Starting phenix.real_space_refine on Sun Jan 26 12:24:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ef0_9042/01_2025/6ef0_9042.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ef0_9042/01_2025/6ef0_9042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ef0_9042/01_2025/6ef0_9042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ef0_9042/01_2025/6ef0_9042.map" model { file = "/net/cci-nas-00/data/ceres_data/6ef0_9042/01_2025/6ef0_9042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ef0_9042/01_2025/6ef0_9042.cif" } resolution = 4.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 88 5.16 5 C 15565 2.51 5 N 4292 2.21 5 O 4788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24748 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1864 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1859 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 12, 'TRANS': 237} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 1834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1834 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 238} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1856 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 231} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1885 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 244} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1783 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 227} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1868 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 236} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1831 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 243} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 12, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 122 Chain: "I" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1913 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 11, 'TRANS': 259} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 108 Chain: "J" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2005 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 258} Chain breaks: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "K" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2016 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 259} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 78 Chain: "L" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2057 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 257} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 55 Chain: "M" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1737 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 9, 'TRANS': 248} Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 175 Chain: "s" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 66 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.12, per 1000 atoms: 0.61 Number of scatterers: 24748 At special positions: 0 Unit cell: (136.99, 139.05, 129.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 15 15.00 O 4788 8.00 N 4292 7.00 C 15565 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.05 Conformation dependent library (CDL) restraints added in 3.1 seconds 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6118 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 23 sheets defined 39.6% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 removed outlier: 4.125A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 109 removed outlier: 4.125A pdb=" N ASN A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.535A pdb=" N LEU A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 128 removed outlier: 3.526A pdb=" N ILE A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.545A pdb=" N LYS A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 215 removed outlier: 3.653A pdb=" N GLU A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.557A pdb=" N ILE A 241 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 243 " --> pdb=" O ASN A 240 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 244 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 removed outlier: 3.881A pdb=" N THR B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 27 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 96 removed outlier: 4.111A pdb=" N ASP B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 88 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 109 through 120 removed outlier: 3.731A pdb=" N MET B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 4.202A pdb=" N GLU B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 178 " --> pdb=" O PHE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 198 removed outlier: 4.255A pdb=" N HIS B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'C' and resid 20 through 29 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 81 through 84 removed outlier: 3.674A pdb=" N ALA C 84 " --> pdb=" O THR C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 81 through 84' Processing helix chain 'C' and resid 86 through 103 removed outlier: 4.195A pdb=" N ILE C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS C 94 " --> pdb=" O THR C 90 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 123 removed outlier: 5.052A pdb=" N ASP C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE C 118 " --> pdb=" O ARG C 114 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 177 removed outlier: 3.774A pdb=" N THR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 198 Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 231 through 242 removed outlier: 4.118A pdb=" N ILE C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 27 removed outlier: 3.780A pdb=" N GLU D 21 " --> pdb=" O ILE D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 81 through 100 removed outlier: 3.843A pdb=" N LEU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG D 90 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 removed outlier: 3.700A pdb=" N TYR D 112 " --> pdb=" O TYR D 108 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLN D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 179 removed outlier: 3.523A pdb=" N LYS D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 200 removed outlier: 3.713A pdb=" N LEU D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 203 No H-bonds generated for 'chain 'D' and resid 201 through 203' Processing helix chain 'D' and resid 216 through 220 removed outlier: 3.509A pdb=" N ASP D 220 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 239 removed outlier: 3.690A pdb=" N TYR D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN D 235 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 30 removed outlier: 4.359A pdb=" N GLU E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA E 30 " --> pdb=" O TYR E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 103 removed outlier: 4.419A pdb=" N THR E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 95 " --> pdb=" O HIS E 91 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 118 removed outlier: 4.104A pdb=" N GLN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 122 removed outlier: 3.603A pdb=" N ARG E 122 " --> pdb=" O LEU E 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 119 through 122' Processing helix chain 'E' and resid 176 through 185 removed outlier: 3.639A pdb=" N ALA E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLU E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 208 removed outlier: 3.928A pdb=" N LEU E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS E 202 " --> pdb=" O LEU E 198 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE E 203 " --> pdb=" O LEU E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 232 through 240 Processing helix chain 'E' and resid 241 through 248 removed outlier: 3.567A pdb=" N LYS E 244 " --> pdb=" O LYS E 241 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU E 245 " --> pdb=" O GLU E 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 32 removed outlier: 3.684A pdb=" N GLU F 23 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA F 28 " --> pdb=" O TYR F 24 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 95 removed outlier: 3.573A pdb=" N ARG F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN F 91 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS F 92 " --> pdb=" O LEU F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 119 removed outlier: 3.574A pdb=" N GLY F 109 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASP F 114 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 175 Processing helix chain 'F' and resid 185 through 196 removed outlier: 4.045A pdb=" N LEU F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE F 190 " --> pdb=" O PRO F 186 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.356A pdb=" N ALA F 229 " --> pdb=" O ASP F 226 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS F 232 " --> pdb=" O ALA F 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 33 Processing helix chain 'G' and resid 82 through 104 removed outlier: 3.688A pdb=" N LEU G 88 " --> pdb=" O ASP G 84 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA G 97 " --> pdb=" O ARG G 93 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 120 removed outlier: 4.582A pdb=" N GLN G 118 " --> pdb=" O ASP G 114 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 124 Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 168 through 181 removed outlier: 3.575A pdb=" N ALA G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU G 175 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 204 removed outlier: 3.833A pdb=" N ALA G 192 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE G 199 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE G 200 " --> pdb=" O ALA G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 208 removed outlier: 4.135A pdb=" N LYS G 208 " --> pdb=" O GLU G 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 221 through 225 Processing helix chain 'G' and resid 233 through 246 removed