT: J 269 GLN cc_start: 0.8463 (tm-30) cc_final: 0.7980 (tm-30) REVERT: J 357 ASP cc_start: 0.8696 (p0) cc_final: 0.8209 (p0) REVERT: J 367 MET cc_start: 0.8524 (mmp) cc_final: 0.7972 (mmm) REVERT: K 221 MET cc_start: 0.7140 (ptp) cc_final: 0.6695 (ptp) REVERT: K 319 ASN cc_start: 0.8073 (m110) cc_final: 0.7683 (m-40) REVERT: K 320 ARG cc_start: 0.7071 (tmm160) cc_final: 0.6870 (ttp80) REVERT: L 271 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8474 (ttmt) REVERT: L 307 GLU cc_start: 0.7989 (tp30) cc_final: 0.7427 (tm-30) REVERT: L 394 CYS cc_start: 0.6099 (p) cc_final: 0.5854 (p) REVERT: M 307 GLU cc_start: 0.8090 (tt0) cc_final: 0.7727 (tp30) outliers start: 1 outliers final: 0 residues processed: 480 average time/residue: 0.1690 time to fit residues: 127.2847 Evaluate side-chains 352 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 77 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 65 optimal weight: 0.0970 chunk 290 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 124 GLN E 73 HIS F 4 ASN H 356 ASN ** I 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 352 ASN J 295 ASN K 285 GLN L 175 GLN L 208 GLN L 273 HIS L 364 HIS M 253 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.080572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.069554 restraints weight = 69363.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.070710 restraints weight = 44721.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.071084 restraints weight = 31884.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.071567 restraints weight = 26243.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.071613 restraints weight = 22602.224| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25059 Z= 0.113 Angle : 0.649 16.306 34025 Z= 0.320 Chirality : 0.045 0.267 3977 Planarity : 0.004 0.052 4395 Dihedral : 5.611 65.115 3592 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.04 % Allowed : 0.73 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.15), residues: 3260 helix: -0.72 (0.14), residues: 1282 sheet: -1.52 (0.23), residues: 503 loop : -1.61 (0.16), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 231 TYR 0.019 0.001 TYR C 137 PHE 0.020 0.001 PHE M 279 TRP 0.037 0.002 TRP M 376 HIS 0.012 0.001 HIS F 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (25059) covalent geometry : angle 0.64915 / 0.32 (34025) hydrogen bonds : bond 0.03031 / 2.00 ( 807) hydrogen bonds : angle 4.54153 / 3.12 ( 2271) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 449 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8090 (p0) cc_final: 0.7831 (p0) REVERT: A 81 MET cc_start: 0.8837 (ttp) cc_final: 0.8605 (ttp) REVERT: B 4 ARG cc_start: 0.7575 (ttp80) cc_final: 0.7285 (ttp80) REVERT: B 21 ILE cc_start: 0.8538 (pt) cc_final: 0.8282 (mt) REVERT: B 57 MET cc_start: 0.8110 (mpp) cc_final: 0.7883 (mtp) REVERT: C 68 LYS cc_start: 0.9019 (tttt) cc_final: 0.8805 (tttm) REVERT: C 88 ILE cc_start: 0.8569 (pt) cc_final: 0.8202 (mt) REVERT: C 173 GLN cc_start: 0.8456 (mm110) cc_final: 0.8138 (tp40) REVERT: C 212 GLU cc_start: 0.8249 (pm20) cc_final: 0.7912 (pm20) REVERT: D 5 ASP cc_start: 0.7431 (p0) cc_final: 0.7204 (p0) REVERT: D 107 GLU cc_start: 0.7370 (tp30) cc_final: 0.6862 (tp30) REVERT: D 139 ASP cc_start: 0.8525 (t0) cc_final: 0.8318 (t0) REVERT: D 148 TYR cc_start: 0.8608 (m-10) cc_final: 0.7292 (m-10) REVERT: D 162 GLN cc_start: 0.8818 (tp40) cc_final: 0.8385 (tp40) REVERT: E 28 LEU cc_start: 0.9095 (mm) cc_final: 0.8657 (mp) REVERT: E 134 MET cc_start: 0.8448 (mtp) cc_final: 0.7817 (mtm) REVERT: E 151 ASP cc_start: 0.7803 (p0) cc_final: 0.7391 (m-30) REVERT: F 60 GLN cc_start: 0.7722 (mt0) cc_final: 0.7287 (mt0) REVERT: G 9 ASP cc_start: 0.8128 (m-30) cc_final: 0.7886 (m-30) REVERT: G 167 LYS cc_start: 0.7907 (mmmt) cc_final: 0.7646 (mmtm) REVERT: G 218 TRP cc_start: 0.8437 (p-90) cc_final: 0.7884 (p-90) REVERT: H 310 GLU cc_start: 0.8170 (tp30) cc_final: 0.7766 (mm-30) REVERT: H 333 MET cc_start: 0.8506 (ttt) cc_final: 0.8207 (ttt) REVERT: H 352 MET cc_start: 0.8458 (ptp) cc_final: 0.8251 (ptp) REVERT: H 396 MET cc_start: 0.8771 (mtp) cc_final: 0.8440 (mmt) REVERT: I 259 ASP cc_start: 0.7510 (p0) cc_final: 0.7073 (p0) REVERT: I 306 MET cc_start: 0.8564 (ttp) cc_final: 0.8119 (ttt) REVERT: I 376 ASN cc_start: 0.7863 (t0) cc_final: 0.7610 (t0) REVERT: I 421 GLU cc_start: 0.8311 (pp20) cc_final: 0.7884 (tm-30) REVERT: J 243 SER cc_start: 0.9316 (t) cc_final: 0.9014 (p) REVERT: J 269 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8014 (tm-30) REVERT: J 288 ILE cc_start: 0.8964 (mm) cc_final: 0.8695 (mm) REVERT: J 367 MET cc_start: 0.8280 (mmp) cc_final: 0.7784 (mmm) REVERT: K 221 MET cc_start: 0.7195 (ptp) cc_final: 0.6685 (ptp) REVERT: K 319 ASN cc_start: 0.8152 (m110) cc_final: 0.7698 (m-40) REVERT: L 191 ARG cc_start: 0.6951 (ptm-80) cc_final: 0.6450 (ptm-80) REVERT: L 271 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8504 (ttmt) REVERT: L 307 GLU cc_start: 0.7923 (tp30) cc_final: 0.7438 (tm-30) REVERT: L 394 CYS cc_start: 0.6111 (p) cc_final: 0.5878 (p) REVERT: M 182 ASP cc_start: 0.7582 (t70) cc_final: 0.7312 (t70) REVERT: M 307 GLU cc_start: 0.8084 (tt0) cc_final: 0.7714 (tp30) REVERT: M 421 GLU cc_start: 0.8353 (tt0) cc_final: 0.8123 (tt0) outliers start: 1 outliers final: 1 residues processed: 450 average time/residue: 0.1569 time to fit residues: 114.0236 Evaluate side-chains 358 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 39 optimal weight: 9.9990 chunk 293 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 85 optimal weight: 0.0470 chunk 95 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 21 GLN C 124 GLN D 122 GLN D 209 ASN F 4 ASN J 295 ASN K 285 GLN L 175 GLN L 208 GLN L 273 HIS L 364 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.078331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.067402 restraints weight = 70249.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.068686 restraints weight = 43698.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.069145 restraints weight = 30970.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.069585 restraints weight = 25337.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.069612 restraints weight = 21257.631| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25059 Z= 0.154 Angle : 0.678 12.138 34025 Z= 0.338 Chirality : 0.046 0.269 3977 Planarity : 0.004 0.059 4395 Dihedral : 5.742 67.169 3592 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.15), residues: 3260 helix: -0.71 (0.14), residues: 1297 sheet: -1.40 (0.23), residues: 494 loop : -1.66 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 261 TYR 0.019 0.001 TYR J 222 PHE 0.022 0.002 PHE J 382 TRP 0.035 0.002 TRP M 376 HIS 0.011 0.001 HIS F 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (25059) covalent geometry : angle 0.67772 / 0.34 (34025) hydrogen bonds : bond 0.03344 / 2.23 ( 807) hydrogen bonds : angle 4.65805 / 3.21 ( 2271) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8072 (p0) cc_final: 0.7827 (p0) REVERT: C 53 THR cc_start: 0.7942 (m) cc_final: 0.7498 (p) REVERT: C 88 ILE cc_start: 0.8611 (pt) cc_final: 0.8227 (mt) REVERT: D 162 GLN cc_start: 0.8869 (tp40) cc_final: 0.8420 (tp40) REVERT: E 28 LEU cc_start: 0.9091 (mm) cc_final: 0.8665 (mp) REVERT: E 134 MET cc_start: 0.8574 (mtp) cc_final: 0.7922 (mtm) REVERT: E 151 ASP cc_start: 0.7759 (p0) cc_final: 0.7086 (t0) REVERT: F 60 GLN cc_start: 0.7834 (mt0) cc_final: 0.7387 (mt0) REVERT: G 218 TRP cc_start: 0.8464 (p-90) cc_final: 0.7862 (p-90) REVERT: H 310 GLU cc_start: 0.8191 (tp30) cc_final: 0.7755 (mm-30) REVERT: H 333 MET cc_start: 0.8602 (ttt) cc_final: 0.8341 (ttt) REVERT: H 352 MET cc_start: 0.8433 (ptp) cc_final: 0.8211 (ptp) REVERT: I 259 ASP cc_start: 0.7498 (p0) cc_final: 0.6970 (p0) REVERT: I 306 MET cc_start: 0.8573 (ttp) cc_final: 0.8117 (ttt) REVERT: I 376 ASN cc_start: 0.7903 (t0) cc_final: 0.7635 (t0) REVERT: I 421 GLU cc_start: 0.8366 (pp20) cc_final: 0.7939 (tm-30) REVERT: J 229 MET cc_start: 0.7071 (mtt) cc_final: 0.6810 (mtt) REVERT: J 243 SER cc_start: 0.9329 (t) cc_final: 0.8805 (m) REVERT: J 269 GLN cc_start: 0.8585 (tm-30) cc_final: 0.7957 (tm-30) REVERT: J 367 MET cc_start: 0.8238 (mmp) cc_final: 0.7510 (mmm) REVERT: K 221 MET cc_start: 0.7448 (ptp) cc_final: 0.7222 (ptp) REVERT: K 375 ASN cc_start: 0.8853 (p0) cc_final: 0.8629 (p0) REVERT: L 191 ARG cc_start: 0.6929 (ptm-80) cc_final: 0.6642 (ptm-80) REVERT: L 271 LYS cc_start: 0.8774 (mtpp) cc_final: 0.8480 (ttmt) REVERT: L 307 GLU cc_start: 0.8160 (tp30) cc_final: 0.7667 (tm-30) REVERT: L 312 MET cc_start: 0.8333 (ptp) cc_final: 0.8052 (ptm) REVERT: M 182 ASP cc_start: 0.7522 (t70) cc_final: 0.7255 (t70) REVERT: M 307 GLU cc_start: 0.8109 (tt0) cc_final: 0.7723 (tp30) REVERT: M 421 GLU cc_start: 0.8478 (tt0) cc_final: 0.8221 (tt0) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.1647 time to fit residues: 114.5255 Evaluate side-chains 356 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 200 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 237 optimal weight: 0.0030 chunk 79 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 270 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 36 optimal weight: 8.9990 overall best weight: 0.5348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 124 GLN F 4 ASN H 356 ASN I 311 ASN K 285 GLN L 273 HIS L 364 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.080799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.069973 restraints weight = 69297.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.071093 restraints weight = 44674.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.071617 restraints weight = 33030.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.071909 restraints weight = 25574.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.071998 restraints weight = 23907.178| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25059 Z= 0.110 Angle : 0.651 10.969 34025 Z= 0.320 Chirality : 0.045 0.261 3977 Planarity : 0.004 0.047 4395 Dihedral : 5.567 67.775 3592 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.08 % Allowed : 0.49 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.15), residues: 3260 helix: -0.59 (0.15), residues: 1299 sheet: -1.35 (0.23), residues: 499 loop : -1.52 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 113 TYR 0.022 0.001 TYR F 171 PHE 0.021 0.001 PHE L 180 TRP 0.035 0.002 TRP M 376 HIS 0.011 0.001 HIS F 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (25059) covalent geometry : angle 0.65110 / 0.32 (34025) hydrogen bonds : bond 0.02934 / 1.94 ( 807) hydrogen bonds : angle 4.48678 / 3.08 ( 2271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3632.90 seconds wall clock time: 63 minutes 53.07 seconds (3833.07 seconds total)