outlier: 3.629A pdb=" N GLN G 237 " --> pdb=" O GLY G 233 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP G 241 " --> pdb=" O GLN G 237 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE G 242 " --> pdb=" O GLU G 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 221 removed outlier: 4.390A pdb=" N GLU H 219 " --> pdb=" O LYS H 215 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS H 220 " --> pdb=" O ASP H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 237 removed outlier: 4.513A pdb=" N THR H 237 " --> pdb=" O GLU H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 removed outlier: 4.054A pdb=" N ALA H 260 " --> pdb=" O LYS H 256 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL H 263 " --> pdb=" O CYS H 259 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 269 Processing helix chain 'H' and resid 275 through 280 removed outlier: 4.069A pdb=" N LEU H 279 " --> pdb=" O ILE H 275 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL H 280 " --> pdb=" O GLY H 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 275 through 280' Processing helix chain 'H' and resid 286 through 299 Processing helix chain 'H' and resid 311 through 316 Processing helix chain 'H' and resid 318 through 322 removed outlier: 4.022A pdb=" N ASP H 321 " --> pdb=" O ARG H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 341 removed outlier: 4.401A pdb=" N ASP H 341 " --> pdb=" O ILE H 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 387 Processing helix chain 'H' and resid 405 through 410 Processing helix chain 'H' and resid 418 through 427 Processing helix chain 'H' and resid 428 through 434 Processing helix chain 'H' and resid 440 through 451 removed outlier: 3.509A pdb=" N LEU H 444 " --> pdb=" O GLU H 440 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS H 449 " --> pdb=" O LYS H 445 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 450 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE H 451 " --> pdb=" O VAL H 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 198 removed outlier: 3.974A pdb=" N ILE I 194 " --> pdb=" O GLN I 190 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS I 195 " --> pdb=" O ILE I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 204 Processing helix chain 'I' and resid 205 through 212 removed outlier: 3.700A pdb=" N GLU I 209 " --> pdb=" O PRO I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 240 removed outlier: 3.637A pdb=" N ALA I 237 " --> pdb=" O ALA I 233 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ASN I 238 " --> pdb=" O LYS I 234 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN I 239 " --> pdb=" O ALA I 235 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 253 removed outlier: 3.710A pdb=" N ILE I 253 " --> pdb=" O SER I 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 250 through 253' Processing helix chain 'I' and resid 260 through 274 removed outlier: 3.980A pdb=" N CYS I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG I 265 " --> pdb=" O PRO I 261 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE I 268 " --> pdb=" O CYS I 264 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS I 269 " --> pdb=" O ARG I 265 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL I 270 " --> pdb=" O GLN I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 Processing helix chain 'I' and resid 298 through 316 removed outlier: 3.542A pdb=" N ILE I 302 " --> pdb=" O GLY I 298 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU I 308 " --> pdb=" O ARG I 304 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU I 309 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP I 314 " --> pdb=" O LEU I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 360 removed outlier: 3.509A pdb=" N LYS I 360 " --> pdb=" O SER I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 367 Processing helix chain 'I' and resid 376 through 380 Processing helix chain 'I' and resid 391 through 405 removed outlier: 4.248A pdb=" N GLY I 400 " --> pdb=" O CYS I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 412 through 427 removed outlier: 3.901A pdb=" N PHE I 416 " --> pdb=" O THR I 412 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN I 426 " --> pdb=" O ARG I 422 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 139 removed outlier: 3.969A pdb=" N LEU J 136 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET J 138 " --> pdb=" O SER J 135 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL J 139 " --> pdb=" O LEU J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 161 Processing helix chain 'J' and resid 161 through 166 removed outlier: 4.117A pdb=" N LEU J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 205 removed outlier: 4.339A pdb=" N ALA J 203 " --> pdb=" O ALA J 199 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS J 204 " --> pdb=" O ARG J 200 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS J 205 " --> pdb=" O ALA J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 241 removed outlier: 4.249A pdb=" N SER J 227 " --> pdb=" O ILE J 223 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE J 234 " --> pdb=" O VAL J 230 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL J 235 " --> pdb=" O ARG J 231 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA J 237 " --> pdb=" O LEU J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 276 removed outlier: 3.541A pdb=" N MET J 272 " --> pdb=" O VAL J 268 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU J 274 " --> pdb=" O ARG J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 306 removed outlier: 4.532A pdb=" N LEU J 305 " --> pdb=" O ASP J 301 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG J 306 " --> pdb=" O PRO J 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 301 through 306' Processing helix chain 'J' and resid 320 through 331 removed outlier: 3.569A pdb=" N ALA J 325 " --> pdb=" O VAL J 321 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU J 326 " --> pdb=" O ALA J 322 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N HIS J 331 " --> pdb=" O ILE J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 344 through 350 Processing helix chain 'J' and resid 357 through 371 removed outlier: 3.707A pdb=" N ALA J 365 " --> pdb=" O VAL J 361 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY J 366 " --> pdb=" O CYS J 362 " (cutoff:3.500A) Processing helix chain 'J' and resid 378 through 391 removed outlier: 4.215A pdb=" N PHE J 382 " --> pdb=" O THR J 378 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY J 387 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL J 389 " --> pdb=" O ALA J 385 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET J 390 " --> pdb=" O VAL J 386 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN J 391 " --> pdb=" O GLY J 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 189 removed outlier: 3.546A pdb=" N ILE K 184 " --> pdb=" O GLN K 180 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ARG K 185 " --> pdb=" O LYS K 181 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA K 187 " --> pdb=" O GLU K 183 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL K 188 " --> pdb=" O ILE K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 194 Processing helix chain 'K' and resid 195 through 200 Processing helix chain 'K' and resid 221 through 229 removed outlier: 4.069A pdb=" N ALA K 225 " --> pdb=" O MET K 221 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL K 226 " --> pdb=" O LEU K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 265 removed outlier: 4.347A pdb=" N ASP K 256 " --> pdb=" O ARG K 252 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL K 257 " --> pdb=" O MET K 253 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE K 258 " --> pdb=" O VAL K 254 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG K 259 " --> pdb=" O ARG K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 274 through 278 removed outlier: 3.657A pdb=" N ALA K 278 " --> pdb=" O ASP K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 305 removed outlier: 3.771A pdb=" N ILE K 295 " --> pdb=" O GLU K 291 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU K 299 " --> pdb=" O ILE K 295 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP K 304 " --> pdb=" O LEU K 300 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 359 removed outlier: 3.723A pdb=" N ARG K 349 " --> pdb=" O ASP K 345 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG K 350 " --> pdb=" O ARG K 346 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU K 351 " --> pdb=" O ARG K 347 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY K 354 " --> pdb=" O ARG K 350 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS K 359 " --> pdb=" O THR K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 381 through 396 removed outlier: 4.004A pdb=" N ALA K 385 " --> pdb=" O ALA K 381 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLY K 391 " --> pdb=" O MET K 387 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU K 392 " --> pdb=" O GLN K 388 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA K 394 " --> pdb=" O ALA K 390 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG K 396 " --> pdb=" O LEU K 392 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 415 removed outlier: 3.946A pdb=" N GLU K 408 " --> pdb=" O GLN K 404 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA K 412 " --> pdb=" O GLU K 408 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR K 413 " --> pdb=" O GLU K 409 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN K 414 " --> pdb=" O ALA K 410 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL K 415 " --> pdb=" O TYR K 411 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 171 removed outlier: 4.574A pdb=" N THR L 171 " --> pdb=" O VAL L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 183 removed outlier: 3.554A pdb=" N GLY L 182 " --> pdb=" O THR L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 211 removed outlier: 3.822A pdb=" N GLN L 208 " --> pdb=" O PRO L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 240 removed outlier: 3.550A pdb=" N VAL L 235 " --> pdb=" O LEU L 231 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ALA L 236 " --> pdb=" O ALA L 232 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA L 237 " --> pdb=" O LYS L 233 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR L 238 " --> pdb=" O ALA L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 272 removed outlier: 3.826A pdb=" N ILE L 262 " --> pdb=" O GLU L 258 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG L 264 " --> pdb=" O ALA L 260 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA L 268 " --> pdb=" O ARG L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 287 Processing helix chain 'L' and resid 298 through 312 removed outlier: 3.802A pdb=" N GLN L 302 " --> pdb=" O ASP L 298 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU L 307 " --> pdb=" O ARG L 303 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU L 308 " --> pdb=" O THR L 304 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET L 312 " --> pdb=" O LEU L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 339 removed outlier: 3.772A pdb=" N LEU L 338 " --> pdb=" O ASP L 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 366 removed outlier: 4.356A pdb=" N ILE L 360 " --> pdb=" O GLY L 356 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE L 361 " --> pdb=" O ARG L 357 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS L 364 " --> pdb=" O ILE L 360 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR L 365 " --> pdb=" O PHE L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 385 removed outlier: 4.204A pdb=" N ASP L 384 " --> pdb=" O LYS L 381 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY L 385 " --> pdb=" O MET L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 389 through 403 removed outlier: 4.449A pdb=" N ASN L 393 " --> pdb=" O ALA L 389 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY L 399 " --> pdb=" O ALA L 395 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE L 403 " --> pdb=" O GLY L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 428 removed outlier: 3.558A pdb=" N ALA L 418 " --> pdb=" O ASP L 414 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA L 423 " --> pdb=" O VAL L 419 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU L 424 " --> pdb=" O ARG L 420 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL L 425 " --> pdb=" O LYS L 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 194 removed outlier: 3.588A pdb=" N ILE M 190 " --> pdb=" O LEU M 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 202 removed outlier: 4.624A pdb=" N LEU M 199 " --> pdb=" O GLU M 195 " (cutoff:3.500A) Proline residue: M 200 - end of helix Processing helix chain 'M' and resid 206 through 211 Processing helix chain 'M' and resid 227 through 236 removed outlier: 3.588A pdb=" N ALA M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 251 Processing helix chain 'M' and resid 257 through 271 removed outlier: 3.746A pdb=" N ARG M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE M 267 " --> pdb=" O VAL M 263 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA M 268 " --> pdb=" O ARG M 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 311 removed outlier: 3.510A pdb=" N ARG M 303 " --> pdb=" O ARG M 299 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU M 306 " --> pdb=" O GLN M 302 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU M 307 " --> pdb=" O ARG M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 364 removed outlier: 3.619A pdb=" N ALA M 358 " --> pdb=" O GLU M 354 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLN M 359 " --> pdb=" O ASP M 355 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE M 360 " --> pdb=" O SER M 356 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE M 363 " --> pdb=" O GLN M 359 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 380 Processing helix chain 'M' and resid 387 through 404 removed outlier: 3.765A pdb=" N LYS M 392 " --> pdb=" O GLY M 388 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA M 393 " --> pdb=" O ALA M 389 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL M 394 " --> pdb=" O GLN M 390 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR M 395 " --> pdb=" O LEU M 391 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL M 396 " --> pdb=" O LYS M 392 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLU M 397 " --> pdb=" O ALA M 393 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET M 400 " --> pdb=" O VAL M 396 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA M 402 " --> pdb=" O ALA M 398 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU M 403 " --> pdb=" O GLY M 399 " (cutoff:3.500A) Processing helix chain 'M' and resid 415 through 420 removed outlier: 4.251A pdb=" N SER M 420 " --> pdb=" O VAL M 416 " (cutoff:3.500A) Processing helix chain 'M' and resid 421 through 423 No H-bonds generated for 'chain 'M' and resid 421 through 423' Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.535A pdb=" N LEU A 43 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 52 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.711A pdb=" N TYR A 155 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A 154 " --> pdb=" O TYR A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.711A pdb=" N PHE A 234 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.525A pdb=" N VAL B 44 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 47 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 210 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 213 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 236 " --> pdb=" O ILE B 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.745A pdb=" N LEU B 67 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 163 through 164 removed outlier: 3.947A pdb=" N ILE C 38 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 45 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU C 46 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA C 214 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 74 through 75 removed outlier: 4.093A pdb=" N GLY C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA9, first strand: chain 'C' and resid 149 through 150 Processing sheet with id=AB1, first strand: chain 'D' and resid 161 through 164 removed outlier: 3.549A pdb=" N GLN D 162 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 164 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 44 " --> pdb=" O THR D 213 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR D 213 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL D 222 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 72 through 74 removed outlier: 3.648A pdb=" N ALA D 136 " --> pdb=" O VAL D 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 169 through 171 removed outlier: 3.605A pdb=" N GLY E 39 " --> pdb=" O LYS E 170 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL E 47 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL E 46 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN E 218 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS E 229 " --> pdb=" O CYS E 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.785A pdb=" N LEU E 143 " --> pdb=" O ALA E 77 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 35 through 39 removed outlier: 3.739A pdb=" N LEU F 38 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA F 214 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 48 " --> pdb=" O SER F 212 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR F 223 " --> pdb=" O ILE F 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 63 through 67 removed outlier: 3.937A pdb=" N CYS F 66 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY F 71 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU F 133 " --> pdb=" O SER F 73 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY F 136 " --> pdb=" O HIS F 143 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS F 143 " --> pdb=" O GLY F 136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR F 154 " --> pdb=" O GLU F 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 37 through 41 removed outlier: 3.520A pdb=" N ILE G 38 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA G 49 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL G 50 " --> pdb=" O GLU G 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 37 through 41 removed outlier: 3.520A pdb=" N ILE G 38 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA G 49 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS G 219 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.589A pdb=" N GLN G 68 " --> pdb=" O CYS G 76 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS G 76 " --> pdb=" O GLN G 68 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY G 75 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE G 137 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AC2, first strand: chain 'H' and resid 246 through 248 removed outlier: 7.120A pdb=" N LEU H 247 " --> pdb=" O VAL H 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'I' and resid 246 through 248 removed outlier: 3.844A pdb=" N ASP I 282 " --> pdb=" O ILE I 247 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 291 through 293 removed outlier: 3.693A pdb=" N ILE J 314 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR J 188 " --> pdb=" O ILE J 314 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 218 through 219 removed outlier: 6.884A pdb=" N VAL L 218 " --> pdb=" O MET L 325 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.89 Time building geometry restraints manager: 6.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8160 1.34 - 1.45: 4299 1.45 - 1.57: 12509 1.57 - 1.69: 26 1.69 - 1.81: 147 Bond restraints: 25141 Sorted by residual: bond pdb=" C4 ATP I 501 " pdb=" C5 ATP I 501 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C4 ATP J 501 " pdb=" C5 ATP J 501 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.72e+01 bond pdb=" C4 ATP K 501 " pdb=" C5 ATP K 501 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.59e+01 bond pdb=" C5 ATP K 501 " pdb=" C6 ATP K 501 " ideal model delta sigma weight residual 1.409 1.466 -0.057 1.00e-02 1.00e+04 3.29e+01 bond pdb=" C5 ATP I 501 " pdb=" N7 ATP I 501 " ideal model delta sigma weight residual 1.387 1.331 0.056 1.00e-02 1.00e+04 3.12e+01 ... (remaining 25136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.75: 33932 4.75 - 9.51: 173 9.51 - 14.26: 1 14.26 - 19.01: 1 19.01 - 23.76: 5 Bond angle restraints: 34112 Sorted by residual: angle pdb=" PB ATP J 501 " pdb=" O3B ATP J 501 " pdb=" PG ATP J 501 " ideal model delta sigma weight residual 139.87 116.11 23.76 1.00e+00 1.00e+00 5.65e+02 angle pdb=" PB ATP K 501 " pdb=" O3B ATP K 501 " pdb=" PG ATP K 501 " ideal model delta sigma weight residual 139.87 118.79 21.08 1.00e+00 1.00e+00 4.44e+02 angle pdb=" PB ATP I 501 " pdb=" O3B ATP I 501 " pdb=" PG ATP I 501 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PA ATP I 501 " pdb=" O3A ATP I 501 " pdb=" PB ATP I 501 " ideal model delta sigma weight residual 136.83 117.43 19.40 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PA ATP J 501 " pdb=" O3A ATP J 501 " pdb=" PB ATP J 501 " ideal model delta sigma weight residual 136.83 117.48 19.35 1.00e+00 1.00e+00 3.74e+02 ... (remaining 34107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 15139 35.73 - 71.45: 153 71.45 - 107.18: 11 107.18 - 142.90: 2 142.90 - 178.63: 2 Dihedral angle restraints: 15307 sinusoidal: 5786 harmonic: 9521 Sorted by residual: dihedral pdb=" C5' ADP L 501 " pdb=" O5' ADP L 501 " pdb=" PA ADP L 501 " pdb=" O2A ADP L 501 " ideal model delta sinusoidal sigma weight residual 300.00 121.38 178.63 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP L 501 " pdb=" O3A ADP L 501 " pdb=" PA ADP L 501 " pdb=" PB ADP L 501 " ideal model delta sinusoidal sigma weight residual -60.00 115.03 -175.03 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CA ILE I 361 " pdb=" C ILE I 361 " pdb=" N LEU I 362 " pdb=" CA LEU I 362 " ideal model delta harmonic sigma weight residual -180.00 -145.56 -34.44 0 5.00e+00 4.00e-02 4.75e+01 ... (remaining 15304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3389 0.081 - 0.161: 556 0.161 - 0.242: 30 0.242 - 0.322: 0 0.322 - 0.403: 1 Chirality restraints: 3976 Sorted by residual: chirality pdb=" CB ILE H 431 " pdb=" CA ILE H 431 " pdb=" CG1 ILE H 431 " pdb=" CG2 ILE H 431 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CB VAL D 116 " pdb=" CA VAL D 116 " pdb=" CG1 VAL D 116 " pdb=" CG2 VAL D 116 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL C 75 " pdb=" CA VAL C 75 " pdb=" CG1 VAL C 75 " pdb=" CG2 VAL C 75 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 3973 not shown) Planarity restraints: 4421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU J 173 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C LEU J 173 " -0.061 2.00e-02 2.50e+03 pdb=" O LEU J 173 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE J 174 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP H 362 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO H 363 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 363 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 363 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 130 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO G 131 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO G 131 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 131 " -0.032 5.00e-02 4.00e+02 ... (remaining 4418 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 735 2.65 - 3.21: 27179 3.21 - 3.78: 37074 3.78 - 4.34: 50102 4.34 - 4.90: 76401 Nonbonded interactions: 191491 Sorted by model distance: nonbonded pdb=" OG1 THR K 220 " pdb=" O3B ATP K 501 " model vdw 2.089 3.040 nonbonded pdb=" OG1 THR I 230 " pdb=" O1B ATP I 501 " model vdw 2.099 3.040 nonbonded pdb=" OG1 THR M 370 " pdb=" O VAL M 410 " model vdw 2.147 3.040 nonbonded pdb=" O ALA H 430 " pdb=" N ARG H 435 " model vdw 2.172 3.120 nonbonded pdb=" O GLN F 166 " pdb=" OG1 THR F 170 " model vdw 2.184 3.040 ... (remaining 191486 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.760 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: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.190 Set scattering table: 0.200 Process input model: 52.250 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.117 25141 Z= 0.704 Angle : 1.074 23.763 34112 Z= 0.630 Chirality : 0.057 0.403 3976 Planarity : 0.006 0.060 4421 Dihedral : 13.016 178.628 9189 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.76 % Favored : 83.24 % Rotamer: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.24 (0.12), residues: 3288 helix: -3.88 (0.10), residues: 979 sheet: -4.35 (0.18), residues: 363 loop : -3.19 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 159 HIS 0.018 0.003 HIS L 273 PHE 0.032 0.003 PHE D 11 TYR 0.027 0.003 TYR A 162 ARG 0.017 0.002 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 641 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.7442 (m-10) cc_final: 0.7174 (m-10) REVERT: A 49 ASP cc_start: 0.8616 (t70) cc_final: 0.8163 (t0) REVERT: A 89 ASP cc_start: 0.8463 (p0) cc_final: 0.7453 (t0) REVERT: A 106 TYR cc_start: 0.7791 (t80) cc_final: 0.6624 (m-10) REVERT: B 97 TYR cc_start: 0.6933 (t80) cc_final: 0.6508 (t80) REVERT: B 99 ARG cc_start: 0.8282 (mtt90) cc_final: 0.7897 (mtt90) REVERT: B 111 VAL cc_start: 0.9021 (p) cc_final: 0.8761 (t) REVERT: B 241 GLN cc_start: 0.7637 (pm20) cc_final: 0.7279 (pm20) REVERT: C 1 MET cc_start: 0.5345 (ptm) cc_final: 0.4811 (ptt) REVERT: C 27 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7874 (tm-30) REVERT: C 129 ARG cc_start: 0.8664 (ptt-90) cc_final: 0.8446 (ptt90) REVERT: C 213 PHE cc_start: 0.8274 (p90) cc_final: 0.7761 (p90) REVERT: C 235 ILE cc_start: 0.8816 (mt) cc_final: 0.8563 (mt) REVERT: D 149 GLN cc_start: 0.7091 (tm130) cc_final: 0.6544 (tm-30) REVERT: E 90 GLU cc_start: 0.8517 (tt0) cc_final: 0.7850 (tp30) REVERT: E 182 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7581 (tm-30) REVERT: F 24 TYR cc_start: 0.8846 (m-80) cc_final: 0.8412 (m-80) REVERT: F 173 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8185 (mt-10) REVERT: G 86 ARG cc_start: 0.7723 (tpp-160) cc_final: 0.7322 (tpt170) REVERT: G 132 PHE cc_start: 0.7681 (m-10) cc_final: 0.7475 (m-10) REVERT: G 212 PHE cc_start: 0.8622 (p90) cc_final: 0.8216 (p90) REVERT: G 225 ASN cc_start: 0.7292 (t0) cc_final: 0.7089 (t0) REVERT: G 242 PHE cc_start: 0.7279 (t80) cc_final: 0.6937 (t80) REVERT: H 376 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6605 (tm-30) REVERT: H 392 HIS cc_start: 0.8050 (m-70) cc_final: 0.7539 (m90) REVERT: I 222 TYR cc_start: 0.6680 (m-80) cc_final: 0.6414 (m-80) REVERT: I 306 MET cc_start: 0.8760 (tmm) cc_final: 0.8513 (tmm) REVERT: I 348 ILE cc_start: 0.8812 (mp) cc_final: 0.8521 (mp) REVERT: I 398 GLU cc_start: 0.8492 (tp30) cc_final: 0.8260 (tp30) REVERT: J 137 MET cc_start: 0.8779 (pmm) cc_final: 0.8492 (pmm) REVERT: J 156 GLN cc_start: 0.8940 (mp10) cc_final: 0.8275 (mp10) REVERT: J 227 SER cc_start: 0.9206 (m) cc_final: 0.8697 (t) REVERT: J 247 MET cc_start: 0.8762 (mtt) cc_final: 0.8276 (mtt) REVERT: J 292 MET cc_start: 0.8458 (ttm) cc_final: 0.8223 (mtm) REVERT: J 327 ILE cc_start: 0.9415 (mm) cc_final: 0.9185 (mm) REVERT: J 368 TYR cc_start: 0.7698 (t80) cc_final: 0.6931 (t80) REVERT: K 164 ASN cc_start: 0.8762 (p0) cc_final: 0.8549 (p0) REVERT: K 196 ASP cc_start: 0.9037 (p0) cc_final: 0.8778 (p0) REVERT: K 238 ASN cc_start: 0.9102 (p0) cc_final: 0.8893 (p0) REVERT: K 289 ASP cc_start: 0.8695 (p0) cc_final: 0.8384 (p0) REVERT: K 322 ASP cc_start: 0.8251 (p0) cc_final: 0.8042 (p0) REVERT: K 346 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.7594 (ppt170) REVERT: L 221 TYR cc_start: 0.8390 (p90) cc_final: 0.8136 (p90) REVERT: L 279 PHE cc_start: 0.8592 (t80) cc_final: 0.7744 (t80) REVERT: L 328 ASN cc_start: 0.8898 (m110) cc_final: 0.8471 (m-40) REVERT: L 359 GLU cc_start: 0.9302 (mp0) cc_final: 0.8994 (mp0) outliers start: 0 outliers final: 0 residues processed: 641 average time/residue: 0.4322 time to fit residues: 411.4407 Evaluate side-chains 422 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 275 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 166 optimal weight: 0.1980 chunk 132 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN A 181 ASN B 218 ASN C 21 GLN C 103 ASN C 177 GLN D 16 HIS D 19 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN F 210 ASN I 418 GLN K 244 HIS L 311 GLN L 328 ASN ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.087714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.074751 restraints weight = 88530.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.076421 restraints weight = 56982.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.077547 restraints weight = 40616.099| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25141 Z= 0.248 Angle : 0.782 7.845 34112 Z= 0.402 Chirality : 0.048 0.177 3976 Planarity : 0.005 0.068 4421 Dihedral : 9.877 153.531 3694 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.20 % Allowed : 5.04 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.13), residues: 3288 helix: -2.61 (0.12), residues: 1146 sheet: -3.42 (0.22), residues: 385 loop : -2.82 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 160 HIS 0.008 0.001 HIS M 364 PHE 0.021 0.002 PHE A 205 TYR 0.021 0.002 TYR H 249 ARG 0.009 0.001 ARG K 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 597 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8529 (t70) cc_final: 0.8210 (t0) REVERT: A 89 ASP cc_start: 0.8370 (p0) cc_final: 0.7725 (t0) REVERT: A 162 TYR cc_start: 0.6863 (p90) cc_final: 0.6576 (p90) REVERT: A 175 GLN cc_start: 0.8192 (pm20) cc_final: 0.7656 (pm20) REVERT: B 75 TYR cc_start: 0.8134 (p90) cc_final: 0.7789 (p90) REVERT: B 99 ARG cc_start: 0.8302 (mtt90) cc_final: 0.8100 (mtt90) REVERT: B 117 ILE cc_start: 0.8986 (mm) cc_final: 0.8643 (mm) REVERT: B 241 GLN cc_start: 0.7771 (pm20) cc_final: 0.7340 (pm20) REVERT: C 1 MET cc_start: 0.5456 (ptm) cc_final: 0.4885 (ptt) REVERT: C 114 ARG cc_start: 0.8833 (tpm170) cc_final: 0.8515 (tpp-160) REVERT: C 120 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8340 (tm-30) REVERT: C 213 PHE cc_start: 0.8301 (p90) cc_final: 0.8064 (p90) REVERT: D 56 ASP cc_start: 0.7478 (t70) cc_final: 0.6875 (m-30) REVERT: D 120 TYR cc_start: 0.8134 (m-80) cc_final: 0.7446 (m-80) REVERT: D 149 GLN cc_start: 0.7448 (tm-30) cc_final: 0.7087 (tm-30) REVERT: D 163 THR cc_start: 0.9493 (p) cc_final: 0.9178 (t) REVERT: E 84 ASP cc_start: 0.8779 (p0) cc_final: 0.8449 (p0) REVERT: E 88 MET cc_start: 0.8718 (mtm) cc_final: 0.8513 (mtp) REVERT: E 90 GLU cc_start: 0.8419 (tt0) cc_final: 0.7668 (tp30) REVERT: F 24 TYR cc_start: 0.8745 (m-80) cc_final: 0.8374 (m-10) REVERT: F 144 LEU cc_start: 0.9082 (tp) cc_final: 0.8835 (tp) REVERT: F 145 LEU cc_start: 0.8819 (mt) cc_final: 0.8612 (mt) REVERT: F 147 PHE cc_start: 0.8616 (t80) cc_final: 0.7975 (t80) REVERT: F 228 GLU cc_start: 0.8512 (mp0) cc_final: 0.8257 (mm-30) REVERT: G 18 ASP cc_start: 0.9015 (p0) cc_final: 0.8709 (p0) REVERT: G 53 LEU cc_start: 0.8625 (tt) cc_final: 0.8054 (pp) REVERT: G 212 PHE cc_start: 0.8688 (p90) cc_final: 0.8390 (p90) REVERT: G 225 ASN cc_start: 0.7236 (t0) cc_final: 0.6923 (t0) REVERT: H 392 HIS cc_start: 0.7559 (m-70) cc_final: 0.7079 (m90) REVERT: H 448 ASP cc_start: 0.8821 (t0) cc_final: 0.8614 (t0) REVERT: I 194 ILE cc_start: 0.8244 (mp) cc_final: 0.8040 (mm) REVERT: I 326 MET cc_start: 0.8491 (pmm) cc_final: 0.8230 (pmm) REVERT: I 352 ASN cc_start: 0.8312 (m-40) cc_final: 0.8088 (m-40) REVERT: I 395 MET cc_start: 0.8886 (tpp) cc_final: 0.8604 (tpp) REVERT: I 417 LYS cc_start: 0.9219 (tttm) cc_final: 0.8921 (tptt) REVERT: J 327 ILE cc_start: 0.9364 (mm) cc_final: 0.9111 (mm) REVERT: J 359 LYS cc_start: 0.9159 (ptmt) cc_final: 0.8789 (tttt) REVERT: J 368 TYR cc_start: 0.7766 (t80) cc_final: 0.7077 (t80) REVERT: K 161 MET cc_start: 0.7504 (ppp) cc_final: 0.7145 (ppp) REVERT: K 285 GLN cc_start: 0.9228 (mm-40) cc_final: 0.8934 (mm-40) REVERT: K 292 VAL cc_start: 0.9181 (m) cc_final: 0.8810 (p) REVERT: K 322 ASP cc_start: 0.7923 (p0) cc_final: 0.7705 (p0) REVERT: L 167 VAL cc_start: 0.8877 (t) cc_final: 0.8496 (p) REVERT: L 306 MET cc_start: 0.8329 (mtt) cc_final: 0.7867 (mtt) REVERT: L 328 ASN cc_start: 0.8665 (m-40) cc_final: 0.8268 (m-40) REVERT: L 359 GLU cc_start: 0.8963 (mp0) cc_final: 0.8718 (mp0) REVERT: M 303 ARG cc_start: 0.8513 (mtt90) cc_final: 0.8062 (ptp-170) REVERT: M 368 MET cc_start: 0.6729 (ptp) cc_final: 0.6343 (ptt) outliers start: 5 outliers final: 2 residues processed: 600 average time/residue: 0.3936 time to fit residues: 360.1614 Evaluate side-chains 450 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 448 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 219 optimal weight: 10.0000 chunk 290 optimal weight: 2.9990 chunk 132 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 274 optimal weight: 0.1980 chunk 226 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 262 optimal weight: 9.9990 chunk 245 optimal weight: 0.8980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 84 ASN A 209 HIS B 123 GLN B 218 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN M 310 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.073916 restraints weight = 87628.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.075662 restraints weight = 56985.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.077452 restraints weight = 37728.468| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 25141 Z= 0.241 Angle : 0.722 8.627 34112 Z= 0.369 Chirality : 0.046 0.167 3976 Planarity : 0.004 0.053 4421 Dihedral : 8.893 125.107 3694 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 0.04 % Allowed : 5.97 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.14), residues: 3288 helix: -2.04 (0.13), residues: 1170 sheet: -2.83 (0.22), residues: 418 loop : -2.45 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 218 HIS 0.008 0.001 HIS A 209 PHE 0.014 0.002 PHE C 213 TYR 0.016 0.001 TYR L 221 ARG 0.008 0.001 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 555 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8455 (t70) cc_final: 0.7965 (t0) REVERT: A 89 ASP cc_start: 0.8417 (p0) cc_final: 0.7611 (t0) REVERT: A 231 ASP cc_start: 0.7498 (t70) cc_final: 0.7284 (t70) REVERT: B 75 TYR cc_start: 0.8260 (p90) cc_final: 0.7960 (p90) REVERT: B 99 ARG cc_start: 0.8248 (mtt90) cc_final: 0.7974 (mtt90) REVERT: B 117 ILE cc_start: 0.8969 (mm) cc_final: 0.8670 (mm) REVERT: B 241 GLN cc_start: 0.7796 (pm20) cc_final: 0.7482 (pm20) REVERT: C 1 MET cc_start: 0.5262 (ptm) cc_final: 0.4971 (ptt) REVERT: C 114 ARG cc_start: 0.8924 (tpm170) cc_final: 0.8607 (tpp-160) REVERT: C 120 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8400 (tm-30) REVERT: D 16 HIS cc_start: 0.8588 (m90) cc_final: 0.8190 (m90) REVERT: D 56 ASP cc_start: 0.7527 (t70) cc_final: 0.7129 (m-30) REVERT: D 120 TYR cc_start: 0.8102 (m-80) cc_final: 0.7526 (m-80) REVERT: D 149 GLN cc_start: 0.7571 (tm-30) cc_final: 0.6996 (tm-30) REVERT: E 90 GLU cc_start: 0.8347 (tt0) cc_final: 0.8088 (tt0) REVERT: E 121 LEU cc_start: 0.7712 (mt) cc_final: 0.7445 (tp) REVERT: F 24 TYR cc_start: 0.8885 (m-80) cc_final: 0.8660 (m-10) REVERT: F 147 PHE cc_start: 0.8298 (t80) cc_final: 0.8087 (t80) REVERT: G 18 ASP cc_start: 0.9073 (p0) cc_final: 0.8735 (p0) REVERT: G 44 ASP cc_start: 0.8425 (t0) cc_final: 0.8199 (t0) REVERT: G 53 LEU cc_start: 0.8685 (tt) cc_final: 0.8239 (pp) REVERT: G 84 ASP cc_start: 0.8414 (p0) cc_final: 0.8198 (p0) REVERT: G 104 LYS cc_start: 0.3210 (mttt) cc_final: 0.2887 (mttp) REVERT: G 110 PRO cc_start: 0.9148 (Cg_exo) cc_final: 0.8842 (Cg_endo) REVERT: G 138 PHE cc_start: 0.8569 (p90) cc_final: 0.8362 (p90) REVERT: G 206 ASP cc_start: 0.8933 (p0) cc_final: 0.8713 (p0) REVERT: G 212 PHE cc_start: 0.8775 (p90) cc_final: 0.8447 (p90) REVERT: G 225 ASN cc_start: 0.7313 (t0) cc_final: 0.6981 (t0) REVERT: H 387 ASN cc_start: 0.8697 (m-40) cc_final: 0.8404 (m110) REVERT: H 392 HIS cc_start: 0.7382 (m-70) cc_final: 0.6882 (m90) REVERT: H 448 ASP cc_start: 0.9031 (t0) cc_final: 0.8757 (t0) REVERT: I 180 SER cc_start: 0.5313 (t) cc_final: 0.5068 (m) REVERT: I 193 GLU cc_start: 0.8172 (mp0) cc_final: 0.7727 (mp0) REVERT: I 194 ILE cc_start: 0.8326 (mp) cc_final: 0.8007 (mm) REVERT: I 253 ILE cc_start: 0.8817 (mp) cc_final: 0.8578 (mm) REVERT: I 340 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.8124 (mtm-85) REVERT: I 343 ARG cc_start: 0.6966 (mtt90) cc_final: 0.6383 (mtt90) REVERT: I 395 MET cc_start: 0.8930 (tpp) cc_final: 0.8570 (tpp) REVERT: I 417 LYS cc_start: 0.9217 (tttm) cc_final: 0.8856 (tptt) REVERT: J 239 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7839 (tm-30) REVERT: J 249 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7346 (mm-30) REVERT: J 327 ILE cc_start: 0.9345 (mm) cc_final: 0.9126 (mm) REVERT: J 359 LYS cc_start: 0.9180 (ptmt) cc_final: 0.8779 (tttt) REVERT: J 368 TYR cc_start: 0.7702 (t80) cc_final: 0.7297 (t80) REVERT: K 161 MET cc_start: 0.7737 (ppp) cc_final: 0.7370 (ppp) REVERT: K 221 MET cc_start: 0.7905 (ppp) cc_final: 0.7546 (ppp) REVERT: K 222 LEU cc_start: 0.8990 (tt) cc_final: 0.8761 (tt) REVERT: K 285 GLN cc_start: 0.9256 (mm-40) cc_final: 0.9026 (mm-40) REVERT: K 292 VAL cc_start: 0.8839 (m) cc_final: 0.8505 (p) REVERT: K 298 GLU cc_start: 0.8388 (pp20) cc_final: 0.8182 (pp20) REVERT: K 322 ASP cc_start: 0.7954 (p0) cc_final: 0.7665 (p0) REVERT: K 346 ARG cc_start: 0.5506 (ptt90) cc_final: 0.5257 (tmt170) REVERT: L 281 ASP cc_start: 0.7737 (p0) cc_final: 0.6374 (p0) REVERT: L 311 GLN cc_start: 0.8018 (tp40) cc_final: 0.7804 (tp40) REVERT: L 328 ASN cc_start: 0.8591 (m-40) cc_final: 0.8176 (m-40) REVERT: L 359 GLU cc_start: 0.8955 (mp0) cc_final: 0.8689 (mp0) REVERT: M 397 GLU cc_start: 0.8745 (mp0) cc_final: 0.8526 (mp0) outliers start: 1 outliers final: 0 residues processed: 555 average time/residue: 0.3835 time to fit residues: 326.3240 Evaluate side-chains 438 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 216 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 chunk 272 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 chunk 305 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 304 optimal weight: 8.9990 chunk 323 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 310 optimal weight: 20.0000 chunk 152 optimal weight: 0.9980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 84 ASN B 119 GLN B 218 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.082663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.069400 restraints weight = 88807.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.071136 restraints weight = 55985.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.072282 restraints weight = 39393.223| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25141 Z= 0.302 Angle : 0.742 9.157 34112 Z= 0.383 Chirality : 0.048 0.205 3976 Planarity : 0.005 0.069 4421 Dihedral : 8.555 97.555 3694 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.14), residues: 3288 helix: -1.77 (0.14), residues: 1197 sheet: -2.42 (0.23), residues: 436 loop : -2.31 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 218 HIS 0.008 0.001 HIS A 209 PHE 0.026 0.002 PHE D 174 TYR 0.024 0.002 TYR D 232 ARG 0.008 0.001 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 529 time to evaluate : 2.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8686 (t70) cc_final: 0.8166 (t0) REVERT: A 89 ASP cc_start: 0.8427 (p0) cc_final: 0.7723 (t0) REVERT: A 231 ASP cc_start: 0.7733 (t70) cc_final: 0.7479 (t70) REVERT: B 75 TYR cc_start: 0.8560 (p90) cc_final: 0.8360 (p90) REVERT: B 99 ARG cc_start: 0.8299 (mtt90) cc_final: 0.7990 (mtt90) REVERT: C 1 MET cc_start: 0.5290 (ptm) cc_final: 0.5088 (ptt) REVERT: C 93 ILE cc_start: 0.8601 (pt) cc_final: 0.8389 (mt) REVERT: C 114 ARG cc_start: 0.8988 (tpm170) cc_final: 0.8677 (tpp-160) REVERT: D 16 HIS cc_start: 0.8734 (m90) cc_final: 0.8079 (m90) REVERT: D 56 ASP cc_start: 0.7968 (t70) cc_final: 0.7253 (m-30) REVERT: E 84 ASP cc_start: 0.8759 (p0) cc_final: 0.8455 (p0) REVERT: E 90 GLU cc_start: 0.8479 (tt0) cc_final: 0.8235 (mt-10) REVERT: E 206 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7931 (tm-30) REVERT: F 19 LEU cc_start: 0.8853 (mp) cc_final: 0.8557 (mp) REVERT: F 102 LYS cc_start: 0.8237 (mmmt) cc_final: 0.7480 (mtmt) REVERT: F 147 PHE cc_start: 0.8406 (t80) cc_final: 0.8203 (t80) REVERT: F 228 GLU cc_start: 0.8494 (mp0) cc_final: 0.8248 (mm-30) REVERT: G 9 ASP cc_start: 0.7304 (p0) cc_final: 0.6987 (p0) REVERT: G 18 ASP cc_start: 0.9061 (p0) cc_final: 0.8771 (p0) REVERT: G 53 LEU cc_start: 0.8606 (tt) cc_final: 0.8319 (pp) REVERT: G 84 ASP cc_start: 0.8471 (p0) cc_final: 0.8260 (p0) REVERT: G 86 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7593 (ttm-80) REVERT: G 104 LYS cc_start: 0.3033 (mttt) cc_final: 0.2735 (mttp) REVERT: G 110 PRO cc_start: 0.9198 (Cg_exo) cc_final: 0.8923 (Cg_endo) REVERT: G 206 ASP cc_start: 0.9011 (p0) cc_final: 0.8802 (p0) REVERT: G 212 PHE cc_start: 0.8846 (p90) cc_final: 0.8582 (p90) REVERT: G 225 ASN cc_start: 0.7526 (t0) cc_final: 0.7240 (t0) REVERT: I 193 GLU cc_start: 0.8460 (mp0) cc_final: 0.7980 (mp0) REVERT: I 253 ILE cc_start: 0.9114 (mp) cc_final: 0.8856 (mm) REVERT: I 307 LEU cc_start: 0.9196 (tp) cc_final: 0.8966 (tp) REVERT: I 343 ARG cc_start: 0.7290 (mtt90) cc_final: 0.6835 (mtt90) REVERT: I 395 MET cc_start: 0.8962 (tpp) cc_final: 0.8632 (tpp) REVERT: J 239 GLU cc_start: 0.8243 (tm-30) cc_final: 0.8014 (tm-30) REVERT: J 249 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7416 (mm-30) REVERT: J 311 ASP cc_start: 0.8631 (p0) cc_final: 0.8335 (m-30) REVERT: J 327 ILE cc_start: 0.9363 (mm) cc_final: 0.9119 (mm) REVERT: J 359 LYS cc_start: 0.9269 (ptmt) cc_final: 0.9058 (tttt) REVERT: J 362 CYS cc_start: 0.9069 (t) cc_final: 0.8850 (t) REVERT: K 161 MET cc_start: 0.8069 (ppp) cc_final: 0.7713 (ppp) REVERT: K 204 ASP cc_start: 0.8450 (p0) cc_final: 0.8066 (p0) REVERT: K 221 MET cc_start: 0.8218 (ppp) cc_final: 0.7881 (ppp) REVERT: K 222 LEU cc_start: 0.9257 (tt) cc_final: 0.8990 (tt) REVERT: K 292 VAL cc_start: 0.9116 (m) cc_final: 0.8822 (p) REVERT: K 322 ASP cc_start: 0.8099 (p0) cc_final: 0.7875 (p0) REVERT: L 203 ASN cc_start: 0.8875 (p0) cc_final: 0.8617 (p0) REVERT: L 255 TYR cc_start: 0.8630 (m-10) cc_final: 0.8422 (m-10) REVERT: L 328 ASN cc_start: 0.8664 (m-40) cc_final: 0.8202 (m-40) REVERT: L 359 GLU cc_start: 0.9095 (mp0) cc_final: 0.8742 (mp0) REVERT: M 397 GLU cc_start: 0.8963 (mp0) cc_final: 0.8617 (mp0) outliers start: 1 outliers final: 0 residues processed: 529 average time/residue: 0.3808 time to fit residues: 309.7981 Evaluate side-chains 435 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 281 optimal weight: 9.9990 chunk 245 optimal weight: 0.0010 chunk 301 optimal weight: 4.9990 chunk 253 optimal weight: 0.8980 chunk 260 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 306 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 84 ASN B 218 ASN D 178 ASN D 204 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN I 190 GLN I 254 GLN J 204 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.085667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.072198 restraints weight = 87839.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.073981 restraints weight = 55731.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.075196 restraints weight = 39225.715| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25141 Z= 0.192 Angle : 0.689 9.208 34112 Z= 0.347 Chirality : 0.046 0.192 3976 Planarity : 0.004 0.076 4421 Dihedral : 8.027 92.265 3694 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.12 % Allowed : 4.22 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.14), residues: 3288 helix: -1.48 (0.14), residues: 1186 sheet: -2.06 (0.24), residues: 436 loop : -2.21 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 160 HIS 0.014 0.001 HIS G 204 PHE 0.025 0.002 PHE D 174 TYR 0.021 0.001 TYR L 269 ARG 0.010 0.000 ARG L 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 527 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8423 (p0) cc_final: 0.7623 (t0) REVERT: A 231 ASP cc_start: 0.7694 (t70) cc_final: 0.7197 (t70) REVERT: B 75 TYR cc_start: 0.8620 (p90) cc_final: 0.8390 (p90) REVERT: B 99 ARG cc_start: 0.8272 (mtt90) cc_final: 0.7962 (mtt90) REVERT: B 103 GLU cc_start: 0.8304 (pm20) cc_final: 0.8031 (pm20) REVERT: B 149 GLN cc_start: 0.8532 (tm-30) cc_final: 0.7915 (tm-30) REVERT: C 93 ILE cc_start: 0.8681 (pt) cc_final: 0.8464 (mt) REVERT: C 114 ARG cc_start: 0.8908 (tpm170) cc_final: 0.8545 (tpp-160) REVERT: D 16 HIS cc_start: 0.8697 (m90) cc_final: 0.8124 (m90) REVERT: D 19 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8174 (mm-40) REVERT: D 56 ASP cc_start: 0.7680 (t70) cc_final: 0.7275 (m-30) REVERT: D 108 TYR cc_start: 0.8341 (t80) cc_final: 0.8089 (t80) REVERT: D 120 TYR cc_start: 0.8023 (m-80) cc_final: 0.7520 (m-80) REVERT: E 84 ASP cc_start: 0.8746 (p0) cc_final: 0.8365 (p0) REVERT: F 19 LEU cc_start: 0.8803 (mp) cc_final: 0.8518 (mp) REVERT: F 60 GLN cc_start: 0.7264 (tp40) cc_final: 0.7018 (tp40) REVERT: F 147 PHE cc_start: 0.8386 (t80) cc_final: 0.8131 (t80) REVERT: G 9 ASP cc_start: 0.7203 (p0) cc_final: 0.6954 (p0) REVERT: G 18 ASP cc_start: 0.9087 (p0) cc_final: 0.8833 (p0) REVERT: G 53 LEU cc_start: 0.8581 (tt) cc_final: 0.8359 (pp) REVERT: G 104 LYS cc_start: 0.2998 (mttt) cc_final: 0.2792 (mttt) REVERT: G 110 PRO cc_start: 0.9235 (Cg_exo) cc_final: 0.8976 (Cg_endo) REVERT: G 212 PHE cc_start: 0.8798 (p90) cc_final: 0.8508 (p90) REVERT: G 225 ASN cc_start: 0.7413 (t0) cc_final: 0.7140 (t0) REVERT: I 253 ILE cc_start: 0.9173 (mp) cc_final: 0.8950 (mm) REVERT: I 417 LYS cc_start: 0.9214 (tttm) cc_final: 0.8733 (tptt) REVERT: J 311 ASP cc_start: 0.8614 (p0) cc_final: 0.8353 (m-30) REVERT: J 327 ILE cc_start: 0.9309 (mm) cc_final: 0.9077 (mm) REVERT: J 332 SER cc_start: 0.9026 (p) cc_final: 0.7727 (p) REVERT: J 359 LYS cc_start: 0.9212 (ptmt) cc_final: 0.8952 (tttt) REVERT: J 362 CYS cc_start: 0.8880 (t) cc_final: 0.8607 (t) REVERT: K 161 MET cc_start: 0.8027 (ppp) cc_final: 0.7687 (ppp) REVERT: K 164 ASN cc_start: 0.8166 (p0) cc_final: 0.7836 (p0) REVERT: K 204 ASP cc_start: 0.8419 (p0) cc_final: 0.7880 (p0) REVERT: K 221 MET cc_start: 0.8243 (ppp) cc_final: 0.7813 (ppp) REVERT: K 222 LEU cc_start: 0.9208 (tt) cc_final: 0.8875 (tt) REVERT: K 292 VAL cc_start: 0.8991 (m) cc_final: 0.8613 (p) REVERT: L 203 ASN cc_start: 0.8897 (p0) cc_final: 0.8672 (p0) REVERT: L 328 ASN cc_start: 0.8644 (m-40) cc_final: 0.8175 (m-40) REVERT: L 359 GLU cc_start: 0.9024 (mp0) cc_final: 0.8672 (mp0) REVERT: M 303 ARG cc_start: 0.8515 (mtt90) cc_final: 0.8087 (mtm-85) REVERT: M 397 GLU cc_start: 0.8919 (mp0) cc_final: 0.8600 (mp0) outliers start: 3 outliers final: 0 residues processed: 527 average time/residue: 0.3684 time to fit residues: 303.0754 Evaluate side-chains 422 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 211 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 227 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 245 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 27 GLN A 84 ASN B 218 ASN C 152 ASN D 178 ASN D 204 GLN F 86 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.085230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.071938 restraints weight = 86543.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.073675 restraints weight = 54745.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.074910 restraints weight = 38531.456| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25141 Z= 0.194 Angle : 0.679 10.035 34112 Z= 0.343 Chirality : 0.045 0.165 3976 Planarity : 0.004 0.049 4421 Dihedral : 7.715 83.442 3694 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.12 % Allowed : 3.13 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.14), residues: 3288 helix: -1.28 (0.14), residues: 1182 sheet: -1.95 (0.23), residues: 444 loop : -2.07 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 160 HIS 0.004 0.001 HIS A 209 PHE 0.036 0.001 PHE D 174 TYR 0.015 0.001 TYR D 108 ARG 0.016 0.001 ARG L 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 516 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ILE cc_start: 0.9260 (pt) cc_final: 0.9001 (mm) REVERT: A 89 ASP cc_start: 0.8519 (p0) cc_final: 0.7663 (t0) REVERT: A 92 ASN cc_start: 0.8723 (p0) cc_final: 0.8461 (p0) REVERT: A 231 ASP cc_start: 0.7512 (t70) cc_final: 0.7080 (t70) REVERT: B 103 GLU cc_start: 0.8327 (pm20) cc_final: 0.7917 (pm20) REVERT: C 93 ILE cc_start: 0.8711 (pt) cc_final: 0.8499 (mt) REVERT: C 114 ARG cc_start: 0.8909 (tpm170) cc_final: 0.8543 (tpp-160) REVERT: C 134 SER cc_start: 0.9404 (t) cc_final: 0.9080 (m) REVERT: C 233 GLN cc_start: 0.8471 (mm-40) cc_final: 0.7568 (tm-30) REVERT: D 16 HIS cc_start: 0.8742 (m90) cc_final: 0.8202 (m90) REVERT: D 56 ASP cc_start: 0.7847 (t70) cc_final: 0.7348 (m-30) REVERT: D 108 TYR cc_start: 0.8412 (t80) cc_final: 0.8109 (t80) REVERT: D 120 TYR cc_start: 0.7984 (m-80) cc_final: 0.7478 (m-80) REVERT: D 167 ASN cc_start: 0.9021 (m110) cc_final: 0.8726 (m-40) REVERT: D 204 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7053 (pp30) REVERT: E 84 ASP cc_start: 0.8726 (p0) cc_final: 0.8394 (p0) REVERT: F 60 GLN cc_start: 0.7294 (tp40) cc_final: 0.7025 (tp40) REVERT: F 102 LYS cc_start: 0.8403 (mmmt) cc_final: 0.7642 (mtmt) REVERT: G 9 ASP cc_start: 0.7183 (p0) cc_final: 0.6956 (p0) REVERT: G 18 ASP cc_start: 0.9127 (p0) cc_final: 0.8846 (p0) REVERT: G 53 LEU cc_start: 0.8603 (tt) cc_final: 0.8396 (pp) REVERT: G 84 ASP cc_start: 0.8539 (p0) cc_final: 0.8227 (p0) REVERT: G 86 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7303 (ttm-80) REVERT: G 110 PRO cc_start: 0.9193 (Cg_exo) cc_final: 0.8938 (Cg_endo) REVERT: G 212 PHE cc_start: 0.8728 (p90) cc_final: 0.8520 (p90) REVERT: G 225 ASN cc_start: 0.7411 (t0) cc_final: 0.7144 (t0) REVERT: I 200 LEU cc_start: 0.7603 (tt) cc_final: 0.7352 (tt) REVERT: I 253 ILE cc_start: 0.9217 (mp) cc_final: 0.8961 (mm) REVERT: I 417 LYS cc_start: 0.9217 (tttm) cc_final: 0.8761 (tptt) REVERT: J 183 LYS cc_start: 0.7235 (pttp) cc_final: 0.6962 (ptmt) REVERT: J 240 HIS cc_start: 0.7730 (m90) cc_final: 0.6819 (m90) REVERT: J 249 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7401 (mm-30) REVERT: J 311 ASP cc_start: 0.8495 (p0) cc_final: 0.8249 (m-30) REVERT: J 327 ILE cc_start: 0.9293 (mm) cc_final: 0.9074 (mm) REVERT: J 359 LYS cc_start: 0.9233 (ptmt) cc_final: 0.8984 (tttt) REVERT: K 161 MET cc_start: 0.8075 (ppp) cc_final: 0.7864 (ppp) REVERT: K 179 MET cc_start: 0.8735 (ppp) cc_final: 0.8368 (ppp) REVERT: K 221 MET cc_start: 0.8290 (ppp) cc_final: 0.7881 (ppp) REVERT: K 222 LEU cc_start: 0.9280 (tt) cc_final: 0.8932 (tt) REVERT: K 292 VAL cc_start: 0.9087 (m) cc_final: 0.8752 (p) REVERT: L 203 ASN cc_start: 0.8875 (p0) cc_final: 0.8615 (p0) REVERT: L 328 ASN cc_start: 0.8727 (m-40) cc_final: 0.8311 (m-40) REVERT: L 359 GLU cc_start: 0.8968 (mp0) cc_final: 0.8657 (mp0) REVERT: M 303 ARG cc_start: 0.8505 (mtt90) cc_final: 0.8077 (ptp-170) REVERT: M 397 GLU cc_start: 0.8931 (mp0) cc_final: 0.8601 (mp0) outliers start: 3 outliers final: 0 residues processed: 518 average time/residue: 0.3723 time to fit residues: 299.8882 Evaluate side-chains 421 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 420 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 233 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 278 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 27 GLN A 84 ASN B 218 ASN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN E 180 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 217 GLN K 302 GLN ** M 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.084202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.070858 restraints weight = 88295.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.072612 restraints weight = 55595.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.073866 restraints weight = 39012.016| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25141 Z= 0.219 Angle : 0.697 11.236 34112 Z= 0.351 Chirality : 0.046 0.230 3976 Planarity : 0.004 0.051 4421 Dihedral : 7.593 79.997 3694 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.08 % Allowed : 2.32 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.14), residues: 3288 helix: -1.16 (0.14), residues: 1189 sheet: -1.92 (0.23), residues: 446 loop : -1.99 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 404 HIS 0.004 0.001 HIS G 204 PHE 0.028 0.002 PHE D 174 TYR 0.016 0.001 TYR G 201 ARG 0.011 0.000 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 499 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8448 (ppp) cc_final: 0.8223 (ptt) REVERT: A 89 ASP cc_start: 0.8468 (p0) cc_final: 0.7648 (t0) REVERT: A 175 GLN cc_start: 0.7680 (pm20) cc_final: 0.7260 (pm20) REVERT: A 231 ASP cc_start: 0.7316 (t70) cc_final: 0.6960 (t70) REVERT: B 108 LYS cc_start: 0.6950 (ttpt) cc_final: 0.6624 (tmtt) REVERT: C 114 ARG cc_start: 0.8947 (tpm170) cc_final: 0.8579 (tpp-160) REVERT: C 120 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8555 (tm-30) REVERT: D 16 HIS cc_start: 0.8738 (m90) cc_final: 0.7952 (m90) REVERT: D 56 ASP cc_start: 0.7794 (t70) cc_final: 0.7501 (m-30) REVERT: D 120 TYR cc_start: 0.7978 (m-80) cc_final: 0.7456 (m-80) REVERT: E 84 ASP cc_start: 0.8731 (p0) cc_final: 0.8390 (p0) REVERT: F 102 LYS cc_start: 0.8330 (mmmt) cc_final: 0.7618 (mtmt) REVERT: F 197 ILE cc_start: 0.9037 (mp) cc_final: 0.8761 (mm) REVERT: G 18 ASP cc_start: 0.9116 (p0) cc_final: 0.8876 (p0) REVERT: G 84 ASP cc_start: 0.8589 (p0) cc_final: 0.8265 (p0) REVERT: G 86 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7297 (ttm-80) REVERT: G 110 PRO cc_start: 0.9216 (Cg_exo) cc_final: 0.8987 (Cg_endo) REVERT: G 225 ASN cc_start: 0.7439 (t0) cc_final: 0.7148 (t0) REVERT: H 428 MET cc_start: 0.6228 (tpt) cc_final: 0.5772 (ttm) REVERT: I 253 ILE cc_start: 0.9226 (mp) cc_final: 0.8976 (mm) REVERT: J 183 LYS cc_start: 0.7186 (pttp) cc_final: 0.6925 (ptmt) REVERT: J 240 HIS cc_start: 0.7650 (m90) cc_final: 0.6836 (m90) REVERT: J 249 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7412 (mm-30) REVERT: J 269 GLN cc_start: 0.9123 (tt0) cc_final: 0.8461 (tm-30) REVERT: J 327 ILE cc_start: 0.9320 (mm) cc_final: 0.8886 (tt) REVERT: J 359 LYS cc_start: 0.9253 (ptmt) cc_final: 0.9049 (tttt) REVERT: J 362 CYS cc_start: 0.8901 (t) cc_final: 0.8677 (t) REVERT: K 161 MET cc_start: 0.8212 (ppp) cc_final: 0.7977 (ppp) REVERT: K 164 ASN cc_start: 0.8203 (p0) cc_final: 0.7954 (p0) REVERT: K 221 MET cc_start: 0.8284 (ppp) cc_final: 0.7921 (ppp) REVERT: K 222 LEU cc_start: 0.9310 (tt) cc_final: 0.8970 (tt) REVERT: K 292 VAL cc_start: 0.9116 (m) cc_final: 0.8807 (p) REVERT: L 203 ASN cc_start: 0.8906 (p0) cc_final: 0.8385 (p0) REVERT: L 206 ILE cc_start: 0.7858 (mm) cc_final: 0.7065 (mm) REVERT: L 328 ASN cc_start: 0.8732 (m-40) cc_final: 0.8305 (m-40) REVERT: L 359 GLU cc_start: 0.9139 (mp0) cc_final: 0.8799 (mp0) REVERT: L 382 MET cc_start: 0.7917 (ppp) cc_final: 0.7570 (ppp) REVERT: M 303 ARG cc_start: 0.8562 (mtt90) cc_final: 0.8085 (ptp-170) REVERT: M 397 GLU cc_start: 0.8978 (mp0) cc_final: 0.8633 (mp0) outliers start: 2 outliers final: 0 residues processed: 501 average time/residue: 0.3547 time to fit residues: 282.0064 Evaluate side-chains 422 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 303 optimal weight: 9.9990 chunk 309 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 212 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 27 GLN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN D 178 ASN D 204 GLN E 180 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 204 HIS ** M 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.083631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.070529 restraints weight = 87500.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.072252 restraints weight = 54683.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.073476 restraints weight = 38220.084| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25141 Z= 0.221 Angle : 0.696 8.295 34112 Z= 0.351 Chirality : 0.046 0.162 3976 Planarity : 0.004 0.045 4421 Dihedral : 7.475 87.155 3694 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.08 % Allowed : 1.99 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.14), residues: 3288 helix: -1.07 (0.15), residues: 1186 sheet: -1.85 (0.23), residues: 446 loop : -1.93 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 160 HIS 0.007 0.001 HIS J 240 PHE 0.028 0.002 PHE D 174 TYR 0.031 0.001 TYR D 156 ARG 0.009 0.000 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 489 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8503 (p0) cc_final: 0.7584 (t0) REVERT: A 175 GLN cc_start: 0.7616 (pm20) cc_final: 0.7137 (pm20) REVERT: A 231 ASP cc_start: 0.7439 (t70) cc_final: 0.7113 (t70) REVERT: B 108 LYS cc_start: 0.6901 (ttpt) cc_final: 0.6637 (tmtt) REVERT: B 241 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8091 (tp40) REVERT: C 114 ARG cc_start: 0.8955 (tpm170) cc_final: 0.8603 (tpp-160) REVERT: D 16 HIS cc_start: 0.8760 (m90) cc_final: 0.8097 (m90) REVERT: D 120 TYR cc_start: 0.7995 (m-80) cc_final: 0.7454 (m-80) REVERT: D 151 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7576 (tm-30) REVERT: D 204 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.7075 (pp30) REVERT: E 22 PHE cc_start: 0.7894 (m-80) cc_final: 0.7660 (m-10) REVERT: E 84 ASP cc_start: 0.8665 (p0) cc_final: 0.8378 (p0) REVERT: F 60 GLN cc_start: 0.7507 (tp40) cc_final: 0.7246 (tp40) REVERT: F 102 LYS cc_start: 0.8308 (mmmt) cc_final: 0.7692 (mtmt) REVERT: F 190 ILE cc_start: 0.8934 (pt) cc_final: 0.8454 (mt) REVERT: G 18 ASP cc_start: 0.9148 (p0) cc_final: 0.8916 (p0) REVERT: G 84 ASP cc_start: 0.8635 (p0) cc_final: 0.8372 (p0) REVERT: G 86 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.7491 (ttm-80) REVERT: G 110 PRO cc_start: 0.9269 (Cg_exo) cc_final: 0.9031 (Cg_endo) REVERT: G 212 PHE cc_start: 0.8740 (p90) cc_final: 0.8539 (p90) REVERT: G 225 ASN cc_start: 0.7377 (t0) cc_final: 0.7106 (t0) REVERT: H 428 MET cc_start: 0.6406 (tpt) cc_final: 0.5881 (ttm) REVERT: J 183 LYS cc_start: 0.7543 (pttp) cc_final: 0.7000 (ptmt) REVERT: J 311 ASP cc_start: 0.8625 (p0) cc_final: 0.8274 (m-30) REVERT: J 327 ILE cc_start: 0.9292 (mm) cc_final: 0.8894 (tt) REVERT: J 359 LYS cc_start: 0.9255 (ptmt) cc_final: 0.9021 (tttt) REVERT: K 161 MET cc_start: 0.8237 (ppp) cc_final: 0.7997 (ppp) REVERT: K 179 MET cc_start: 0.8749 (ppp) cc_final: 0.8537 (ppp) REVERT: K 221 MET cc_start: 0.8312 (ppp) cc_final: 0.7946 (ppp) REVERT: K 222 LEU cc_start: 0.9314 (tt) cc_final: 0.8941 (tt) REVERT: K 303 MET cc_start: 0.8840 (mtp) cc_final: 0.8473 (tpp) REVERT: L 203 ASN cc_start: 0.8904 (p0) cc_final: 0.8367 (p0) REVERT: L 206 ILE cc_start: 0.7879 (mm) cc_final: 0.6999 (mm) REVERT: L 311 GLN cc_start: 0.7976 (tp40) cc_final: 0.7697 (tp40) REVERT: L 328 ASN cc_start: 0.8841 (m-40) cc_final: 0.8430 (m-40) REVERT: L 359 GLU cc_start: 0.9088 (mp0) cc_final: 0.8737 (mp0) REVERT: L 382 MET cc_start: 0.8015 (ppp) cc_final: 0.7643 (ppp) REVERT: M 303 ARG cc_start: 0.8582 (mtt90) cc_final: 0.8092 (ptp-170) REVERT: M 397 GLU cc_start: 0.9033 (mp0) cc_final: 0.8533 (mp0) outliers start: 2 outliers final: 0 residues processed: 491 average time/residue: 0.3581 time to fit residues: 279.9309 Evaluate side-chains 413 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 412 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 285 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 264 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 225 optimal weight: 0.2980 chunk 58 optimal weight: 0.4980 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 27 GLN C 152 ASN D 178 ASN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 240 HIS ** M 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.085096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.071838 restraints weight = 87763.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.073600 restraints weight = 55225.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.074842 restraints weight = 38556.631| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25141 Z= 0.176 Angle : 0.701 12.436 34112 Z= 0.347 Chirality : 0.045 0.170 3976 Planarity : 0.004 0.043 4421 Dihedral : 7.237 86.993 3694 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.04 % Allowed : 0.61 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.14), residues: 3288 helix: -0.98 (0.15), residues: 1192 sheet: -1.78 (0.23), residues: 453 loop : -1.80 (0.16), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 160 HIS 0.010 0.001 HIS J 240 PHE 0.049 0.001 PHE D 174 TYR 0.019 0.001 TYR D 108 ARG 0.009 0.000 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 497 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8539 (p0) cc_final: 0.7448 (t0) REVERT: A 175 GLN cc_start: 0.7517 (pm20) cc_final: 0.7103 (pm20) REVERT: B 108 LYS cc_start: 0.6894 (ttpt) cc_final: 0.6679 (tptp) REVERT: B 241 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8251 (tp40) REVERT: C 114 ARG cc_start: 0.8854 (tpm170) cc_final: 0.8502 (tpp-160) REVERT: C 120 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8550 (tm-30) REVERT: C 233 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7552 (tm-30) REVERT: D 16 HIS cc_start: 0.8731 (m90) cc_final: 0.8159 (m90) REVERT: D 56 ASP cc_start: 0.7433 (m-30) cc_final: 0.6666 (m-30) REVERT: D 120 TYR cc_start: 0.7945 (m-80) cc_final: 0.7464 (m-80) REVERT: D 151 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7613 (tm-30) REVERT: E 78 MET cc_start: 0.8385 (mtp) cc_final: 0.8074 (mmm) REVERT: E 84 ASP cc_start: 0.8647 (p0) cc_final: 0.8293 (p0) REVERT: E 143 LEU cc_start: 0.8655 (mt) cc_final: 0.8445 (mt) REVERT: F 60 GLN cc_start: 0.7453 (tp40) cc_final: 0.7226 (tp40) REVERT: F 90 GLN cc_start: 0.8162 (mp10) cc_final: 0.7784 (mp10) REVERT: F 102 LYS cc_start: 0.8237 (mmmt) cc_final: 0.7630 (mtmt) REVERT: F 190 ILE cc_start: 0.8928 (pt) cc_final: 0.8415 (mt) REVERT: G 18 ASP cc_start: 0.9160 (p0) cc_final: 0.8916 (p0) REVERT: G 110 PRO cc_start: 0.9270 (Cg_exo) cc_final: 0.9065 (Cg_endo) REVERT: G 225 ASN cc_start: 0.7321 (t0) cc_final: 0.7033 (t0) REVERT: H 226 GLU cc_start: 0.8285 (pm20) cc_final: 0.7904 (pm20) REVERT: H 428 MET cc_start: 0.6420 (tpt) cc_final: 0.5904 (ttm) REVERT: I 193 GLU cc_start: 0.8636 (mp0) cc_final: 0.7799 (mp0) REVERT: I 219 VAL cc_start: 0.8484 (p) cc_final: 0.8055 (m) REVERT: J 183 LYS cc_start: 0.7486 (pttp) cc_final: 0.6898 (ptmt) REVERT: J 269 GLN cc_start: 0.9064 (tt0) cc_final: 0.8578 (tm-30) REVERT: J 311 ASP cc_start: 0.8523 (p0) cc_final: 0.8225 (m-30) REVERT: J 327 ILE cc_start: 0.9248 (mm) cc_final: 0.8838 (tt) REVERT: J 359 LYS cc_start: 0.9244 (ptmt) cc_final: 0.8991 (tttt) REVERT: K 161 MET cc_start: 0.8210 (ppp) cc_final: 0.7970 (ppp) REVERT: K 179 MET cc_start: 0.8703 (ppp) cc_final: 0.8486 (ppp) REVERT: K 221 MET cc_start: 0.8266 (ppp) cc_final: 0.7989 (ppp) REVERT: K 222 LEU cc_start: 0.9301 (tt) cc_final: 0.9006 (tt) REVERT: K 377 SER cc_start: 0.8313 (m) cc_final: 0.8039 (p) REVERT: L 203 ASN cc_start: 0.8880 (p0) cc_final: 0.8358 (p0) REVERT: L 206 ILE cc_start: 0.7808 (mm) cc_final: 0.6977 (mm) REVERT: L 255 TYR cc_start: 0.8357 (m-10) cc_final: 0.8145 (m-80) REVERT: L 280 MET cc_start: 0.7966 (mmm) cc_final: 0.7766 (mmm) REVERT: L 311 GLN cc_start: 0.7916 (tp40) cc_final: 0.7648 (tp40) REVERT: L 328 ASN cc_start: 0.8865 (m-40) cc_final: 0.8448 (m-40) REVERT: L 359 GLU cc_start: 0.9069 (mp0) cc_final: 0.8715 (mp0) REVERT: L 382 MET cc_start: 0.8250 (ppp) cc_final: 0.7835 (ppp) REVERT: M 303 ARG cc_start: 0.8588 (mtt90) cc_final: 0.8065 (ptp-170) REVERT: M 397 GLU cc_start: 0.8990 (mp0) cc_final: 0.8525 (mp0) outliers start: 1 outliers final: 0 residues processed: 498 average time/residue: 0.3517 time to fit residues: 277.0574 Evaluate side-chains 418 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 266 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 167 optimal weight: 20.0000 chunk 230 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 27 GLN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN C 177 GLN D 70 HIS D 178 ASN D 204 GLN E 180 GLN ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.082540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.069142 restraints weight = 87715.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.070845 restraints weight = 55840.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.072026 restraints weight = 39537.276| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25141 Z= 0.274 Angle : 0.735 10.564 34112 Z= 0.373 Chirality : 0.047 0.152 3976 Planarity : 0.004 0.043 4421 Dihedral : 7.399 88.402 3694 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.08 % Allowed : 0.77 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.15), residues: 3288 helix: -0.97 (0.15), residues: 1191 sheet: -1.75 (0.23), residues: 457 loop : -1.81 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 160 HIS 0.006 0.001 HIS J 240 PHE 0.044 0.002 PHE D 174 TYR 0.014 0.002 TYR K 198 ARG 0.013 0.001 ARG G 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 468 time to evaluate : 2.784 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: 0.8570 (t0) cc_final: 0.8209 (t0) REVERT: A 89 ASP cc_start: 0.8527 (p0) cc_final: 0.7753 (t0) REVERT: B 78 MET cc_start: 0.8299 (tpp) cc_final: 0.8086 (tpp) REVERT: B 103 GLU cc_start: 0.8432 (pm20) cc_final: 0.8232 (pm20) REVERT: B 108 LYS cc_start: 0.7092 (ttpt) cc_final: 0.6888 (tmtt) REVERT: B 117 ILE cc_start: 0.8973 (mm) cc_final: 0.8767 (mm) REVERT: B 241 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8317 (tp40) REVERT: C 114 ARG cc_start: 0.8989 (tpm170) cc_final: 0.8646 (tpp-160) REVERT: C 212 GLU cc_start: 0.8067 (pt0) cc_final: 0.7816 (pm20) REVERT: D 16 HIS cc_start: 0.8835 (m90) cc_final: 0.8092 (m90) REVERT: D 56 ASP cc_start: 0.7379 (m-30) cc_final: 0.6702 (m-30) REVERT: D 120 TYR cc_start: 0.8017 (m-80) cc_final: 0.7369 (m-80) REVERT: D 151 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7615 (tm-30) REVERT: D 204 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6870 (pp30) REVERT: E 78 MET cc_start: 0.8455 (mtp) cc_final: 0.8213 (mtp) REVERT: E 84 ASP cc_start: 0.8671 (p0) cc_final: 0.8450 (p0) REVERT: F 60 GLN cc_start: 0.7286 (tp40) cc_final: 0.7022 (tp40) REVERT: F 102 LYS cc_start: 0.8309 (mmmt) cc_final: 0.7744 (mtmt) REVERT: F 190 ILE cc_start: 0.8945 (pt) cc_final: 0.8459 (mt) REVERT: G 10 LEU cc_start: 0.8614 (pt) cc_final: 0.8059 (tt) REVERT: G 18 ASP cc_start: 0.9198 (p0) cc_final: 0.8968 (p0) REVERT: G 84 ASP cc_start: 0.8656 (p0) cc_final: 0.8347 (p0) REVERT: G 86 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7336 (ttm-80) REVERT: G 110 PRO cc_start: 0.9232 (Cg_exo) cc_final: 0.9013 (Cg_endo) REVERT: G 225 ASN cc_start: 0.7467 (t0) cc_final: 0.7206 (t0) REVERT: H 226 GLU cc_start: 0.8373 (pm20) cc_final: 0.7992 (pm20) REVERT: J 183 LYS cc_start: 0.7595 (pttp) cc_final: 0.7201 (ptmt) REVERT: J 249 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7579 (mm-30) REVERT: J 327 ILE cc_start: 0.9289 (mm) cc_final: 0.8934 (tt) REVERT: J 359 LYS cc_start: 0.9300 (ptmt) cc_final: 0.9088 (tttt) REVERT: K 179 MET cc_start: 0.8807 (ppp) cc_final: 0.8578 (ppp) REVERT: K 221 MET cc_start: 0.8376 (ppp) cc_final: 0.8128 (ppp) REVERT: K 222 LEU cc_start: 0.9353 (tt) cc_final: 0.9101 (tp) REVERT: K 270 PHE cc_start: 0.8883 (t80) cc_final: 0.8575 (t80) REVERT: L 203 ASN cc_start: 0.8880 (p0) cc_final: 0.8290 (p0) REVERT: L 206 ILE cc_start: 0.7847 (mm) cc_final: 0.6988 (mm) REVERT: L 255 TYR cc_start: 0.8550 (m-10) cc_final: 0.8317 (m-80) REVERT: L 280 MET cc_start: 0.8040 (mmm) cc_final: 0.7837 (mmm) REVERT: L 328 ASN cc_start: 0.8916 (m-40) cc_final: 0.8505 (m-40) REVERT: L 359 GLU cc_start: 0.9064 (mp0) cc_final: 0.8730 (mp0) REVERT: L 382 MET cc_start: 0.8334 (ppp) cc_final: 0.7781 (ppp) REVERT: M 397 GLU cc_start: 0.9062 (mp0) cc_final: 0.8529 (mp0) outliers start: 2 outliers final: 0 residues processed: 470 average time/residue: 0.3591 time to fit residues: 267.6497 Evaluate side-chains 397 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 396 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 320 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 0.0010 chunk 269 optimal weight: 4.9990 chunk 323 optimal weight: 0.0670 chunk 75 optimal weight: 9.9990 chunk 233 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.1928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 27 GLN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS C 152 ASN D 178 ASN ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.083960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.070746 restraints weight = 87704.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.072478 restraints weight = 54914.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.073700 restraints weight = 38547.112| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25141 Z= 0.189 Angle : 0.711 11.724 34112 Z= 0.352 Chirality : 0.045 0.171 3976 Planarity : 0.004 0.041 4421 Dihedral : 7.137 80.362 3694 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.04 % Allowed : 0.41 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.15), residues: 3288 helix: -0.91 (0.15), residues: 1194 sheet: -1.62 (0.23), residues: 453 loop : -1.76 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 160 HIS 0.003 0.001 HIS E 73 PHE 0.043 0.001 PHE D 174 TYR 0.016 0.001 TYR B 156 ARG 0.012 0.001 ARG G 169 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: